Found the following significant warnings:
  Warning: Obsolescent feature: DATA statement at (1) after the first executable statement
See ‘/data/gannet/ripley/R/packages/tests-devel/mvgb.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) bal.Rd:156: Escaped LaTeX specials: \&
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) MVNtestchar-package.Rd:16-17: Lost braces; missing escapes or markup?
    16 | {Provides a test of multivariate normality of a sample which does not require estimation of the nuisance parameters, the mean      vector and covariance matrix.  Rather, a sequence of transformations removes these nuisance parameters, resulting in a set of    sample matrices that are positive definite.  If, and only if the original data is multivariate normal, these matrices are       uniformly distributed on the space of positive definite matrices in the unit hyper-rectangle.  The package performs a goodness    of fit test of this hypothesis. In addition to the test, functions in the package give visualizations of the  support region    of positive definite matrices for p equals 2.
       | ^
checkRd: (-1) pkb.Rd:14: Escaped LaTeX specials: \# \# \#
checkRd: (-1) dmvss.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dmvss.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pmvss.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) bbc.Rd:39: Lost braces
    39 | The "nbdev.mxm" (negative binomial deviance) is missing. For more information on these see \code{\link{cv.ses}}. bold{Note} that they come with "".
       |                                                                                                                      ^
checkRd: (-1) cv.fbed.lmm.reg.Rd:32: Lost braces; missing escapes or markup?
    32 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.gomp.Rd:29: Lost braces; missing escapes or markup?
    29 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
checkRd: (-1) cv.ses.Rd:94: Lost braces; missing escapes or markup?
    94 | The folds of the data to use (a list generated by the function generateCVRuns {TunePareto}). If NULL the folds are created internally with the same function.
       |                                                                               ^
Namespaces in Imports field not imported from:
  ‘e1071’ ‘glue’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rTubeDB’
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Requires orphaned package: ‘taxize’
Specified C++11: please drop specification unless essential
checkRd: (-1) mzipmed_data.Rd:22: Lost braces; missing escapes or markup?
    22 | @source {Simulated to serve as an example}
       |         ^
Note: found 50 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Note: found 63 marked UTF-8 strings
Package which this enhances but not available for checking: ‘asreml’
checkRd: (-1) M36NT2PM.dat.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) M36NT2PM.dat.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Note: found 12 marked UTF-8 strings
checkRd: (-1) DSIVdata.Rd:15-23: Lost braces
    15 | for(i in 1:50){
       |               ^
checkRd: (-1) DSIVdata.Rd:17-21: Lost braces
    17 |   for(j in 1:50){
       |                 ^
checkRd: (-1) DSIVdata.Rd:31-39: Lost braces
    31 | for(i in 1:20){
       |               ^
checkRd: (-1) DSIVdata.Rd:33-37: Lost braces
    33 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:10-18: Lost braces
    10 | for(i in 1:200){
       |                ^
checkRd: (-1) DSLIVEdata.Rd:12-16: Lost braces
    12 |   for(j in 1:200){
       |                  ^
checkRd: (-1) DSLIVEdata.Rd:26-34: Lost braces
    26 | for(i in 1:20){
       |               ^
checkRd: (-1) DSLIVEdata.Rd:28-32: Lost braces
    28 |   for(j in 1:20){
       |                 ^
checkRd: (-1) DSLIVEdata.Rd:50-54: Lost braces
    50 | for(kk in 1:length(p)){
       |                       ^
checkRd: (-1) drop_name_crossref.Rd:49: Lost braces; missing escapes or markup?
    49 | Takes one or several dois and extracts information from Crossref, then processes them into visual citations with \code{\link{drop_name}}. Requires {rcrossref} > v1.1, see README for further details.
       |                                                                                                                                                    ^
Note: found 47936 marked UTF-8 strings
checkRd: (-1) fod.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fod.Rd:14: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 2438 marked UTF-8 strings
Package suggested but not available for checking: ‘spatialClust’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following files/directories:
  ‘Crashpad’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (2018-01-22)
    Version  (2017-08-22)
    Version
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Package suggested but not available for checking: ‘gurobi’
Note: found 5 marked Latin-1 strings
  Note: found 7187 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 140 marked UTF-8 strings
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                 ^
checkRd: (-1) NbClust.Rd:50: Lost braces; missing escapes or markup?
    50 |       \item \bold{Average} : The distance \eqn{D_{ij}}{D_ij} between two clusters \eqn{C_{i}}{C_i} and \eqn{C_{j}}{C_j} is the mean of the distances between the pair of points {x} and {y}, where \eqn{x \in C_{i}, y \in C_{j}}{x in C_i, y in C_j}.
       |                                                                                                                                                                                         ^
checkRd: (-1) nbconvert.Rd:49: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) nbconvert.Rd:50: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘rrpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘magick’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) ncpen.Rd:108: Lost braces; missing escapes or markup?
   108 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
checkRd: (-1) ncpen.reg.Rd:109: Lost braces; missing escapes or markup?
   109 |   \item{gamma}{extra shrinkage parameter for \code{classo} and {sridge} only.}
       |                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) norm_tests.Rd:69: Lost braces
    69 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
checkRd: (-1) t_neat.Rd:243: Lost braces
   243 | Anderson-Darling test." See url{https://github.com/Lakens/perfect-t-test} for
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Running ‘checkmodule.R’
  Running ‘spelling.R’
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...3,27d2
< > # This file is copied and modified from runjags package
< > # Copyright (C) 2013 Matthew Denwood <matthewdenwood@mac.com> and Achmad Syahrul Choir <madsyair@gmail.com>
< > # 
< > # This code allows the distributions provided by the neojags module
< > # to be tested from within R.  
< > # 
< > # This version of the module is compatible with JAGS version 3 and 4.
< > # Some necessary modifications are controlled using the INCLUDERSCALARDIST
< > # macro which is defined by makevars if JAGS version 3 is detected.
< > # Once JAGS version 3 becomes obsolete the redundant code will be
< > # removed from neojags.
< > # 
< > # neojags is free software: you can redistribute it and/or modify
< > # it under the terms of the GNU General Public License as published by
< > # the Free Software Foundation, either version 3 of the License, or
< > # (at your option) any later version.
< > # 
< > # neojags is distributed in the hope that it will be useful,
< > # but WITHOUT ANY WARRANTY; without even the implied warranty of
< > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
< > # GNU General Public License for more details.
< > # 
< > # You should have received a copy of the GNU General Public License
< > # along with runjags  If not, see <http://www.gnu.org/licenses/>.
< > 
31c6
< NULL
---
> All Done!
  Running ‘testthat.R’
Note: found 1008 marked UTF-8 strings
checkRd: (-1) color_palette.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) color_palette.Rd:29: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) GSS.Rd:17: Lost braces
    17 | code{2016}.}
       |     ^
checkRd: (-1) partial_correlation.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) partial_correlation.Rd:29: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘ggraph’ ‘reshape2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fastshp’
Note: found 2 marked UTF-8 strings
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) PVmodule.Rd:27: Lost braces; missing escapes or markup?
    27 | In the resulting netSEM model, time was used as a proxy for damp heat exposure stress (S) variable and $P_{max}$ (maximum power generated by the modules) was used as the performance level response ($R$) variable, several mechanistic variables ($M$) were obtained through chemical evaluation methods, including FTIR and TGA  on EVA encapsulant. 
       |                                                                                                           ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                     ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                ^
checkRd: (-1) netSEMp1.Rd:55: Lost braces
    55 | For example, in the quadratic functional form y ~ b0 + b1x + b2x^2, the three P-values correspond two those of \\hat{b0}, \\hat{b1} and \\hat{b2}, respectively. 
       |                                                                                                                                              ^
checkRd: (-1) spec_clust.Rd:33: Lost braces; missing escapes or markup?
    33 | A label vector of size n x 1 with elements in {1,2,...,K}
       |                                               ^
checkRd: (-1) nettskjema_get_data.Rd:64-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_get_data.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_get_data.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_token2renviron.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_write_codebook.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nettskjema_write_codebook.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rc.plot.ideogram.Rd:20: Lost braces; missing escapes or markup?
    20 |  \item{las}{numeric in {0,1,2,3}; the style of chromosome labels. 0, always parallel to the track [default]; 1, always horizontal; 2, always perpendicular to the track; 3, always vertical.}
       |                        ^
checkRd: (-1) NetworkChange.Rd:163: Escaped LaTeX specials: \&
checkRd: (-1) NetworkChangeRobust.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) NetworkStatic.Rd:142: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) harry_potter.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:47-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) harry_potter.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vanDeBunt_students.Rd:49: Lost braces in \itemize; meant \describe ?
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
checkRd: (-1) nodeLogic.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nodeLogic.Rd:46: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘map.png’ ‘maze.html’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
checkRd: (-1) networktree.Rd:56: Lost braces; missing escapes or markup?
    56 | with a matrix response {y}. \code{x1} and \code{x2} are used as
       |                        ^
Note: found 2 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'ANTsR', 'ITKR', 'extrantsr', 'MNITemplate', 'RAVEL', 'neurodata'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Note: found 5170 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘quickcode’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
checkRd: (-1) load_schedules.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) load_schedules.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘nflfastR’
  All declared Imports should be used.
Specified C++14: please drop specification unless essential
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'NGCHMDemoData', 'NGCHMSupportFiles'
'LazyData' is specified without a 'data' directory
checkRd: (-1) NHANES.Rd:278: Lost braces
   278 | \code{AgeFirstMarij}{Age participant first tried marijuana. Reported for participants aged 18 to 59 years.}
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) graphresU.fun.Rd:72: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHSRdatasets’ ‘grid’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) bootstrap_param_est.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootstrap_param_est.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_emission.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) impute_ref.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_data.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sim_data.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) postPredSPD.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) postPredSPD.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘jpndistrict’
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) mcrPlot.Rd:42-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mcrPlot.Rd:45-47: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rxode2parse’
Packages suggested but not available for checking: 'Rvmmin', 'Rcgmin'
checkRd: (-1) dot-make_long_data.Rd:44: Lost braces; missing escapes or markup?
    44 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
checkRd: (-1) dot-make_long_data_nested_cv.Rd:49: Lost braces; missing escapes or markup?
    49 | training sample), psi (the value of this observations Psihat(P_{n,B_n}^0)),
       |                                                                ^
checkRd: (-1) Dmean.Rd:62: Escaped LaTeX specials: \&
checkRd: (-1) Dvar.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) anova.Rd:19: Lost braces
    19 |   Returns an object of class code{anova}.  These objects represent
       |                                  ^
Running ‘spelling.R’
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...3,9c3,6
< > if (requireNamespace("spelling", quietly = TRUE)) {
< +   spelling::spell_check_test(
< +     vignettes = TRUE, error = FALSE,
< +     skip_on_cran = TRUE
< +   )
< + }
< NULL
---
> > if(requireNamespace('spelling', quietly = TRUE))
> +   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
> +                              skip_on_cran = TRUE)
> All Done!
  Running ‘testthat.R’ [15s/21s]
checkRd: (-1) fwtnpperm.Rd:34: Lost braces
    34 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
checkRd: (-1) check_input_event_times.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_input_event_times.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) check_time_unit.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) default_params_doc.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_brts.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nltt_diff_exact_extinct.Rd:39-40: Lost braces in \itemize; meant \describe ?
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Found the following HTML validation problems:
nn2poly.html:129:1 (nn2poly.Rd:75): Warning: trimming empty <li>
nn2poly.html:128:1 (nn2poly.Rd:75): Warning: trimming empty <ol>
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: Obsolescent feature: Computed GOTO at (1)
See ‘/data/gannet/ripley/R/packages/tests-devel/nnls.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) ROCplots.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ROCplots.Rd:40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
checkRd: (-1) match_forecast_county.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_forecast_county.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_forecast_county.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) parse_damage.Rd:29: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:114-117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:118-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePop.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) imp_int_an.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ndmodel.Rd:18: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
checkRd: (-1) set.data.Rd:14: Lost braces; missing escapes or markup?
    14 |   \item{shape}{either \code{wide} or {long}. Default \code{wide}. See Details.}
       |                                      ^
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) mle_parameters.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mle_parameters.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Lcm.Rd:75: Lost braces
    75 |     \item{\code{GetTrace()}:}{retrieve all traced iterations. Returns a list with all the parameters set using the method SetTrace(). See description of snapshot{reference} method for a description of the parameters.  }
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) plot.regression.circular.Rd:35: Lost braces
    35 |               code{plot.type="circle"} and \code{x} is the output of \code{\link{kern.reg.circ.lin}}) or to \code{\link{lines3d}} (if \code{plot.type="circle"})
       |                   ^
checkRd: (-1) DiscHazRateAuxFunctions.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DiscHazRateAuxFunctions.Rd:48: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) nplr.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:52-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:56-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nplr.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nppbib.Rd:28: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) np.reg.test.Rd:148: Lost braces
   148 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
checkRd: (-1) nptest-package.Rd:73: Lost braces
    73 | ter Braak, C. J. F. (1992). Permutation versus bootstrap significance tests in multiple regression and ANOVA. In K. H. J\"{o}ckel, G. Rothe, & W. Sendler (Eds.), Bootstrapping and related techniques. lecture notes in economics and mathematical systems, vol 376 (pp. 79-86). Springer.
       |                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) NSAE.Rd:14: Lost braces; missing escapes or markup?
    14 | {Maintainer}: Saurav Guha \email{saurav.iasri@gmail.com}
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) NScluster-package.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:35-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:44-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NScluster-package.Rd:49-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:44-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:69-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mple.cppm.Rd:113-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:36-87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:90-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:123-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:151-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.cppm.Rd:195-211: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
checkRd: (-1) svr.df.Rd:13: Lost braces
    13 | \item{z}{the vector of zi = min{Xi, Yi}}
       |                                ^
Note: found 1 marked UTF-8 string
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
checkRd: (-1) MSM.fit.Rd:21: Lost braces
    21 | \code{MSM.fit} returns an object of class code{MSM.lm} or \code{MSM.glm}, depending on the input model.
       |                                               ^
checkRd: (-1) SMC.Smooth.Rd:25: Lost braces; missing escapes or markup?
    25 | observation at current time step. It should return {xx} (the samples xt) and
       |                                                    ^
checkRd: (-1) SMC.Smooth.Rd:26: Lost braces; missing escapes or markup?
    26 | {logww} (their corresponding log weight).}
       | ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘optparse’ ‘vcfR’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘pedtools’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) xyz2R.Rd:31: Lost braces
    31 |    \item Finally, code{T} is rotated an angle \code{z} about its NEWEST z-axis.
       |                       ^
'LazyData' is specified without a 'data' directory
Note: found 5 marked UTF-8 strings
Note: found 6409 marked UTF-8 strings
Note: found 7284 marked UTF-8 strings
checkRd: (-1) OBMb.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OBMb.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Suggests orphaned package: ‘taxize’
Note: found 7 marked UTF-8 strings
Note: found 6986 marked UTF-8 strings
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                               ^
checkRd: (-1) ChangepointDetector.Rd:93: Lost braces; missing escapes or markup?
    93 | \code{'sparse'}, then only (S^{diag}, S^{off,d})
       |                                         ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |        ^
checkRd: (-1) ChangepointDetector.Rd:94: Lost braces; missing escapes or markup?
    94 | and (S^{diag}, S^{off,s}) are included in \code{stat} respectively.);
       |                  ^
Note: found 1242 marked UTF-8 strings
checkRd: (-1) onlineCPD.Rd:35: Lost braces
    35 |  function(x, lambda){const_hazard(x, lambda=100)}
       |                     ^
checkRd: (-1) ocsApiUserProvisioningManager.Rd:87: Lost braces
    87 |  \item{code{addToGroup(userid, groupid)}}{
       |            ^
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’ ‘rmarkdown’ ‘tidymodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.ODEmorris.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ODEmorris.Rd:64-65: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                            ^
checkRd: (-1) formula.oglmx.Rd:49: Lost braces
    49 |   \code{\link{oglmx}}, code{\link[lmtest]{lrtest}}, code{\link{formula}}.
       |                                                         ^
Specified C++11: please drop specification unless essential
Note: found 12 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Note: found 842 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘testthat’
  All declared Imports should be used.
checkRd: (-1) dot-discoveryRequest.Rd:15-16: Lost braces
    15 | \item{service}{One of {"locations", "deployments", "deviceCategories", "devices",
       |                       ^
checkRd: (-1) dot-discoveryRequest.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{method}{One of {"get", "getTree"}}
       |                      ^
checkRd: (-1) dot-saveAsFile.Rd:19: Lost braces; missing escapes or markup?
    19 | (numeric) Result code from {0: done, -1: error, -2: fileExists}
       |                            ^
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) summary.blrm_trial.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) summary.blrm_trial.Rd:34: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) oncotree.fit.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) oncotree.fit.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 21 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) one_sample.Rd:40: Lost braces; missing escapes or markup?
    40 | In two sided or one sided interval estimation of \code{sigma^2} of one normal sample, {side} is a parameter used to control whether to compute two sided or one sided interval estimation. When computing the one sided upper limit, input \code{side = -1}; when computing the one sided lower limit, input \code{side = 1}; when computing the two sided limits, input \code{side = 0} (default).
       |                                                                                       ^
Note: found 32 marked UTF-8 strings
Note: found 5766 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
Note: found 42 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘glue’ ‘httpcode’ ‘httr’ ‘jsonlite’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Licence stub is invalid DCF.
GNU make is a SystemRequirements.
Running ‘buffer.R’
  Comparing ‘buffer.Rout’ to ‘buffer.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< > 
  Running ‘kernel.R’
  Comparing ‘kernel.Rout’ to ‘kernel.Rout.save’ ...5,10d4
< > 
< > if (!length(oclPlatforms())) {
< +     cat("== Cannot run tests as there is no platform")
< +     q("no")
< + }
< >
Note: found 4 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3134 marked UTF-8 strings
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: Obsolescent feature: DATA statement at (1) after the first executable statement
See ‘/data/gannet/ripley/R/packages/tests-devel/OpenMx.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
* used C++ compiler: ‘g++-14 (GCC) 14.2.0’
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘openNLPmodels.en’
Note: found 10 marked UTF-8 strings
Requires orphaned package: ‘taxize’
Note: found 167 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) loss.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loss.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mixture-opera.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mixture.Rd:34: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) word_imp.Rd:14: Lost braces
    14 | number of individual records. An \code{n} x code{2} dataframe can
       |                                                 ^
checkRd: (-1) MonteCarlo.Rd:23: Lost braces
    23 | N is computed from \code{p} length. M is code{10^4} by default.
       |                                              ^
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Graph_layout_Doptbd_trtE’
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) optimal_holdout_size.Rd:30: Lost braces; missing escapes or markup?
    30 | List/data frame of dimension (number of evaluations) x (4 + n_par) containing input data and results. Columns \code{size} and \code{cost} are optimal holdout size and cost at this size respectively. Parameters N, k1, theta.1, theta.2,...,theta.{n_par} are input data.
       |                                                                                                                                                                                                                                                     ^
checkRd: (-1) drawdesign.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drawdesign.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gnu_style.Rd:24: Lost braces
    24 | [GNU Command Line Standards]{http://www.gnu.org/prep/standards/standards.html}
       |                             ^
Package which this enhances but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
checkRd: (-1) calc_n_from_c.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Helper function to calculate other n's given n_{1,T} and allocation ratios}
       |                                                       ^
checkRd: (-1) calc_n_from_c.Rd:15: Lost braces; missing escapes or markup?
    15 | Helper function to calculate other n's given n_{1,T} and allocation ratios
       |                                                ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rrelaxiv’
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘Graph_layout_Doptrcd_trtE’
Package suggested but not available for checking: ‘gurobi’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 36 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) internal.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:56-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:62-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) internal.Rd:70: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
checkRd: (-1) minK.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minK.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lra-ord.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lra-ord.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
checkRd: (-1) orf.Rd:74: Lost braces
    74 | matrix of covariates \code{X} and a vector of outcomes 'code{Y} to the \code{orf}
       |                                                             ^
Found the following files/directories:
  ‘cluster of fitted mean data.eps’ ‘cluster of fitted mean data.txt’
  ‘cluster of raw data.txt’
checkRd: (-1) distsumlpmin.Rd:69: Lost braces
    69 |   \code{Véase}{Vease} \enc{también}{tambien} \code{\link{distsummin}}, \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |               ^
checkRd: (-1) distsummin.Rd:80: Lost braces
    80 | \code{Véase}{Vease} \enc{también}{tambien} \code{\link{orloca.es-package}}, \code{\link{loca.p}} y \code{\link{distsum}}.
       |             ^
checkRd: (-1) hillEquation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hillEquation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:88-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qiba.Rd:91-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) polynomial.derivatives.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.derivatives.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polynomial.integrals.Rd:21: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) oscar.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{print}{Level of verbosity in Fortran (may not be visible on all terminals); should be an integer between {range, range}, Default: 3}
       |                                                                                                                ^
checkRd: (-1) oscar.control.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{start}{Starting point generation method, see vignettes for details; should be an integer between {range,range}, Default: 2}
       |                                                                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RLum.OSL_decomposition.Rd:90-91: Lost braces
    90 | \item \link{optimise_OSLintervals}: {Approximates the optimal integration intervals. Uses the global
       |                                     ^
checkRd: (-1) RLum.OSL_decomposition.Rd:92-94: Lost braces
    92 | \item \link{decompose_OSLcurve}: {Calculates component intensities for \strong{all} \code{record_type} measurements.
       |                                  ^
checkRd: (-1) fit_OSLcurve.Rd:97: Lost braces; missing escapes or markup?
    97 | fitting with the \emph{RSS_{K-1}} value of the previous fitting and calculates
       |                            ^
Note: found 5889 marked UTF-8 strings
File ‘osmdata/libs/osmdata.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 35 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                ^
checkRd: (-1) otp_create_surface.Rd:33: Lost braces; missing escapes or markup?
    33 | The file will be named surface_{id}.tiff, with {id} replaced by the OTP id assigned
       |                                                ^
checkRd: (-1) imput_cov.Rd:79: Lost braces
    79 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                     ^
checkRd: (-1) indiv_grp_closest.Rd:47: Lost braces; missing escapes or markup?
    47 | The function \code{indiv_grp_closest} is an intermediate function used in the implementation of an algorithm called {OUTCOME} (and its enrichment {R-OUTCOME}, see the reference (2) for more details) dedicated to the solving of recoding problems in data fusion using Optimal Transportation theory.
       |                                                                                                                                                   ^
checkRd: (-1) merge_dbs.Rd:179: Lost braces
   179 | \item van Buuren, S., Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1–67. url{https://www.jstatsoft.org/v45/i03/}
       |                                                                                                                                                                 ^
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘astsa’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) fmat.Rd:15: Lost braces; missing escapes or markup?
    15 | \item outcome: codes {I, P, R, NC, O, UH, UO, eUH, eUO, NE}
       |                      ^
checkRd: (-1) fmat.Rd:24: Lost braces; missing escapes or markup?
    24 | The input parameters given by the user are {I, P, R, NC, O, UH, UO} and
       |                                            ^
checkRd: (-1) fmat.Rd:25: Lost braces; missing escapes or markup?
    25 | the parameter 'e'. The parameter e is multiplied by {UH, UO} internally so as to
       |                                                     ^
checkRd: (-1) fmat.Rd:26: Lost braces; missing escapes or markup?
    26 | produce {eUH, eUO}.
       |         ^
checkRd: (-1) middleearth.Rd:14: Lost braces; missing escapes or markup?
    14 | \item \strong{code:} one of the outcome codes {I, P, R, NC, O, UH, UO, UH, UO, NE}
       |                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) lint_package.Rd:20: Lost braces
    20 | code{\link[lintr:lint_package]{lintr::lint_package}} where we hardcode the
       |     ^
checkRd: (-1) provide_news_rd.Rd:22: Lost braces
    22 | Christian Vonderach uses the index thus wants file{inst/NEWS.rd} to
       |                                                   ^
checkRd: (-1) provide_news_rd.Rd:23: Lost braces
    23 | automatically be in sync with file{./NEWS.md}.
       |                                   ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Changes
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
checkRd: (-1) residuals_paco.Rd:10: Escaped LaTeX specials: \$
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
checkRd: (-1) MICS2014Ch.Rd:296: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Ch.Rd:297: Lost braces in \enumerate; meant \describe ?
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
checkRd: (-1) MICS2014HH.Rd:214: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HH.Rd:215: Lost braces in \enumerate; meant \describe ?
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
checkRd: (-1) MICS2014HL.Rd:109: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014HL.Rd:110: Lost braces in \enumerate; meant \describe ?
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
checkRd: (-1) MICS2014Wm.Rd:336: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) MICS2014Wm.Rd:337: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:88: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018bh.Rd:89: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:308: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018fs.Rd:309: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:362: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018hh.Rd:363: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mm.Rd:70: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:243: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) PakPMICS2018mn.Rd:244: Lost braces in \enumerate; meant \describe ?
Note: found 4 marked UTF-8 strings
Note: found 314 marked UTF-8 strings
Package suggested but not available for checking: ‘CorShrink’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Pandoc.convert.Rd:42: Lost braces
    42 | Calling John MacFarlane's great program to convert specified file (see \code{f} parameter below) or character vector {see \code{text} paramater} to other formats like \code{HTML}, \code{pdf}, \code{docx}, \code{odt} etc.
       |                                                                                                                      ^
checkRd: (-1) btsdemo.Rd:22: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:23: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:25: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:26: Escaped LaTeX specials: \_
checkRd: (-1) btsdemo.Rd:30: Escaped LaTeX specials: \_
checkRd: (-1) panelsummary.Rd:112: Lost braces; missing escapes or markup?
   112 | \item `"{exp(estimate) * std.error}"
       |         ^
checkRd: (-1) panelsummary_raw.Rd:90: Lost braces; missing escapes or markup?
    90 | \item `"{exp(estimate) * std.error}"
       |         ^
Found the following HTML validation problems:
pvargmm.html:141:282 (pvargmm.Rd:79): Warning: trimming empty <p>
'LazyData' is specified without a 'data' directory
checkRd: (-1) hvidovre.Rd:11: Lost braces
    11 |     \item{\code{roof_tile}}{a numeric vector, roof_tile}{dummy, roof made out of tiles =1}
       |                                                         ^
checkRd: (-1) hvidovre.Rd:25: Lost braces
    25 |     \item{\code{railways}}{a numeric vector, railways}{distance to nearest railway in meters}
       |                                                       ^
checkRd: (-1) hvidovre.Rd:26: Lost braces
    26 |     \item{\code{nature_SLD}}{a numeric vector, nature_SLD}{distance to nearest nature area in meters}
       |                                                           ^
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
checkRd: (-1) apa_print.htest.Rd:58: Lost braces
    58 | [here]{https://github.com/crsh/papaja/issues} (please include
       |       ^
checkRd: (-1) init_apa_results.Rd:15-16: Lost braces
    15 | \item{\code{full_result}}{A (named list of) character strings comprised of \code{estimate} and \verb{statistic`` for each factor.\} \\item\{}table`}{A data frame containing all results; can, for example, be passed to \code{\link[=apa_table]{apa_table()}}.
       |                                                                                                                                                     ^
Found the following HTML validation problems:
apa_barplot.html:83:1 (apa_barplot.Rd:50): Warning: trimming empty <dt>
apa_beeplot.html:84:1 (apa_beeplot.Rd:51): Warning: trimming empty <dt>
apa_interval.html:96:1 (apa_interval.Rd:68): Warning: trimming empty <dt>
apa_lineplot.html:84:1 (apa_lineplot.Rd:51): Warning: trimming empty <dt>
apa_print.emmGrid.html:77:1 (apa_print.emmGrid.Rd:37): Warning: trimming empty <dt>
apa_print.glm.html:107:1 (apa_print.glm.Rd:62): Warning: trimming empty <dt>
apa_print.htest.html:90:1 (apa_print.htest.Rd:45): Warning: trimming empty <dt>
apa_print.papaja_wsci.html:50:1 (apa_print.papaja_wsci.Rd:15): Warning: trimming empty <dt>
revision_letter_pdf.html:43:1 (revision_letter_pdf.Rd:13): Warning: trimming empty <dt>
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
checkRd: (-1) agreement.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) agreement.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) papciUI.Rd:39: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘MicrobiotaProcess’
Specified C++11: please drop specification unless essential
checkRd: (-1) getParamNr.Rd:15: Lost braces
    15 | Default is code{FALSE}.}
       |                ^
checkRd: (-1) getRequirements.Rd:16: Lost braces
    16 | code{TRUE}.}
       |     ^
checkRd: (-1) sampleValue.Rd:15: Lost braces; missing escapes or markup?
    15 | Default is code {FALSE}.}
       |                 ^
checkRd: (-1) sampleValues.Rd:18: Lost braces; missing escapes or markup?
    18 | Default is code {FALSE}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) returns.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{...}{Other options including {type} which refers to the
       |                                      ^
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) PPS.fit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PPS.fit.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) forbes400.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) forbes400.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:8: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) turkey.Rd:11: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
checkRd: (-1) summary.parsec.Rd:13-14: Lost braces in \itemize; meant \describe ?
File ‘parsedate/libs/parsedate.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘co2’ ‘co2.1’ ‘co2.2’ ‘co2s.1’ ‘co2s.2’ ‘ctm.1’ ‘ctm.2’ ‘m’ ‘m.1’
  ‘m.2’ ‘test’ ‘test.1’ ‘test.2’ ‘testa.1’ ‘testa.2’ ‘xfile.1’
  ‘xfile.2’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) PAS-package.Rd:30: Lost braces
    30 |     {\code{bin model}}{\cr Zhiqiu Hu, Zhiquan Wang, and Shizhong Xu (2012) An infinitesimal model for quantitative trait genomic value prediction. PloS ONE 7: e41336.}
       |                       ^
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
Namespaces in Imports field not imported from:
  ‘ComplexHeatmap’ ‘mathjaxr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
checkRd: (-1) as_config.Rd:32: Lost braces; missing escapes or markup?
    32 | with `{config}` package, which requires existence of default key.
       |       ^
checkRd: (-1) as_config.Rd:28: Lost braces; missing escapes or markup?
    28 | list compatible with `{config}` package
       |                       ^
'LazyData' is specified without a 'data' directory
Note: found 180 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clusterProfiler’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
checkRd: (-1) plotHeat.Rd:113: Lost braces
   113 | code{\link[patternize]{patPCA}}, as 'one' when visualizing single image or as 'multi' for multi
       |     ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
---- unloading
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
checkRd: (-1) pbd_loglik.Rd:31: Lost braces
    31 |     \code{pars2[1]} {set the conditioning on non-extinction of the clade (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:32: Lost braces
    32 |     \code{pars2[2]} {sets whether the likelihood is for the branching times (0) or the phylogeny (1) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:33: Lost braces
    33 |     \code{pars2[3]} {sets whether the first element of the branching times is the stem (1) or the crown (2) age \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:34: Lost braces
    34 |     \code{pars2[4]} {sets whether the parameters and likelihood should be shown on screen (1) or not (0) \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:35: Lost braces
    35 |     \code{pars2[5]} {sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details. \cr \cr}
       |                     ^
checkRd: (-1) pbd_loglik.Rd:36: Lost braces
    36 |     \code{pars2[6]}{Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}
       |                    ^
checkRd: (-1) pbd_loglik.Rd:37: Lost braces
    37 |     \code{pars2[7]}{Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)\cr \cr}  
       |                    ^
Found the following significant warnings:
  Warning: Obsolescent feature: Computed GOTO at (1)
  Warning: Obsolescent feature: Old-style character length at (1)
See ‘/data/gannet/ripley/R/packages/tests-devel/pbdSLAP.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
'LazyData' is specified without a 'data' directory
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘PBSmodelling/libs/PBSmodelling.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) twoby2Calibrate.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:85-86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:87-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:97-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:108-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) twoby2Calibrate.Rd:111-116: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
checkRd: (-1) PCM_ABC.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:108-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:117: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:205-207: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:208-211: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:212-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:221-224: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:225-228: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:229-231: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:232: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:233: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:234: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:235: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:236: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:237: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:238: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:239: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PCM_ABC.Rd:240: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate_phylproc.Rd:67: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MiniBenchmarkRvsCpp.Rd:18: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) getPCRAData.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getPCRAData.Rd:29: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 11 marked UTF-8 strings
checkRd: (-1) pcvpcr.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
checkRd: (-1) pcvpls.Rd:42: Lost braces; missing escapes or markup?
    42 | set {X, y} and cross-validation.
       |     ^
Package suggested but not available for checking: ‘cmdstanr’
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘PythonInR’
checkRd: (-1) keyword_directory.Rd:48: Lost braces
    48 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                        ^
checkRd: (-1) keyword_directory.Rd:48: Lost braces
    48 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                                     ^
checkRd: (-1) keyword_search.Rd:59: Lost braces
    59 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                        ^
checkRd: (-1) keyword_search.Rd:59: Lost braces
    59 | Default pattern is "\\p{WHITE_SPACE}{3,}" which can be interpreted as: 
       |                                     ^
'LazyData' is specified without a 'data' directory
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ncvreg’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
checkRd: (-1) get_training_data.Rd:6-14: Lost braces
     6 | where <- function(name, env = parent.frame()) {
       |                                               ^
checkRd: (-1) get_training_data.Rd:7-9: Lost braces
     7 |   if (identical(env, emptyenv())) {
       |                                   ^
checkRd: (-1) get_training_data.Rd:9-11: Lost braces
     9 |   } else if (exists(name, envir = env, inherits = FALSE)) {
       |                                                           ^
checkRd: (-1) get_training_data.Rd:11-13: Lost braces
    11 |   } else {
       |          ^
checkRd: (-1) get_training_data.Rd:20-28: Lost braces
    20 | where <- function(name, env = parent.frame()) {
       |                                               ^
checkRd: (-1) get_training_data.Rd:21-23: Lost braces
    21 |   if (identical(env, emptyenv())) {
       |                                   ^
checkRd: (-1) get_training_data.Rd:23-25: Lost braces
    23 |   } else if (exists(name, envir = env, inherits = FALSE)) {
       |                                                           ^
checkRd: (-1) get_training_data.Rd:25-27: Lost braces
    25 |   } else {
       |          ^
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) pdkMeans.Rd:63: Lost braces
    63 | \cite{C18}{pdSpecEst} for more details. Note that this comes at the cost of increased computation time in comparison to one
       |           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) embedded.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) embedded.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) ensemble.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) ensemble.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
checkRd: (-1) staged.blocks.Rd:39: Lost braces
    39 | \item{miv.threshold}{MIV (marginal information value) entrance threshold applicable only for code{"stepMIV"} method.
       |                                                                                                  ^
checkRd: (-1) staged.blocks.Rd:44: Lost braces
    44 | \item{m.ch.p.val}{Significance level of p-value for marginal chi-square test applicable only for code{"stepMIV"} method.
       |                                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Peacock.test-package.Rd:28: Escaped LaTeX specials: \_
'LazyData' is specified without a 'data' directory
checkRd: (-1) variogramGuess.Rd:94: Lost braces
    94 | Method \code{"b"} was proposed by \doi{10.1016/0098-3004(95)00095-X}{Jian et al. (1996)} and
       |                                                                     ^
checkRd: (-1) variogramGuess.Rd:98: Lost braces
    98 | \doi{10.1016/j.cageo.2008.10.011}{Hiemstra et al. (2009)}.
       |                                  ^
checkRd: (-1) variogramGuess.Rd:100: Lost braces
   100 | Method \code{"d"} was developed by \doi{10.1007/s11004-012-9434-1}{Desassis & Renard (2012)}.
       |                                                                   ^
Note: found 4860 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
GNU make is a SystemRequirements.
checkRd: (-1) 5.1.pems.plots.Rd:212: Lost braces; missing escapes or markup?
   212 |   (Logical or character) For {WatsonPlot}, how to 
       |                              ^
checkRd: (-1) 5.1.pems.plots.Rd:221: Lost braces; missing escapes or markup?
   221 |   (numeric) For {WatsonPlot}, pre-set plot types: 
       |                 ^
checkRd: (-1) 6.2.check.functions.Rd:189: Lost braces
   189 |   If a parent function is identified as \code{fun.name} and the check case (code{input}, 
       |                                                                                 ^
checkRd: (-1) 7.1.vsp.code.Rd:89: Lost braces
    89 |   code{\link{common.calculations}} for further details.
       |       ^
checkRd: (-1) 7.2.emissions.code.Rd:90: Lost braces
    90 |   emissions calculation methods. It accepts an input code{conc} which it checks and passes 
       |                                                          ^
checkRd: (-1) 8.1.tidyverse.tools.Rd:139: Lost braces
   139 |    (\code{pems}, code{data.frame}, etc) to 
       |                      ^
Specified C++11: please drop specification unless essential
checkRd: (-1) breslow.Rd:27: Escaped LaTeX specials: \# \#
checkRd: (-1) my.bspline.Rd:38: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) my.bspline.Rd:21: Escaped LaTeX specials: \$ \$ \$ \$ \$ \$
checkRd: (-1) my.bspline.Rd:27: Escaped LaTeX specials: \$ \$ \$
checkRd: (-1) pendensity.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:57: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:82: Escaped LaTeX specials: \$ \$
checkRd: (-1) pendensity.Rd:96: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:100: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:105: Escaped LaTeX specials: \$
checkRd: (-1) pendensity.Rd:109: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘fixest’
  All declared Imports should be used.
checkRd: (-1) mc3_pep.Rd:53: Lost braces; missing escapes or markup?
    53 | is not 2^{p} but the number of unique models `visited' by the 
       |          ^
Note: found 4 marked UTF-8 strings
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) CAPM.RiskPremium.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) Return.portfolio.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:110-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:114-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:119-122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:123-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Return.portfolio.Rd:130-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chart.ECDF.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) managers.Rd:8: Escaped LaTeX specials: \&
Found the following HTML validation problems:
Return.Geltner.html:58:32 (Return.Geltner.Rd:27): Warning: trimming empty <code>
centeredmoments.html:24:32 (centeredmoments.Rd:37): Warning: trimming empty <code>
Package suggested but not available for checking: ‘DMwR’
checkRd: (-1) classificationMetrics.Rd:85: Lost braces; missing escapes or markup?
    85 |   will use some extra notation, namely: TP = #{p == + & t == +} ; FP =
       |                                               ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |    ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                              ^
checkRd: (-1) classificationMetrics.Rd:86: Lost braces; missing escapes or markup?
    86 |   #{p == + & t == -} ; TN = #{p == - & t == -}; FN = #{p == - & t == +}
       |                                                       ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |          ^
checkRd: (-1) classificationMetrics.Rd:87: Lost braces; missing escapes or markup?
    87 |   ; P = #{t == +} ; N = #{t == -}; Finally, for some descriptions
       |                          ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
checkRd: (-1) jackal.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 201 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 1782 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Fixed issues
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_PN.Rd:15: Lost braces
    15 | A code{\link{marked_petrinet}}
       |       ^
'LazyData' is specified without a 'data' directory
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) PatentsRD.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRD.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) PatentsRDUS.Rd:4: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) DTV.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTV.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘animation.gif’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) PhageCocktail.Rd:100-103: Lost braces
   100 | "Result": {
       |           ^
checkRd: (-1) PhageCocktail.Rd:105-112: Lost braces
   105 | "BacteriaLysed": {
       |                  ^
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^
checkRd: (-1) phasePlaneAnalysis.Rd:84: Lost braces; missing escapes or markup?
    84 | identified {see (3) above}, if this point is a saddle then the manifolds are
       |            ^
Note: found 4 marked UTF-8 strings
Found the following files/directories:
  ‘test.pdf’
Namespaces in Imports field not imported from:
  ‘C50’ ‘HDclassif’ ‘MASS’ ‘MLmetrics’ ‘Matrix’ ‘adabag’ ‘base’
  ‘caTools’ ‘e1071’ ‘earth’ ‘evtree’ ‘frbs’ ‘glmnet’ ‘hda’ ‘ipred’
  ‘kernlab’ ‘kknn’ ‘klaR’ ‘mda’ ‘nnet’ ‘party’ ‘pls’ ‘randomForest’
  ‘rpartScore’ ‘sparseLDA’ ‘themis’
  All declared Imports should be used.
Note: found 114 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) connectedSets.Rd:27: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:29: Escaped LaTeX specials: \_ \_
checkRd: (-1) connectedSets.Rd:31: Escaped LaTeX specials: \_ \_
checkRd: (-1) maxConnectedSet.Rd:35: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:37: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:39: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:41: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:45: Escaped LaTeX specials: \_ \_ \_ \_ \_ \_ \_ \_ \_ \_
checkRd: (-1) maxConnectedSet.Rd:47: Escaped LaTeX specials: \_ \_
Specified C++11: please drop specification unless essential
Found the following HTML validation problems:
estimate.probability.html:33:1 (estimate.probability.Rd:25): Warning: trimming empty <li>
estimate.probability.html:35:1 (estimate.probability.Rd:26): Warning: trimming empty <li>
Note: found 13 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘tidyverse’ ‘usethis’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
checkRd: (-1) 11_d.init.method.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.method.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:21-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:24-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:27-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) 11_d.init.procedure.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.star.tree.Rd:29: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) GarlandJanis.IC.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.IC.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.Original.Rd:6: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) GarlandJanis.varcov.Rd:7: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) fitgom.Rd:87: Lost braces
    87 |   \item \code{theta} The ncol{counts} by K matrix of estimated
       |                              ^
checkRd: (-1) fitgom.Rd:89: Lost braces
    89 |   \item \code{omega} The nrow{counts} by K matrix of estimated
       |                              ^
checkRd: (-1) phylter.Rd:51: Lost braces; missing escapes or markup?
    51 | the output ({out$DiscardedGenes}).}
       |             ^
checkRd: (-1) pa-internal.Rd:11: Lost braces
    11 | code{l2df}: convert list to data.frame
       |     ^
checkRd: (-1) pa-internal.Rd:14: Lost braces
    14 | code{convertTZ}: force a new timezone on datetime
       |     ^
checkRd: (-1) pa-internal.Rd:16: Lost braces
    16 | code{createTime}: create datetime variable
       |     ^
checkRd: (-1) pa-internal.Rd:18: Lost braces
    18 | code{addDayIndex}: create ID_day variable from timestamp
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) IvesGodfray.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) IvesGodfray.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Kcalc.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) phylocom.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylocom.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) phylosignal.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) sample2matrix.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sample2matrix.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) traitgram.Rd:14: Escaped LaTeX specials: \$
checkRd: (-1) utility.Rd:37: Escaped LaTeX specials: \$ \$
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘pinnacle.API’
Note: found 2048 marked UTF-8 strings
checkRd: (-1) pinp.Rd:60: Lost braces; missing escapes or markup?
    60 |   {current date}"}
       |   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_pixels.Rd:27-29: Lost braces
    27 | if (interactive()) {
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sprinkle_colnames.Rd:26-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sprinkle_colnames.Rd:29-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:63-68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:69-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:74-77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_levels_labels.Rd:78-83: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deps.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deps.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) deps.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pkgdepR-package.Rd:18: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) write.pkgbib.Rd:44: Lost braces; missing escapes or markup?
    44 | The Old version of this function {write.bib} has now been integrated
       |                                  ^
Found the following HTML validation problems:
options.html:83:1 (options.Rd:36): Warning: trimming empty <dt>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘BH’
  All declared Imports should be used.
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                       ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                 ^
checkRd: (-1) adjacency.Rd:27: Lost braces; missing escapes or markup?
    27 | item j. For example, in the ranking \\{1\\} > \\{3, 4\\} > \\{2\\},
       |                                                              ^
checkRd: (-1) rankings.Rd:127: Lost braces; missing escapes or markup?
   127 | rank skipped. For example {1, 0, 2, 1}, ranks the first and fourth items in
       |                           ^
Note: found 150 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘robustbase’
  All declared Imports should be used.
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.html’ ‘P2Run.png’
checkRd: (-1) one_design.Rd:125-126: Lost braces
   125 | function serves for the purpose of spot-testing for any pre-specified {n,
       |                                                                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) plgraphics-internal.Rd:19: Lost braces
    19 |     \item{RNAMES}{code{row.names} if \code{x} is a matrix or data.frame,
       |                       ^
Found the following HTML validation problems:
efourier_power.html:100:1 (efourier_power.Rd:35): Warning: trimming empty <li>
checkRd: (-1) check_hwe.Rd:103: Lost braces; missing escapes or markup?
   103 | {'ALL', 'AFF', 'UNAFF', 'ALL(QT)', 'ALL(NP)'}), A1 (Allele 1; usually minor),
       | ^
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
3c3
< > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
---
> > assign(".oldSearch", search(), pos = 'CheckExEnv')
14a15
> > ### Keywords: models
17a19
> > 
230a233,248
> > ## Not run: 
> > ##D ### Raw data
> > ##D data(item9cat5)
> > ##D 
> > ##D ## ML estimation
> > ##D nrmleplnout<-nrmlepln(item9cat5, ncat=5)
> > ##D print(nrmleplnout)
> > ##D 
> > ##D ## BCL estimation
> > ##D nrbcplnout<-nrbcpln(item9cat5, ncat=5, se=FALSE)
> > ##D print(nrbcplnout)
> > ##D 
> > ##D ## ML Rasch estimation
> > ##D nrmleraschout<-nrmlerasch(item9cat5, ncat=5)
> > ##D print(nrmleraschout)
> > ## End(Not run)
244a263
> > ### Keywords: models
247a267
> > 
336a357
> > 
344c365
< > ### Title: Starting values for polytomous logit-normit model
---
> > ### Title: Starting values for polytymous logit-normit model
348a370
> > 
387c409,410
< > ## Matrix of response patterns and frequencies
---
> > 
> > ### Matrix of response patterns and frequencies
'LazyData' is specified without a 'data' directory
checkRd: (-1) delta2a.Rd:21: Lost braces; missing escapes or markup?
    21 | delta_k = log(a_k - a_{k+1})
       |                       ^
checkRd: (-1) ordprob.mple.Rd:29: Lost braces
    29 | logical. If code{TRUE} all the q variable are assumed to have the same mean.
       |                 ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Note: found 12992 marked UTF-8 strings
checkRd: (-1) add_bars.Rd:15: Lost braces
    15 | When \\code{y0} is not specified, the lowest value of the y-axis is used.}
       |            ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |       ^
checkRd: (-1) add_bars.Rd:24: Lost braces
    24 | \\code{\\link[graphics]{par}}.}
       |                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
checkRd: (-1) plotluck.Rd:129: Lost braces
   129 |  in factors are are shown as a special factor level code{"?"}. They can be
       |                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein-package.Rd:20: Lost braces
    20 | code{\link{help}}
       |     ^
checkRd: (-1) plotprotein.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
checkRd: (-1) plu_more.Rd:16: Lost braces; missing escapes or markup?
    16 | Additional arguments are replaced with "{n} more".
       |                                         ^
Namespaces in Imports field not imported from:
  ‘base’ ‘grDevices’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pmartRdata’
checkRd: (-1) PMCMR-deprecated.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PMCMR-deprecated.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 62 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                              ^
checkRd: (-1) pmledecon.Rd:113: Lost braces; missing escapes or markup?
   113 |     likelihood less than $10^{-10}$ are replaced by $10^{-10}$.
       |                                                         ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                   ^
checkRd: (-1) ahp.Rd:16: Lost braces; missing escapes or markup?
    16 | an ``A'' matrix. It should be a square matrix with diagonal values equal 1 and $a_{ij} = 1/a_{ij}$.
       |                                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot_scm.Rd:106: Lost braces; missing escapes or markup?
   106 | \item{lookupDF}{A data frame containing a lookup table for node labels. By default, {plot_scm} will use the PSN model names. If a lookup table containing the fields `Model` and `Alias` is provided, model names in `Model` will be replaced in the output plots by mtaching labels in `Alias`.}
       |                                                                                     ^
checkRd: (-1) rnm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnm.Rd:71: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 7256 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
checkRd: (-1) estimate.functional.Rd:34: Lost braces; missing escapes or markup?
    34 | \item{bw}{function describing bandwidth selection (see ?gmm for alternatives). Standard is that the bandwidth depends on the sample length $T$ by $m(T)=T^{1/5}$.}
       |                                                                                                                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pois.fe.robust.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pois.fe.robust.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pois.fe.robust.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 437 marked UTF-8 strings
checkRd: (-1) carcinoma.Rd:8: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) poLCA.Rd:69: Escaped LaTeX specials: \&
Note: found 70 marked UTF-8 strings
Note: found 21 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘formula.tools’ ‘ggplot2’ ‘gplots’ ‘graphics’ ‘purrr’
  ‘rstatix’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Note: found 52 marked UTF-8 strings
Note: found 805 marked Latin-1 strings
  Note: found 12681 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
Running examples in ‘pollimetry-Ex.R’ failed
The error most likely occurred in:

> ### Name: bodysize
> ### Title: Converts the intertegular distance (IT) and co-variates to body
> ###   size in dry weight (mg) for bees or hoverflies.
> ### Aliases: bodysize
> 
> ### ** Examples
> 
> example=cbind.data.frame(IT=c(1.3,2.3),
+                          Sex=c("Female","Male"), 
+                          Subfamily=c("Syrphinae","Eristalinae"),
+                          Region=c("Australasia","Europe"),
+                          Species=c("Sphaerophoria_macrogaster","Myathropa_florea"))
> bodysize(x=example,taxa="hov",type="taxo")
Loading required namespace: pollimetrydata
Failed with error:  ‘there is no package called ‘pollimetrydata’’
Downloading data from: https://github.com/liamkendall/pollimetrydata/raw/master/data/hov_tax_mod.rdata 

SHA-1 hash of the downloaded data file is:
8fabe989dfed6c91d8e5834ad224ff4865b76b7f
Loading required package: rstan
Loading required package: StanHeaders
Error: package or namespace load failed for ‘rstan’ in .doLoadActions(where, attach):
 error in load action .__A__.1 for package rstan: Rcpp::loadModule(module = "class_model_base", what = TRUE, env = ns, : Unable to load module "class_model_base": attempt to apply non-function
Error in .requirePackage(package) : 
  unable to find required package ‘rstan’
Calls: bodysize ... .findInheritedMethods -> getClass -> getClassDef -> .requirePackage
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) inputData.Rd:94: Lost braces
    94 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) inputData.Rd:95: Lost braces
    95 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) preprocessData.Rd:81: Lost braces
    81 | recommend using either \sQuote{code{.}} (a period) or
       |                                    ^
checkRd: (-1) preprocessData.Rd:82: Lost braces
    82 | \sQuote{code{_}} (an underscore) rather than a space.
       |             ^
checkRd: (-1) stat_quantile_prob.Rd:14: Lost braces; missing escapes or markup?
    14 | Number {25, 50, 75}
       |        ^
checkRd: (-1) calculateDIC.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculateDIC.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) polySegratioMM-package.Rd:70-72: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘test-data.R’ ‘test-inits.R’ ‘test.bug’ ‘test.cmd’
checkRd: (-1) MLM_Model.Rd:31: Lost braces; missing escapes or markup?
    31 |   the weight vectors \bold{{w}^{i}} corresponds to class \eqn{i}{i}.
       |                                ^
checkRd: (-1) MLM_Model.Rd:33: Lost braces; missing escapes or markup?
    33 | We set \eqn{{\bold{{w}}^{h}} = 0} and the parameters to be learned are the weight vectors \bold{{w}^{i}}
       |                                                                                                     ^
Running examples in ‘pool-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbPool
> ### Title: Create a pool of database connections
> ### Aliases: dbPool
> 
> ### ** Examples
> 
> # You use a dbPool in the same way as a standard DBI connection
> pool <- dbPool(RSQLite::SQLite())
> pool
<Pool> of SQLiteConnection objects
  Objects checked out: 0
  Available in pool: 1
  Max size: Inf
  Valid: TRUE
> 
> DBI::dbWriteTable(pool, "mtcars", mtcars)
> dbGetQuery(pool, "SELECT * FROM mtcars LIMIT 4")
   mpg cyl disp  hp drat    wt  qsec vs am gear carb
1 21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
2 21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
3 22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
4 21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
> 
> # Always close a pool when you're done using it
> poolClose(pool)
> 
> # Using the RMySQL package
> if (requireNamespace("RMySQL", quietly = TRUE)) {
+   pool <- dbPool(
+     drv = RMySQL::MySQL(),
+     dbname = "shinydemo",
+     host = "shiny-demo.csa7qlmguqrf.us-east-1.rds.amazonaws.com",
+     username = "guest",
+     password = "guest"
+   )
+ 
+   dbGetQuery(pool, "SELECT * from City LIMIT 5;")
+ 
+   poolClose(pool)
+ }
Error in .local(drv, ...) : 
  Failed to connect to database: Error: Unknown server host 'shiny-demo.csa7qlmguqrf.us-east-1.rds.amazonaws.com' (-2)
Calls: dbPool ... <Anonymous> -> dbConnect -> dbConnect -> .local -> .Call
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘why-pool.Rmd’ using rmarkdown

Quitting from lines 34-75 [unnamed-chunk-2] (why-pool.Rmd)
Error: processing vignette 'why-pool.Rmd' failed with diagnostics:
Failed to connect to database: Error: Unknown server host 'shiny-demo.csa7qlmguqrf.us-east-1.rds.amazonaws.com' (-2)

--- failed re-building ‘why-pool.Rmd’

SUMMARY: processing the following file failed:
  ‘why-pool.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.tfam.Rd:17: Lost braces
    17 | objects created using code{tfam_inertia}.}
       |                           ^
checkRd: (-1) popdemo-package.Rd:32: Lost braces
    32 |        code{\link{inertia}} measures asymptotic population density relative to stable
       |            ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |     ^
checkRd: (-1) tfa_inertia.Rd:33: Lost braces
    33 | item{inertia}{inertias of perturbed matrices}
       |              ^
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘population/libs/population.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ActCR’ ‘ActFrag’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) summary.POUMM.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{stats}{a named list of functions of the form function(par) { number },
       |                                                                  ^
Note: found 3208 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) coalesce_xy.Rd:22: Lost braces; missing escapes or markup?
    22 | the \code{conflict} argument of {powerjoin}'s join functions. \code{coalesce_xy()} is
       |                                 ^
checkRd: (-1) power_left_join.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{by}{As in {dplyr}, but extended so user can supply a formula or a list
       |                 ^
checkRd: (-1) power_left_join.Rd:79: Lost braces; missing escapes or markup?
    79 | \item{keep}{A boolean for compatibility with {dplyr}, or a value among "left",
       |                                              ^
checkRd: (-1) preprocess_inputs.Rd:37: Lost braces; missing escapes or markup?
    37 | only be used in the \code{x} and \code{y} arguments of {powerjoin} join functions. No
       |                                                        ^
checkRd: (-1) bira2.Rd:91: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:144: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:146: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) bira2.Rd:150: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:126: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:219: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:221: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:223: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:225: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:227: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:229: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:231: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:233: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:235: Escaped LaTeX specials: \&
checkRd: (-1) cra2.Rd:237: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:301: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:303: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:305: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:307: Escaped LaTeX specials: \&
checkRd: (-1) cra3.Rd:309: Escaped LaTeX specials: \&
checkRd: (-1) med_pn.Rd:129: Escaped LaTeX specials: \&
Note: found 1548 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) ccp_ppm.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{model}{Determines of model fit is such that there are p_{it}s (model=1) or
       |                                                               ^
checkRd: (-1) curve_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) gaussian_ppmx.Rd:143: Lost braces; missing escapes or markup?
   143 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) gaussian_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each subjects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
checkRd: (-1) ordinal_ppmx.Rd:145: Lost braces; missing escapes or markup?
   145 | \item mu - a matrix  of dimension (T, N) containing MCMC iterates associated with each subjects mean parameter (mu*_{c_i}).
       |                                                                                                                     ^
checkRd: (-1) ordinal_ppmx.Rd:147: Lost braces; missing escapes or markup?
   147 | \item sig2 - a matrix of dimension (T, N) containing MCMC iterates associated with each sujbects variance parameter (sigma2*_{c_i})
       |                                                                                                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘rpart’ ‘withr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) pqrBayes.Rd:58: Lost braces; missing escapes or markup?
    58 | When {sparse=TRUE} (default), spike--and--slab priors are adopted. Otherwise, Laplacian shrinkage will be used.
       |      ^
checkRd: (-1) pqrBayes.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pqrBayes.Rd:63: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘bslib’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’ ‘numDeriv’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lmtest’
  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) PRDA.Rd:8: Lost braces; missing escapes or markup?
     8 | Given an hypothetical value of effect size, {PRDA} performs a prospective
       |                                             ^
checkRd: (-1) PRDA.Rd:22: Lost braces; missing escapes or markup?
    22 | In {PRDA} there are two main functions:
       |    ^
checkRd: (-1) PRDA.Rd:51: Lost braces; missing escapes or markup?
    51 | Alternatively, {PRDA} allows users to specify a distribution of plausible
       |                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) diagnose_expressions.Rd:39: Lost braces
    39 | \item wrapping a function argument in two curly braces (e.g. `{{arg}} > 0) means
       |                                                               ^
File ‘precondition/libs/precondition.so’:
  Found non-API calls to R: ‘PRENV’, ‘R_PromiseExpr’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) dev_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dev_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gusto.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) val_data.Rd:14: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: replacing previous import ‘knitr::clean_cache’ by ‘pkgdown::clean_cache’ when loading ‘preferably’
See ‘/data/gannet/ripley/R/packages/tests-devel/preferably.Rcheck/00install.out’ for details.
checkRd: (-1) preference-package.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:58-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:61-63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:78-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference-package.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:24-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) preference.Rd:26-27: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) prereg_initialize.Rd:20: Lost braces; missing escapes or markup?
    20 | the (pre)registration form specification (in {preregr} format), see the
       |                                              ^
checkRd: (-1) prereg_initialize.Rd:23: Lost braces; missing escapes or markup?
    23 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
checkRd: (-1) prereg_initialize.Rd:26: Lost braces; missing escapes or markup?
    26 | For an introduction to working with {preregr} (pre)registrations,
       |                                     ^
checkRd: (-1) rmd_templates.Rd:75: Lost braces; missing escapes or markup?
    75 | This function creates an R Markdown template from a {preregr}
       |                                                     ^
checkRd: (-1) rmd_templates.Rd:77: Lost braces; missing escapes or markup?
    77 | Sheet holding the (pre)registration form specification (in {preregr}
       |                                                            ^
checkRd: (-1) rmd_templates.Rd:81: Lost braces; missing escapes or markup?
    81 | specification, or a loaded or imported {preregr} (pre)registration form.
       |                                        ^
Note: found 96 marked UTF-8 strings
checkRd: (-1) format_number.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) format_number.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) format_number.Rd:38: Lost braces in \itemize; meant \describe ?
Note: found 42966 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘hista.png’ ‘plotcd.png’ ‘test.R’ ‘test.html’ ‘testR2html.R’
  ‘testglm.csv’ ‘testglm.html’ ‘testglm.tab’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 165 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) alogistic.Rd:20: Lost braces
    20 | The user does not put these directly into this function, but rather uses code{ode} in the \code{deSolve} package.
       |                                                                              ^
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
checkRd: (-1) prim.box.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prim.box.Rd:70: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
checkRd: (-1) NesPrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTAllparts.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulab.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulabAll.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulev.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTMulevAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTreg.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) PrInDTregAll.Rd:16: Lost braces
    16 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) RePrInDT.Rd:17: Lost braces
    17 | {see function \code{\link{PrInDT}} for details.}\cr
       | ^
checkRd: (-1) findbeta.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{lower.v}{logical, if TRUE the specified percentile.value is the upper limit for the mean (or the median or the mode) at the specified confidence level (percentile). If {FALSE} the specified percentile.value is the lower limit for the mean (or the median or the mode) at the specified confidence level (percentile). The default is FALSE.}
       |                                                                                                                                                                               ^
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'rcbc'
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
Packages suggested but not available for checking: 'cmdstanr', 'iwmm'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) proc.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) proc.Rd:28: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) paasche.Rd:91: Lost braces
    91 |     \code{OSME} \tab Output-oriented scale-mix efficiency score \emph{(code{orientation = "out"})}\cr
       |                                                                            ^
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) plot.profileModel.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) profileModel.Rd:277: Escaped LaTeX specials: \&
checkRd: (-1) PS.Rd:9: Lost braces
     9 |                 \item{CD}{}{Character disorder scale score}
       |                            ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) proftools-package.Rd:40: Lost braces
    40 |   by the code{kcachegrind} program available on some operating
       |              ^
checkRd: (-1) summary.projections.Rd:33-48: Lost braces
    33 | if (require(incidence)) {
       |                         ^
checkRd: (-1) organize.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) organize.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rebuild.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rebuild.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rebuild.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rebuild.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) prolific_prescreener.Rd:254: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_prescreener.Rd:255: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:96: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:243: Lost braces in \itemize; meant \describe ?
checkRd: (-1) prolific_study.Rd:244: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) impute_plot.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{global}{Logical. If \code{TRUE} ({default}), a global density plot is
       |                                        ^
Note: found 391 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 21 marked Latin-1 strings
  Note: found 150 marked UTF-8 strings
Package suggested but not available for checking: ‘cin’
checkRd: (-1) computeResponseProbability.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{model}{the item model to use. Accepts \code{grm} or {gpcm}.}
       |                                                           ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                  ^
checkRd: (-1) struc_addSimData.Rd:15: Lost braces
    15 | \item{value}{code{data.frame} or code{data.table}}
       |                                      ^
Note: found 4203 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
checkRd: (-1) prototest.univariate.Rd:21: Lost braces
    21 | response variable. Vector of length emph{n}, assumed to be quantitative.
       |                                         ^
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) pr_stem_sentences.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capital letters 
       |                       ^
checkRd: (-1) pr_stem_words.Rd:20: Lost braces; missing escapes or markup?
    20 | Implementation of the {SnowballC} stemmer. Note that punctuation and capitals letters 
       |                       ^
checkRd: (-1) proust_sentiments.Rd:7: Lost braces; missing escapes or markup?
     7 | See the {rfeel} package now: http://github.com/ColinFay/rfeel}
       |         ^
checkRd: (-1) proust_sentiments.Rd:20: Lost braces; missing escapes or markup?
    20 | See the {rfeel} package now: http://github.com/ColinFay/rfeel
       |         ^
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rdt’
File ‘proxy/libs/proxy.so’:
  Found non-API call to R: ‘Rf_NonNullStringMatch’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pryr/libs/pryr.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘NAMED’, ‘PRCODE’,
    ‘PRENV’, ‘PRVALUE’, ‘Rf_findVarInFrame3’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 1 marked UTF-8 string
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) qpc.Rd:43: Lost braces
    43 | S{Sulewski, P. (2020). \emph{Normal Distribution with Plasticizing Component,} Communications in Statistics ? Theory and Method 51(11), 3806-3835.}
       |  ^
checkRd: (-1) riedsid.Rd:92-93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riedsid.Rd:94-96: Lost braces in \itemize; meant \describe ?
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
Note: found 596 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) data1.Rd:14: Lost braces
    14 | The data set from {AbouRizk, S.M., Halpin, D.W., Wilson, J. R. (1994). \emph{Fitting beta distributions based on sample data.} Journal of Construction Engineering and Management 120(2), 288–305.}
       |                   ^
checkRd: (-1) data2.Rd:14: Lost braces; missing escapes or markup?
    14 | The data set presents the height of 99 five-year-old British boys in cm downloaded from {http://www.mas.ncl.ac.uk/njnsm/medfac/docs/intro.pdf.}
       |                                                                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) table1.Rd:14: Lost braces
    14 | The first data set from {Sulewski, P. (2017) \emph{A new test for independence in 2x2 contingency tables,} Acta Universitatis Lodziensis. Folia Oeconomica, 4(330), 55–75}
       |                         ^
checkRd: (-1) table3.Rd:14: Lost braces
    14 | The third data set from {Sulewski, P. (2021). \emph{Logarithmic Minimum Test for Independence in Three Way Con-tingency Table of Small Sizes.} Journal of Statistical Computation and Simulation 91(13), 2780-2799}
       |                         ^
Note: found 26 marked Latin-1 strings
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) dprime.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dprime.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
Namespaces in Imports field not imported from:
  ‘lifecycle’ ‘patchwork’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Note: found 107 marked UTF-8 strings
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
checkRd: (-1) PTE_bootstrap_inference.Rd:39-42: Lost braces
    39 |                                                         continuous = function(Xytrain){ #defalt is OLS regression
       |                                                                                       ^
checkRd: (-1) PTE_bootstrap_inference.Rd:43-47: Lost braces
    43 |                                                         incidence = function(Xytrain){ #default is logistic regression
       |                                                                                      ^
checkRd: (-1) PTE_bootstrap_inference.Rd:48-52: Lost braces
    48 |                                                         survival = function(Xytrain){ #default is Weibull regression
       |                                                                                     ^
checkRd: (-1) PTE_bootstrap_inference.Rd:66-68: Lost braces
    66 |                                         function(mod, Xyleftout){
       |                                                                 ^
checkRd: (-1) PTE_bootstrap_inference.Rd:74-77: Lost braces
    74 |                                         function(results, indices_1_1, indices_0_0, indices_0_1, indices_1_0){
       |                                                                                                              ^
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 28898 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) ptw-package.Rd:20-28: Lost braces
    20 | @Article{Bloemberg2010,
       |         ^
checkRd: (-1) ptw-package.Rd:30-38: Lost braces
    30 | Article{Wehrens2015,
       |        ^
checkRd: (-1) ma.Rd:62: Lost braces
    62 | \item{yi}{Numeric vector of length code{k} with observed effect size
       |                                        ^
checkRd: (-1) ma.Rd:65: Lost braces
    65 | \item{vi}{Numeric vector of length code{k} with sampling variances.}
       |                                        ^
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) plotWordCloud.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{PubMed wordcloud using function 'wordcloud' of package {wordcloud}}
       |                                                               ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                  ^
checkRd: (-1) plotWordCloud.Rd:32: Lost braces; missing escapes or markup?
    32 | This function just call 'wordcloud' from package {wordcloud}. See package {wordcloud} for more details about the parameters.
       |                                                                           ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘itsadug’ ‘mgcv’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
File ‘purrrlyr/libs/purrrlyr.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘purrr/libs/purrr.so’:
  Found non-API calls to R: ‘Rf_findVarInFrame3’, ‘SET_BODY’,
    ‘SET_CLOENV’, ‘SET_FORMALS’, ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) DataSets.Rd:10: Lost braces; missing escapes or markup?
    10 | \format{the \code{PvarQuantileDF} is a \code{data.frame} with fields \code{prob} an {Qaunt}. 
       |                                                                                     ^
checkRd: (-1) pvlrt.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
checkRd: (-1) r_contin_table_zip.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{no_zi_idx}{List of pairs {(i, j)} where zero inflation is not allowed. To
       |                                ^
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘progressr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Ch05-detail.Rd:23: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:24: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:31: Escaped LaTeX specials: \#
checkRd: (-1) Ch05-detail.Rd:32: Escaped LaTeX specials: \#
checkRd: (-1) Ch09-CDF-Pval.Rd:72: Lost braces; missing escapes or markup?
    72 |   G(u) = (1-r) u  + r Fc_A(Fc_0^{-1}(u))
       |                                 ^
checkRd: (-1) Ch10-CDF-Pval-HA.Rd:62: Lost braces; missing escapes or markup?
    62 |   G_A(u) = Fc_A(Fc_0^{-1}(u))
       |                      ^
checkRd: (-1) aid_st2.Rd:6: Escaped LaTeX specials: \&
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) crosstab.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) crosstab.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) srswrRe.Rd:10: Lost braces
    10 |   \item{listRanef}{{\emph{ranef(model)}} object where {\emph{model}} is an { \emph{lmer}} object.}
       |                                                                            ^
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) qgcomp.survcurve.boot.Rd:17-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qgcomp.survcurve.boot.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qgcomp.survcurve.boot.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qgcomp.survcurve.boot.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGlink.funcs.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGmvpred.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) QGpred.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:195: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:196: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:197: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:198: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:199: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:200: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:201: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:202: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:203: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:204: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gmap.Rd:206: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘spDataLarge’
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) qif.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qif.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 1459 marked UTF-8 strings
Note: found 76102 marked UTF-8 strings
Note: found 727 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) qmethod-package.Rd:109: Lost braces
   109 |   \item Van Exel, J., and G. de Graaf, 2005. \emph{Q Methodology: A Sneak Preview}\cr \url{https://qmethodblog.files.wordpress.com/2016/01/qmethodologyasneakpreviewreferenceupdate.pdf}{Available at this link}.
       |                                                                                                                                                                                         ^
checkRd: (-1) qmethod-package.Rd:110: Lost braces
   110 |   \item Brown, S. R., 1980. \emph{Political subjectivity: Applications of Q methodology in political science}, New Haven, CT: Yale University Press.\cr \url{https://qmethodblog.files.wordpress.com/2016/01/brown-1980-politicalsubjectivity.pdf}{Available at this link}.
       |                                                                                                                                                                                                                                                   ^
Namespace in Imports field not imported from: ‘missMethods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) hideLocation.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{trueLoc}{A vector of one or more numbers in the set {1, 2, ..., nSubjects} whose locations are to be hidden.}
       |                                                           ^
checkRd: (-1) hideLocation.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{nSubjects}{An integer larger than 1 used to define the set {1, 2, ..., nSubjects}.}
       |                                                                  ^
'LazyData' is specified without a 'data' directory
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
File ‘qs/libs/qs.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘LEVELS’, ‘PRENV’,
    ‘SETLEVELS’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FRAME’,
    ‘SET_HASHTAB’, ‘SET_PRENV’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’,
    ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
checkRd: (-1) IPWE_mean_IndCen.Rd:54-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) IPWE_mean_IndCen.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{case}{string. One of {"a", "b", "c"}, corresponding to three models.}
       |                            ^
checkRd: (-1) simJLSDdata.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simJLSDdata.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) find_lcp.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) find_lcp.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:18-19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summarize_lcps.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) als_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) als_data_qc_mapping.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:22-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qualpal.Rd:30-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cqs.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:33-35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cqs.Rd:37-45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:35-36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) llqr.Rd:38-41: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 4 marked UTF-8 strings
Note: found 35707 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: Obsolescent feature: Computed GOTO at (1)
See ‘/data/gannet/ripley/R/packages/tests-devel/quantreg.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
checkRd: (-1) quarries.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:20-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:23-25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) quarries.Rd:26-28: Lost braces in \itemize; meant \describe ?
Note: found 8504 marked UTF-8 strings
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
checkRd: (-1) display_table.Rd:37: Lost braces; missing escapes or markup?
    37 | \item{normtest}{A character indicating test of normality, the default method is \code{\link{shapiro.test}} when sample size no more than 5000, otherwise \code{\link[nortest]{lillie.test}} {Kolmogorov-Smirnov} is used, see package \strong{nortest} for more methods.Use 'shapiro.test', 'lillie.test', 'ad.test', etc to specify methods.}
       |                                                                                                                                                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 99 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘quotedargs/libs/quotedargs.so’:
  Found non-API calls to R: ‘LEVELS’, ‘PRCODE’, ‘PRENV’, ‘PRVALUE’,
    ‘SETLEVELS’, ‘SET_NAMED’, ‘SET_PRCODE’, ‘SET_PRENV’, ‘SET_PRVALUE’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 12928 marked UTF-8 strings
Found the following HTML validation problems:
confusion_matrix.html:236:1 (confusion_matrix.Rd:73): Warning: trimming empty <li>
confusion_matrix.html:238:1 (confusion_matrix.Rd:74): Warning: trimming empty <li>
confusion_matrix.html:240:1 (confusion_matrix.Rd:75): Warning: trimming empty <li>
confusion_matrix.html:235:1 (confusion_matrix.Rd:73): Warning: trimming empty <ul>
Note: found 63 marked UTF-8 strings
checkRd: (-1) est.R0.ML.Rd:98: Lost braces
    98 | Supplementary Material S1 from \doi{10.1186/1472-6947-12-147}{Obadia et al., 2012}.
       |                                                              ^
checkRd: (-1) plot.R0.R.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from one estimation method.
       |                                                      ^
checkRd: (-1) plot.R0.sR.Rd:20: Lost braces
    20 | Called for side effect. Draws all \eqn{R_{0}} or /eqn{R(t)} values from an
       |                                                      ^
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) do_admb.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) do_admb.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_pars.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_pars.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘ReGenesees’
Namespaces in Imports field not imported from:
  ‘quickcode’ ‘stats’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked Latin-1 strings
  Note: found 347 marked UTF-8 strings
checkRd: (-1) conf2d.Rd:64: Lost braces; missing escapes or markup?
    64 |   compute a smooth surface from \code{x} and {y}. If users already have
       |                                              ^
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘shiny’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘bootmlm’
checkRd: (-1) bugs.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bugs.Rd:166: Lost braces in \itemize; meant \describe ?
Note: found 2 marked UTF-8 strings
checkRd: (-1) r4ss-package.Rd:9: Lost braces; missing escapes or markup?
     9 | A collection of R functions for use with Stock Synthesis, a fisheries stock assessment modeling platform written in ADMB by Dr. Richard D. Methot at the NOAA Northwest Fisheries Science Center. The functions include tools for summarizing and plotting results, manipulating files, visualizing model parameterizations, and various other common stock assessment tasks. This version of '{r4ss}' is compatible with Stock Synthesis versions 3.24 through 3.30 (specifically version 3.30.19.01, from April 2022).
       |                                                                                                                                                                                                                                                                                                                                                                                                ^
Package suggested but not available for checking: ‘gtfstools’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) extract_class.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) extract_class.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
Repository.html:125:1 (Repository.Rd:129): Warning: trimming empty <ul>
checkRd: (-1) post_RA_fits.Rd:61: Lost braces; missing escapes or markup?
    61 |     \item{\code{H(po_{bm_{n.bm}}, po_act)}:}{ last benchmark prior bm_{n.bm} inducing the fit \code{fits.bm[[n.bm]]} and actual prior}
       |                                                                       ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘comat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
checkRd: (-1) plot-methods.Rd:98: Lost braces
    98 |                         The line width, a emph{positive} number, defaulting to \code{1}. The interpretation is device-specific, and some devices do not implement line widths less than one (see the help on the device for details of the interpretation). Note that this paramater can also represent a list of different line widths, with length of the list corresponding to the number of \code{DVH} or \code{DVH.list} objects (if \code{plot.type="individual"}, number of line widths should correspond to number of individual \code{DVH} objects).
       |                                               ^
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) DataSet-class.Rd:25: Lost braces; missing escapes or markup?
    25 | Example: {fromField:"val1", toField:"value"}.}
       |          ^
checkRd: (-1) amTimeSeries.Rd:119: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) amTimeSeries.Rd:122: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getCurrentStockData.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTransformTS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:114: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules-ts.Rd:158: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rAmCharts-shinymodules.Rd:38: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) makeDesignMatrix.Rd:16: Lost braces; missing escapes or markup?
    16 | is randomized to a certain treatment {j}, the entry of \code{(i,j)} of the
       |                                      ^
File ‘randomizr/libs/randomizr.so’:
  Found non-API call to R: ‘SETLENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
checkRd: (-1) auxfun.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) auxfun.Rd:38-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) addRasterLegend.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) addRasterLegend.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Note: found 15 marked UTF-8 strings
checkRd: (-1) grottaBar.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) grottaBar.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rankL2R.Rd:18: Lost braces; missing escapes or markup?
    18 | where the vector dimension is 2^{response.number}.}
       |                                 ^
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) user_log_dir.Rd:48: Lost braces
    48 | \\env{$XDG_CACHE_HOME} if defined
       |      ^
checkRd: (-1) max.Rd:17: Lost braces
    17 | Returns the maximum of all values in a vector by passing \{code{\link{max}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
checkRd: (-1) min.Rd:17: Lost braces
    17 | Returns the minimum of all values in a vector by passing \{code{\link{min}} as \code{fn} argument to \code{\link{univar}} function.
       |                                                                ^
checkRd: (-1) rapport.inputs.Rd:26: Lost braces
    26 |     \item \emph{dataset inputs}, i.e. the inputs that refer to named element of an |code{R} object provided in \code{data} argument in \code{rapport} call. Currently, \code{rapport} supports only \code{data.frame} objects, but that may change in the (near) future.
       |                                                                                         ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RasterList-Package.Rd:20: Lost braces
    20 | {\code{\link{rasterList}}}{: it is the constructor of a  \code{\link{RasterList-class}} object from a generic \code{object}, it also transforms a \code{\link{RasterList-class}} into another one throungh a function argument. }
       |                           ^
checkRd: (-1) RasterList-Package.Rd:22: Lost braces
    22 | {\code{\link{rasterListFun}}}{: it is a function that constructs  a  particular \code{\link{RasterList-class}} object in which the objects are \code{function}-type. }
       |                              ^
checkRd: (-1) RasterList-Package.Rd:24: Lost braces
    24 | {\code{\link{RasterListApply}}}{: it is a function that allows to operate among two or more \code{\link{RasterList-class}} objects defined in the same spatial extent through a generic function \code{fun(x,y,...)} where \code{x} and \code{y} are each cell/element of two \code{\link{RasterList-class}} objects given as arguments \code{x} and \code{y} of \code{\link{RasterListApply}}.}
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) as_mcmc.list.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Convert a rater_fit object to a {coda} \code{mcmc.list} object.}
       |                                        ^
checkRd: (-1) as_mcmc.list.Rd:16: Lost braces; missing escapes or markup?
    16 | Convert a rater_fit object to a {coda} \code{mcmc.list} object.
       |                                 ^
checkRd: (-1) as_mcmc.list.Rd:13: Lost braces; missing escapes or markup?
    13 | A {coda} mcmc.list object.
       |   ^
GNU make is a SystemRequirements.
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:115-120: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:121-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:125-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dbConnect-AthenaDriver-method.Rd:128-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) S1.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{m_bar}{the sample vector of moments for a specified vector $(h_{a,r},y)$}
       |                                                                      ^
checkRd: (-1) S1.Rd:16: Lost braces; missing escapes or markup?
    16 | \item{N_k}{index of the $ h_{a,r}$ function considered}
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) rbm.haplos.power.Rd:35: Lost braces; missing escapes or markup?
    35 |   \item{simus.haplos}{ Which method to simulate the data, if \code{simus.haplos="freqs"}, {rbm.haplos.freqs()} is used, otherwise \code{rbm.haplos.thresholds()} is used.}
       |                                                                                           ^
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rex’
  All declared Imports should be used.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
checkRd: (-1) rbeta.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rbeta.Rd:35-37: Lost braces in \itemize; meant \describe ?
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) ecoperators-methods.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecoperators-methods.Rd:54: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
getblock.html:58:1 (getblock.Rd:23): Warning: trimming empty <h3>
getrawtransaction.html:57:1 (getrawtransaction.Rd:22): Warning: trimming empty <h3>
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
checkRd: (-1) R.cache-package.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) R.cache-package.Rd:31-34: Lost braces in \itemize; meant \describe ?
Note: found 57456 marked Latin-1 strings
Package suggested but not available for checking: ‘rrelaxiv’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’ ‘shinythemes’
  All declared Imports should be used.
checkRd: (-1) mig_calculate_rc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item pre-working age: {a1, alpha1}
       |                        ^
checkRd: (-1) mig_calculate_rc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item working age: {a2, alpha2, mu2, lambda2}
       |                    ^
checkRd: (-1) mig_calculate_rc.Rd:30: Lost braces; missing escapes or markup?
    30 | \item retirement: {a3, alpha3, mu3, lambda3}
       |                   ^
checkRd: (-1) mig_calculate_rc.Rd:31: Lost braces; missing escapes or markup?
    31 | \item post retirement: {a4, lambda4}
       |                        ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘rlemon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘temp.RData’
checkRd: (-1) nc_open_CGLS.Rd:29-32: Lost braces
    29 | if(resolution == "300m"){
       |                         ^
checkRd: (-1) nc_open_CGLS.Rd:33-36: Lost braces
    33 | if(resolution == "1km"){
       |                        ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) Rchoice.Rd:159: Lost braces; missing escapes or markup?
   159 |  \code{ranp}. If the parameters are assumed to be normally distributed \eqn{\beta_i ~ N(\beta, \Sigma)}, then the random parameter are constructed as: \deqn{\beta_{ir}=\beta+L\omega_{ir}} where \eqn{LL'=\Sigma} and \eqn{\omega_{ir}} is the {r}-th draw from standard normal distribution for individual \eqn{i}. 
       |                                                                                                                                                                                                                                                 ^
Found the following files/directories:
  ‘data.csv’
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘outcmaesdisp.dat’
checkRd: (-1) indexplot.Rd:28: Lost braces
    28 |   \item{legend}{keyword (see \code{link}[grapics]{legend}) giving location of the legend if \code{groups} are specified; 
       |                                                  ^
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) RcmdrPlugin.MA-package.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) RcmdrPlugin.MA-package.Rd:23: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘ROpenOffice’
checkRd: (-1) plotCorpusCa.rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCorpusCa.rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCorpusCa.rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotCorpusCa.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recodeTimeVarDlg.Rd:11-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recodeTimeVarDlg.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recodeTimeVarDlg.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vocabularyTable.rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vocabularyTable.rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vocabularyTable.rd:55: Lost braces
    55 | \seealso{\code{\link{vocabularyDlg}}, code{\link{DocumentTermMatrix}}, \code{\link{table}}, }
       |                                           ^
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
checkRd: (-1) nonlinearAR1.sim.Rd:8: Lost braces; missing escapes or markup?
     8 | of the form z_n = g(z_{n-1}) + epsilon. A normal distribution is assumed for the innovations.
       |                       ^
Note: found 345 marked UTF-8 strings
Package suggested but not available for checking: ‘conics’
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
File ‘RcppBDT/libs/RcppBDT.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
‘configure’: /bin/bash is not portable
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
checkRd: (-1) cSMCexamples.Rd:78-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:81-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cSMCexamples.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) linear_RNDPROJ.Rd:45: Lost braces; missing escapes or markup?
    45 | there is a linear map \eqn{f:R^N} to {R^n} such that
       |                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) halfnorm.like.Rd:105: Lost braces; missing escapes or markup?
   105 |   {f(x|a,b,c_1,c_2,...,c_k) = f(x|a,b)(1 + c(1) h_i1(x) + c(2) h_i2(x) + ... + c(k) h_ik(x)). }
       |   ^
checkRd: (-1) secondDeriv.Rd:15: Lost braces
    15 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) farthest_point_sampling.Rd:28: Lost braces; missing escapes or markup?
    28 | space P = {p_1, ..., p_k}, such that each p_i is the farthest 
       |           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) computeCBMeasure.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) computeCBMeasure.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rdm.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘dataui’
'LazyData' is specified without a 'data' directory
checkRd: (-1) reader-package.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reader-package.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘temp.txt’ ‘temp2.csv’ ‘temp3.rda’
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.skip.Rd:15: Lost braces
    15 | line in the file to determine the {code{skip}} value.}
       |                                   ^
checkRd: (-1) get.skip.Rd:15: Lost braces
    15 | line in the file to determine the {code{skip}} value.}
       |                                        ^
checkRd: (-1) readMzXmlDir.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlDir.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readMzXmlFile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ReAD.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
checkRd: (-1) em_hmm.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{pi}{An estimate of the stationary probabilities of four states {(0,0), (0,1), (1,0), (1,1)}.}
       |                                                                      ^
'LazyData' is specified without a 'data' directory
File ‘readr/libs/readr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
'LazyData' is specified without a 'data' directory
checkRd: (-1) Automotive.Rd:29: Lost braces
    29 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). Own postprocessing.
       |                                                           ^
checkRd: (-1) Automotive.Rd:33: Lost braces
    33 | Wikipedia (2018): \dQuote{Automobilindustrie --- Wikipedia{,} Die freie Enzyklopaedie}. \url{https://de.wikipedia.org/wiki/Automobilindustrie} (accessed October 14, 2018). 
       |                                                           ^
Note: found 8 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1036 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) recombinator.Rd:32-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) recombinator.Rd:35-38: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) pseudo.geefit.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.geefit.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.onedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.threedim.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pseudo.twodim.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) simEvent.Rd:112: Lost braces; missing escapes or markup?
   112 | and another argument named {zCoef} for covariate coefficient vector.
       |                            ^
Note: found 9590 marked UTF-8 strings
Running ‘spelling.R’
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ...6c6
< NULL
---
> All Done!
  Running ‘testthat.R’ [6s/20s]
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
File ‘redland/libs/redland.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
checkRd: (-1) make_refreshable.Rd:13: Lost braces
    13 | not that quotes need to be escaped (code{\"}).}
       |                                         ^
Note: found 24832 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘EnvironmentalA.txt’ ‘EnvironmentalB.txt’ ‘Example.txt’
  ‘Example_Predictions.txt’ ‘Example_RRDist.txt’
  ‘Example_RRDistCol.TIF’ ‘Example_RRDistGrey.TIF’ ‘GeneticA.txt’
  ‘GeneticB.txt’ ‘Inds.txt’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 20 marked UTF-8 strings
checkRd: (-1) impute_down_nuts.Rd:21: Lost braces
    21 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
checkRd: (-1) validate_data_frame.Rd:19: Lost braces
    19 | NUTS typologies, defaults to code{"geo_var".}}
       |                                  ^
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) fbase1.binomial.Rd:32: Lost braces; missing escapes or markup?
    32 | In all base log-likelihood functions, we have dropped any additive terms that are independent of the distribution parameter, e.g. constant terms or those terms that are dependent on the response variable only. This is done for computational efficiency. Therefore, these functions cannot be used to obtain the absolute values of log-likelihood functions but only in the context of optimization and/or sampling. Users can write thin wrappers around these functions to add the constant terms to the function value. (Derivatives do not need correction. For binomial family, all factorial terms are ignored since they only depend on \code{n} and {y}.)
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  ^
checkRd: (-1) app_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{input, output, session}{Internal parameters for {shiny}.
       |                                                       ^
checkRd: (-1) plot.ehh.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}} and \code{\link[graphics]{matplot}}). 
       |                                ^
checkRd: (-1) plot.ehhs.Rd:27: Lost braces
    27 | \item{type}{plot type (see code{\link[graphics]{plot.default}}.
       |                                ^
File ‘rehh/libs/rehh.so’:
  Found non-API call to R: ‘SETLENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
checkRd: (-1) polarizacion_Dalton.Rd:26: Lost braces; missing escapes or markup?
    26 | {Pd = sqrt(sum(p_j*(x_j-mean(x_p))/4.5)^2)}
       | ^
checkRd: (-1) reparto_div.Rd:37: Lost braces; missing escapes or markup?
    37 | The set of divisors is formed by the odd numbers, that is {1,3,..,2n+1}.
       |                                                           ^
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
checkRd: (-1) rem.dyad.Rd:121: Lost braces; missing escapes or markup?
   121 | \item Single or multiple covariates, time varying: For \code{CovSnd}, \code{CovRec}, or \code{CovInt}, an \code{m} by \code{p} by {n} array whose respective dimensions index time (i.e., event number), covariate, and actor.  For \code{CovEvent}, a \code{m} by \code{p} by \code{n} by \code{n} array, whose dimensions are analogous to the previous case.
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) rentrez.Rd:17-21: Lost braces
    17 | /enumerated{
       |            ^
Note: found 6034 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: 'sum' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL. [-Wintrinsic-shadow]
  Warning: Obsolescent feature: Computed GOTO at (1)
See ‘/data/gannet/ripley/R/packages/tests-devel/repeated.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
checkRd: (-1) twosidedPValuestobins.Rd:84: Lost braces; missing escapes or markup?
    84 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
checkRd: (-1) ztobins.Rd:90: Lost braces; missing escapes or markup?
    90 | A matrix with \code{n.bins + 1} rows and {ncol(zmat)} columns, representing for each study the discretization chosed. Values are the between bin breaks. First and last values are the edges of the outmost bins.
       |                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) method.A.Rd:200-205: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:206-211: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:231-236: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.A.Rd:237-242: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:201-206: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:207-212: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:232-237: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) method.B.Rd:238-243: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘PackageCites.bib’
'LazyData' is specified without a 'data' directory
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) repo_build.Rd:44-47: Lost braces
    44 | ## chunk "item 1" {
       |                   ^
checkRd: (-1) repo_dependencies.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:49-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) repo_dependencies.Rd:51-53: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 25 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) NCBirths2004.Rd:16: Lost braces
    16 |     \item{\code{Smoker}}{Mother a smoker? code{No}, \code{Yes}}
       |                                               ^
checkRd: (-1) ExpandProbs.Rd:35: Lost braces; missing escapes or markup?
    35 |      {z_probs2 sqrt((n-1)/n) = t_probs,n-1}
       |      ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) cast.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) cast.Rd:46: Escaped LaTeX specials: \_
File ‘reshape2/libs/reshape2.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) as-data-frame-cast-df-v7.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-data-frame-cast-matrix-59.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-df-bu.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) as-matrix-cast-matrix-2y.rd:3: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:19: Escaped LaTeX specials: \_ \_
checkRd: (-1) cast-9g.rd:41: Escaped LaTeX specials: \_
checkRd: (-1) cast-9g.rd:46: Escaped LaTeX specials: \_ \_
checkRd: (-1) clean-vars-rc.rd:13: Escaped LaTeX specials: \_
checkRd: (-1) expand-kx.rd:15: Escaped LaTeX specials: \_
checkRd: (-1) reshape-4u.rd:17: Escaped LaTeX specials: \_ \_
checkRd: (-1) resistance.Rd:52: Lost braces
    52 |     \item B. Bollob\'{a}s, 1998.  \emph{Modern Graph Theory}.  Springer.
       |                      ^
Note: found 1214 marked UTF-8 strings
checkRd: (-1) harmonize_values.Rd:44: Lost braces; missing escapes or markup?
    44 | \item{perl}{Use perl-like regex? Defaults to {FALSE}.}
       |                                              ^
checkRd: (-1) elink.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elink.Rd:74-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) reutils-package.Rd:114: Lost braces
   114 |      code{reutils.test.remote} to \code{TRUE} to run the full suite of tests.
       |          ^
checkRd: (-1) cpUpper.Rd:39: Lost braces
    39 | \code{"fastfloyd"}{ (default) uses an iterative variant of the Floyd-Warshall algorithm, in which the check of consistency of the current observation with a given cluster is done in a single step of the Floyd-Warshall algorithm. Much faster than \code{"floyd"}.}
       |                   ^
checkRd: (-1) cpUpper.Rd:41: Lost braces
    41 | \code{"floyd"}{ uses the algorithm described in Crawford and Pendakur (2013): at each step the complete Floyd-Warshall algorithm is run to check whether each cluster can accomodate the current observation.}
       |               ^
checkRd: (-1) rec.Rd:23: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Note: found 26 marked UTF-8 strings
checkRd: (-1) saveRev.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{use_wd}{logical - If TRUE, the history will be prepended by setwd({'users current working directory'}). This function will set the script's working directory to
       |                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘Rfast/libs/Rfast.so’:
  Found non-API call to R: ‘HASHTAB’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘RFCCA/libs/RFCCA.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) fs_search.Rd:76: Lost braces
    76 | \\code{\link{fs_auth}} \code{\link{fs_browse}}
       |       ^
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RFlocalfdr.data’ ‘vita’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RFpredInterval/libs/RFpredInterval.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
checkRd: (-1) tk.browse.Rd:29: Lost braces
    29 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel (see the 'Typing R commands while browsing' section below), the code{TRUE} value is used essentially in the stand alone version.
       |                                                                                                                                                                                                                                                           ^
checkRd: (-1) tk.convert.Rd:17: Lost braces
    17 |     Single logical value, whether to wait for the interface window to be closed before unfreezing the R console. The \code{FALSE} default let you use R and the interface in parallel, the code{TRUE} is used essentially in the stand alone version.
       |                                                                                                                                                                                                ^
checkRd: (-1) tk.tracks.Rd:8: Lost braces
     8 |   This function allows to load and edit the \code{\linkS4class{drawable.list}} object that is to be passed to \code{\link{tk.browse}} and code{\link{browsePlot}}, using a Tcl-tk interface
       |                                                                                                                                               ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) GenDataPopulation.Rd:21: Lost braces
    21 | {data}{Population of data}
       |       ^
checkRd: (-1) GenDataSample.Rd:23: Lost braces
    23 | {data}{Sample of data}
       |       ^
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘hoardr’
  All declared Imports should be used.
checkRd: (-1) RiemannianMetric.Rd:450-453: Lost braces
   450 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:484-487: Lost braces
   484 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
checkRd: (-1) RiemannianMetric.Rd:588-591: Lost braces
   588 | if (reticulate::py_module_available("geomstats")) {
       |                                                   ^
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
checkRd: (-1) Ghana_2021_school_attendance.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Ghana_2021_school_attendance_geometry.Rd:75: Lost braces in \itemize; meant \describe ?
Found the following files/directories:
  ‘Crashpad’
checkRd: (-1) regCVCF.Rd:52: Lost braces; missing escapes or markup?
    52 | a decision tree with {C4.5} on each one. Using each classifier, a prediction of the whole dataset is obtained.
       |                      ^
checkRd: (-1) summary.rfdata.Rd:17: Lost braces; missing escapes or markup?
    17 | A list including information related to the noise filtering process contained in the object \code{object} of class {rfdata} with the following elements:
       |                                                                                                                    ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘attempt’ ‘curl’ ‘knitr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) code_sawtooth_design.Rd:53: Lost braces
    53 | /url{http://www.sawtoothsoftware.com/help/lighthouse-studio/manual/index.html?hid_web_cbc_exporting.html}
       |     ^
'LazyData' is specified without a 'data' directory
Note: found 1471 marked UTF-8 strings
checkRd: (-1) rhandsontable-package.Rd:8: Lost braces
     8 | R interface for creating tables using Handsontable, url{https://handsontable.com/}
       |                                                        ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘mydata.rda’ ‘thedata.rda’
checkRd: (-1) GenerateClusterData.Rd:34: Lost braces; missing escapes or markup?
    34 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2},
       |                                                ^
checkRd: (-1) GenerateClusterData.Rd:35: Lost braces; missing escapes or markup?
    35 | -v_{(numberOfClusters-1)/2} (if \code{numberOfClusters} is odd)
       |    ^
checkRd: (-1) GenerateClusterData.Rd:36: Lost braces; missing escapes or markup?
    36 | origin, v_1, -v_1, v_2, -v_2, v_3, -v_3,..., v_{(numberOfClusters-1)/2}
       |                                                ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:25-26: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:27-28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:29-30: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:31-32: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:33-34: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:35-36: Lost braces
    35 |    \item{pam_cluster_64_7_5715},{N=64, seven clusters with 5715 vectors per
       |                                 ^
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:37-38: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringDefaultMicrobenchmarks.Rd:39-40: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:21-22: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) GetClusteringExampleMicrobenchmarks.Rd:23-24: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 667 marked UTF-8 strings
Found the following files/directories:
  ‘rnaturalearthhires’
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
Error(s) in re-building vignettes:
--- re-building ‘BadCoordinateID.Rmd’ using rmarkdown
--- finished re-building ‘BadCoordinateID.Rmd’

--- re-building ‘BasicUsage.Rmd’ using rmarkdown
--- finished re-building ‘BasicUsage.Rmd’

--- re-building ‘Fields.Rmd’ using rmarkdown

Quitting from lines 76-99 [unnamed-chunk-4] (Fields.Rmd)
Error: processing vignette 'Fields.Rmd' failed with diagnostics:
replacement has length zero
--- failed re-building ‘Fields.Rmd’

--- re-building ‘FindTissue.Rmd’ using rmarkdown
[WARNING] Div at FindTissue.knit.md line 175 column 1 unclosed at FindTissue.knit.md line 8628 column 1, closing implicitly.
--- finished re-building ‘FindTissue.Rmd’

--- re-building ‘IDDataFlags.Rmd’ using rmarkdown
--- finished re-building ‘IDDataFlags.Rmd’

--- re-building ‘MediaAPIDemo.Rmd’ using rmarkdown
Warning in get_engine(options$engine) :
  Unknown language engine 'undefined' (must be registered via knit_engines$set()).
--- finished re-building ‘MediaAPIDemo.Rmd’

--- re-building ‘ModifiedDataID.Rmd’ using rmarkdown
--- finished re-building ‘ModifiedDataID.Rmd’

--- re-building ‘RecordAPIDemo.Rmd’ using rmarkdown
[WARNING] Div at RecordAPIDemo.knit.md line 200 column 1 unclosed at RecordAPIDemo.knit.md line 11795 column 1, closing implicitly.
--- finished re-building ‘RecordAPIDemo.Rmd’

--- re-building ‘ridigbio.Rmd’ using rmarkdown
--- finished re-building ‘ridigbio.Rmd’

SUMMARY: processing the following file failed:
  ‘Fields.Rmd’

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
checkRd: (-1) iex.chart.Rd:23: Lost braces; missing escapes or markup?
    23 | r takes only of of the values accepted IN API request. {"5y", "2y", "1y", "ytd", "6m", "3m", "1m", "1d"}
       |                                                        ^
checkRd: (-1) descrip.Rd:122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:123: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:124-125: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:126-128: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:129-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:139-140: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:141-144: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:145-146: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:147: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:148: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) descrip.Rd:149: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) correct_sign.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct_sign.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘SET_TYPEOF’, ‘run_Rmainloop’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 169 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘maxLik’
  All declared Imports should be used.
checkRd: (-1) riskParityPortfolio.Rd:163: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:164: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:167: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:168: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) riskParityPortfolio.Rd:170: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       | ^
checkRd: (-1) riskPredict.Rd:38: Lost braces
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |     ^
checkRd: (-1) riskPredict.Rd:38: Lost braces; missing escapes or markup?
    38 | {hat{eta}_c^{(1)}} based on the prediction rule.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       | ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |     ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |             ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                      ^
checkRd: (-1) riskPredictDiff.Rd:34: Lost braces; missing escapes or markup?
    34 | {hat{eta}_c^{(1)}-hat{eta}_c^{(2)}} based on the 2 prediction rules.}
       |                              ^
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Note: found 243 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘B110711CD4.CSV’ ‘inputparam2.txt’ ‘itcout0.pdf’ ‘itcout1.eps’
  ‘origin_data.csv’
'LazyData' is specified without a 'data' directory
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                             ^
checkRd: (-1) RivivcA.Rd:7: Lost braces
     7 | This is the major function to be called where numerical convolution ad/or deconvolution might be used for a linear in vitro in vivo correlation level A. It performes either numerical convolution via /code{NumConv()} or deconvolution via /code{NumDeconv()} and correlates their results with the known.data object via linear regression \code{lm()}. If you just want raw results of convolution/deconvolution then call explicitely \code{\link{NumConv}} or \code{link{NumDeconv}}
       |                                                                                                                                                                                                                                                   ^
Non-standard file/directory found at top level:
  ‘jri’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
Licence stub is invalid DCF.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘RJSONIO/libs/RJSONIO.so’:
  Found non-API call to R: ‘VECTOR_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) Exponential.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) Gamma.Rd:80: Escaped LaTeX specials: \&
checkRd: (-1) college.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) college.Rd:15: Escaped LaTeX specials: \$
Package which this enhances but not available for checking: ‘winch’
File ‘rlang/libs/rlang.so’:
  Found non-API calls to R: ‘ENVFLAGS’, ‘FRAME’, ‘HASHTAB’, ‘LEVELS’,
    ‘NAMED’, ‘PRENV’, ‘PRVALUE’, ‘RDEBUG’, ‘R_PromiseExpr’,
    ‘Rf_findVarInFrame3’, ‘SETLENGTH’, ‘SET_BODY’, ‘SET_CLOENV’,
    ‘SET_ENCLOS’, ‘SET_ENVFLAGS’, ‘SET_FORMALS’, ‘SET_GROWABLE_BIT’,
    ‘SET_RDEBUG’, ‘SET_TRUELENGTH’, ‘SET_TYPEOF’, ‘STRING_PTR’,
    ‘XTRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'DoubletFinder', 'RcppPlanc'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) basic_GS.Rd:42: Lost braces; missing escapes or markup?
    42 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
checkRd: (-1) basic_SSOR.Rd:45: Lost braces; missing escapes or markup?
    45 | \eqn{L} and {U} are strictly lower/upper triangular matrix respectively.
       |             ^
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘rnaturalearthhires’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ms_simplify.Rd:36: Lost braces
    36 | \url{https://github.com/mbloch/mapshaper/wiki/Simplification-Tips}{link}
       |                                                                   ^
Note: found 31 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) setOption.Matlab.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setOption.Matlab.Rd:40-41: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
checkRd: (-1) ComprehensiveTemperatureGenerator.Rd:68: Lost braces; missing escapes or markup?
    68 | \item{exogen_all}{data frame containing exogenous variable formatted like \code{Tx_all} and {Tn_all}. Default is \code{NULL}. 
       |                                                                                             ^
checkRd: (-1) qqplot_RMAWGEN_Tx.Rd:70: Lost braces; missing escapes or markup?
    70 | \code{Tx_gen},{Tn_gen} and \code{main} must have an even number of elements.
       |               ^
GNU make is a SystemRequirements.
checkRd: (-1) RMBC.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBC.Rd:31-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:52-53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:60-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RMBCaux.Rd:62-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robustINIT.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) weightedSestimator.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cGARCHfilter-class.Rd:57: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHfit-class.Rd:59: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHsim-class.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) cGARCHspec-class.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) cgarchsim-methods.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfft-class.Rd:65: Lost braces
    65 | code{dfft(object, index=0)} on an object created from a forecast with 
       |     ^
checkRd: (-1) goGARCHfilter-class.Rd:155: Escaped LaTeX specials: \&
checkRd: (-1) goGARCHfit-class.Rd:166: Escaped LaTeX specials: \&
checkRd: (-1) rmgarch-package.Rd:73: Escaped LaTeX specials: \&
checkRd: (-1) mgraph.Rd:62: Lost braces
    62 |   \item{TC}{target class (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes. If multi-class and TC==-1 then TC is set to 
       |                                                                        ^
checkRd: (-1) mmetric.Rd:112: Lost braces
   112 |   \item{TC}{target class index or vector of indexes (for multi-class classification class) within {1,...,\emph{Nc}}, where \emph{Nc} is the number of classes:<cr>
       |                                                                                                   ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                 ^
checkRd: (-1) mparheuristic.Rd:27: Lost braces
    27 | except for SVM several \code{rbfdot} kernel based models (\code{"ksvm"},\code{"rsvm"},\code{"lssvm"}, which can assume \code{2^}{search-range}; please check the result of this function to confirm if the search is linear or \code{2^}{search-range}). 
       |                                                                                                                                                                                                                                         ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                 ^
checkRd: (-1) histMisclassif.Rd:22: Lost braces
    22 | err_i = 1 - max_{k={1,\ldots,K}} P(Z_i=k|x_i)
       |                    ^
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 7 marked UTF-8 strings
checkRd: (-1) nsgaControl.Rd:20-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:28-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:36-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nsgaControl.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot-methods.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) DO.unit.convert.Rd:24: Lost braces; missing escapes or markup?
    24 |     Units of dissolved oxygen concentration desired, i.e. to be converted to. Must be \code{"mg/L"}, \code{"PP"}, or {"pct"}.
       |                                                                                                                      ^
checkRd: (-1) MR.loops.Rd:80: Lost braces; missing escapes or markup?
    80 | Returns a list of 2. \code{$MR.summary} is of class {data.frame} with 3 columns: \code{$MR} (metabolic rate in user specified units, this is the same as the slope in each linear model), \code{$sd.slope} (standard deviation of slopes calculation), \code{$r.square} (adjusted r square value from each model). This second object is a list of \code{biglm} objects, each one representing a metabolic loop (see McDonnell and Chapman 2016). 
       |                                                     ^
checkRd: (-1) get.pcrit.Rd:27: Lost braces; missing escapes or markup?
    27 | Metabolic rate variable name, formatted as character. Default = \code{NULL}. If this argument takes a value, Pcrit will be calculated by regressing \code{MR.var.name} on \code{DO.var.name}. \code{time.var} and {time.interval} should, in this case, take no value. If \code{MR.var.name} is left as\code{NULL}, then instantaneous metabolic rates (MR) at specified time intervals (see \code{time.interval}) from \code{DO.var.name} and \code{time.var}.
       |                                                                                                                                                                                                                   ^
checkRd: (-1) tot.rss.Rd:35: Lost braces
    35 | code{\link{sumsq}}
       |     ^
checkRd: (-1) tot.rss.Rd:36: Lost braces
    36 | code{\link{get.pcrit}}
       |     ^
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
checkRd: (-1) myTarGetClientList.Rd:33: Lost braces
    33 | {MyTarget API Documenation}{https://target.my.com/doc/api/detailed/#resource_agency_clients}
       |                            ^
Note: found 26259 marked UTF-8 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Note: found 2800 marked UTF-8 strings
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
checkRd: (-1) NCEP.track2kml.Rd:36: Lost braces
    36 |   There are several options for specifying \code{col.scheme}.  A single color may be specified for all points (using e.g. \code{'red'}, \code{2}, or \code{"#FF0000"}), specific colors may be given for each point (e.g. \code{c('red','blue','green', etc.)} or code{c('#FF0000','#0000FF','#00FF00', etc.)}), or the function can automatically assign colors, according to the values in \code{clo.variable}, if \code{col.scheme} is any color palette in \code{\link[RColorBrewer]{display.brewer.all}} or one of the recognizezd R color palettes (i.e. \code{'rainbow'}, \code{'heat.colors'}, \code{'terrain.colors'}, \code{'topo.colors'}, \code{'cm.colors'}, or \code{'bpy.colors'}).  An alpha value (0-255) may be supplied to \code{point.alpha} to adjust transparencies.
       |                                                                                                                                                                                                                                                                       ^
checkRd: (-1) rncl.Rd:53-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:59-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:65-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:73-78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:80-84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:86-90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:92-93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:98-99: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:101-102: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:107-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:112-115: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:117-119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rncl.Rd:121-124: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
checkRd: (-1) NlistServersInCategory.Rd:11: Escaped LaTeX specials: \_
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RNetCDF/libs/RNetCDF.so’:
  Found non-API call to R: ‘Rf_findVarInFrame3’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) nexml_get.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nexml_get.Rd:35: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘RNifti/libs/RNifti.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘RNiftyReg/libs/RNiftyReg.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘attention’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fData.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mfData.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:45-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:55-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:59-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:63-65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:66-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:70-71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) outliergram.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) outliergram.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Note: found 19 marked UTF-8 strings
GNU make is a SystemRequirements.
checkRd: (-1) predict.robu.Rd:36-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:43-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.robu.Rd:50-55: Lost braces in \itemize; meant \describe ?
Note: found 6 marked UTF-8 strings
Specified C++11: please drop specification unless essential
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) descriptiveTable.Rd:18: Lost braces
    18 | other object type that does not fail in code{model.frame(object)}.}
       |                                             ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) performance.Rd:35: Escaped LaTeX specials: \#
checkRd: (-1) performance.Rd:36: Escaped LaTeX specials: \# \# \#
checkRd: (-1) performance.Rd:37: Escaped LaTeX specials: \# \#
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_equality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:27: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:28: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_plugin_build_inequality_constraints.Rd:29: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) ROI_solve.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:28-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ROI_solve.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 261 marked UTF-8 strings
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) update_tidy_omic.Rd:16-17: Lost braces
    16 | in \code{updated_tidy_data} (names) and the table {features, samples,
       |                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) read_ascii.Rd:33: Lost braces
    33 | \item{respondent_pattern}{For use when the file does not contain a line for every card for every respondent (or contains extra lines that correspond to no respondent), a regular expression that matches the file's respondent identifier; e.g., if the respondent number is stored in the first four digits of each line, preceded by a space, "(?<=^\\s)\\d{4}".}
       |                                                                                                                                                                                                                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                       ^
checkRd: (-1) osm_url_spec.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{server_url}{A url using `{x}`, `{y}`, and `{z}` for the x, y, and
       |                                                  ^
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘RandomFields’
checkRd: (-1) Clyde.Rd:8: Lost braces
     8 | These data record the water quality, in terms of dissolved oxygen (\code{DO}) on a percentage scale, at a number of sampling stations (\code{Station}) on the River Clyde.  The date (\code{Day}, \\code{Month}, \code{Year}) is also available, along with the day of the year (\code{Doy} between 1 and 365) and an identified (\code{id}) of the survey on which each measurement was made.
       |                                                                                                                                                                                                         ^
checkRd: (-1) rp.pos.Rd:22-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:25-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:28-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:31-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rp.pos.Rd:43: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) rpivotTable.Rd:60: Lost braces; missing escapes or markup?
    60 | An example is: onRefresh=htmlwidgets::JS("function(config) { Shiny.onInputChange('myPivotData', config); }")
       |                                                            ^
checkRd: (-1) plotImage.blcTree.Rd:17: Lost braces
    17 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) plotImage.glcTree.Rd:16: Lost braces
    16 |   \item{method}{Method to determine width of columns that represent classes: \dQuote{weight} (subject weight in class) or dQuote{binary} (depth in tree).}
       |                                                                                                                                 ^
checkRd: (-1) get.poetry.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{output}{Can be any or a combination of the input terms {'author', 'title', 'lines', 'linecount'}. If NULL, all
       |                                                              ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘SparseM’ ‘nlme’ ‘timeDate’
  All declared Imports should be used.
checkRd: (-1) rpql.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rpql.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.tg.Rd:18: Lost braces; missing escapes or markup?
    18 | Renames the \code{class(tg)["name"]} attribute and sets {class(tg)["type"] <- "TextGrid"} (if it is not already set)
       |                                                         ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) psel.Rd:83: Lost braces; missing escapes or markup?
    83 | For example, a \code{top=1} preference selection on the tuples {(a=1, b=1), (a=1, b=2)}
       |                                                                ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘ROCit’ ‘corrplot’ ‘kableExtra’ ‘purrr’ ‘reshape2’
  All declared Imports should be used.
checkRd: (-1) check_node.Rd:11: Lost braces
    11 | \item{x}{\\code{list}, the node to check}
       |                ^
File ‘RProtoBuf/libs/RProtoBuf.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
checkRd: (-1) rptBinary.Rd:89: Lost braces
    89 |      Note that the distribution might not be symmetrical, in which case the emph{se} is less informative.}
       |                                                                                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ex.Rd:20: Lost braces
    20 | Execute a ops-dag using `code{wrap()}` data as values.
       |                              ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                          ^
checkRd: (-1) sql_node.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{expand_braces}{logical if TRUE use {col} notation to ensure {col} is a column name.}
       |                                                                   ^
checkRd: (-1) R2_lik.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{R2_lik()} is also computed for LMMs and GLMMs in the {MuMIn} package.
       |                                                            ^
checkRd: (-1) R2_pred.Rd:32: Lost braces; missing escapes or markup?
    32 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of R2_resid.
       |                                                                                                            ^
checkRd: (-1) R2_resid.Rd:69: Lost braces; missing escapes or markup?
    69 | Note that the version of \code{binaryPGLMM()} in the package ape is replaced by a version contained within {rr2} that outputs all of the required information for the calculation of \code{R2_resid()}
       |                                                                                                            ^
File ‘rrapply/libs/rrapply.so’:
  Found non-API call to R: ‘Rf_isValidString’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following files/directories:
  ‘HL_H0.pdf’ ‘pi0infer.pdf’ ‘rate.txt’ ‘summary.txt’
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                            ^
checkRd: (-1) Boost.Rd:40: Lost braces; missing escapes or markup?
    40 | \item{niter}{number of boosting iterations (for RRBoost: T_{1,max} + T_{2,max}) (numeric)}
       |                                                                        ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                             ^
checkRd: (-1) Boost.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{niter}{number of iterations for the boosting algorithm (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                                                         ^
checkRd: (-1) Boost.control.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{n_init}{number of iterations for the SBoost step of RRBoost ($T_{1,max}$) (int)}
       |                                                                       ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                  ^
checkRd: (-1) Boost.validation.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{niter}{number of iterations (for RRBoost T_{1,max} + T_{2,max}) (numeric)}
       |                                                              ^
checkRd: (-1) rrecsys.Rd:72: Lost braces; missing escapes or markup?
    72 |  The average deviation rating $dev_{ij}$ between co-rated items is defined by:
       |                                    ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |           ^
checkRd: (-1) rrecsys.Rd:76: Lost braces; missing escapes or markup?
    76 |  Where $c_{ij}$ is the number of co-ratings between items $i$ and $j$ and $r_{ui}$ is an existing rating for user $u$ on item $i$. The Weighted Slope One takes into account both, information from users who rated the same item and the number of observed ratings.
       |                                                                              ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) lateformeeting.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lateformeeting.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lfm_clean.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) regrad.Rd:46: Lost braces; missing escapes or markup?
    46 |  \item \code{x-axis} {1st column: The names of the different institutions}
       |                      ^
checkRd: (-1) regrad.Rd:47: Lost braces; missing escapes or markup?
    47 |  \item \code{y-axis} {2nd column: The value to show completeness}
       |                      ^
Note: found 192 marked UTF-8 strings
checkRd: (-1) rrinf_clust.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}. See \link{example_clustering} for details.}
       |                                                                                  ^
checkRd: (-1) rrtest_clust.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{clustering}{A \code{List} that specifies a clustering of datapoint indexes {1, ..., n}.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) mrrr.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:69-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:71-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mrrr.Rd:74: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) landslides.Rd:11-21: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) landslides.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) landslides.Rd:22-26: Lost braces
    22 | \item \code{dem} {Digital elevation model given as a .Rd grid, i.e. a list
       |                  ^
checkRd: (-1) landslides.Rd:27-28: Lost braces
    27 | \item \code{study_area} {An \code{sf}-object representing the outlines of
       |                         ^
checkRd: (-1) rsaga.get.modules.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rsaga.get.modules.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) rSCA.modeling.Rd:61: Lost braces; missing escapes or markup?
    61 |                 a predefined string to specify how the information of leaf nodes will be stored in the map file. A full list of options for mapvalue is: {mean, max, min, median, interval, radius, variation, random}. Default value is "mean". Use "interval" to get an interval bounded by the minimum and maximum values, (i.e., [min, max]). The option of "radius" will output the mean and the radius [i.e., (max - min) / 2] at the same time. Use "variation" to output the mean and the standard deviation. The option of "random" will output the information as an interval like the "interval" option, but it will use a random value within the interval as the predicted value.
       |                                                                                                                                                          ^
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘keys’ ‘shinyWidgets’ ‘testthat’
  All declared Imports should be used.
checkRd: (-1) remoteDriver-class.Rd:39-40: Lost braces
    39 | browser being used; should be one of {chrome|firefox|htmlunit|
       |                                      ^
checkRd: (-1) remoteDriver-class.Rd:50: Lost braces; missing escapes or markup?
    50 | of {WINDOWS|XP|VISTA|MAC|LINUX|UNIX}. When requesting a new session,
       |    ^
checkRd: (-1) remoteDriver-class.Rd:194-196: Lost braces
   194 |   element, available schemes: {"class name", "css selector",
       |                               ^
checkRd: (-1) webElement-class.Rd:50-52: Lost braces
    50 |     element, available schemes: {"class name", "css selector",
       |                                 ^
checkRd: (-1) webElement-class.Rd:67-69: Lost braces
    67 |     element, available schemes: {"class name", "css selector",
       |                                 ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API calls to R: ‘R_Consolefile’, ‘R_Outputfile’,
    ‘R_TempDir’, ‘R_Visible’, ‘R_curErrorBuf’, ‘ptr_R_Busy’,
    ‘ptr_R_ClearerrConsole’, ‘ptr_R_FlushConsole’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_ResetConsole’, ‘ptr_R_ShowMessage’, ‘ptr_R_WriteConsole’,
    ‘ptr_R_WriteConsoleEx’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 606 marked UTF-8 strings
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MatrixExtra’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) box_m.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) box_m.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wilcox_test.Rd:91: Lost braces; missing escapes or markup?
    91 |  distribution of \code{(u+v)/2}, where \code{u} and {v} are independent, each
       |                                                     ^
Running examples in ‘rstpm2-Ex.R’ failed
The error most likely occurred in:

> ### Name: voptimize
> ### Title: Vectorised One Dimensional Optimization
> ### Aliases: voptimize voptimise
> ### Keywords: optimize
> 
> ### ** Examples
> 
> require(graphics)
> 
> f <- function (x, a) (x - a)^2
> xmin <- voptimize(f, lower=c(0, 0), upper=c(1,1), tol = 0.0001, a = c(1/3,2/3))
Warning in voptimizeRcpp(function(arg) f(arg, ...), lower, upper, tol) :
  subscript out of bounds (index 1 >= vector size 1)
Error: segfault from C stack overflow
Execution halted
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
checkRd: (-1) RTDE.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) RTDE.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                              ^
checkRd: (-1) LBA-race.Rd:157: Lost braces
   157 |   corresponding (and not first) accumulator winning see /code{/link{LBA}}.
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘test_addPageBreak.doc’ ‘test_addPlot.doc’ ‘test_addSessionInfo.doc’
  ‘test_addTable.doc’
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
GNU make is a SystemRequirements.
checkRd: (-1) tw_options.Rd:22: Lost braces in \itemize; meant \describe ?
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
checkRd: (-1) grapes-.-times-grapes.Rd:6-9: Lost braces
     6 | "round.torch.Tensor" <- function(input) {
       |                                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) rt_GET.Rd:13: Lost braces
    13 | code{\link[httr]{GET}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
checkRd: (-1) rt_POST.Rd:13: Lost braces
    13 | code{\link[httr]{POST}} (\code{TRUE}) or not (\code{FALSE})}
       |     ^
Note: found 37 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Note: found 2023 marked Latin-1 strings
  Note: found 17 marked UTF-8 strings
Package suggested but not available for checking: ‘cmdstanr’
GNU make is a SystemRequirements.
checkRd: (-1) rts.Rd:32: Lost braces
    32 | If a name of a raster time series file is provided for the \code{x} argument, it acts the same as code{\link[rts]{read.rts}}.
       |                                                                                                       ^
Problems with news in ‘NEWS.md’:
No news entries found.
Found the following files/directories:
  ‘Tsttwalk.dat’
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                   ^
checkRd: (-1) rules.Rd:24: Lost braces; missing escapes or markup?
    24 | \item Absent names are replaced with the 'rule__\\{ind\\}' where \\{ind\\} is the
       |                                                                    ^
Package suggested but not available for checking: ‘rxode2et’
'LazyData' is specified without a 'data' directory
'library' or 'require' calls in package code:
  ‘nimble’ ‘nimbleAPT’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) RUVIII.Rd:51: Lost braces
    51 | If code{return.info} is \code{TRUE}, a list is returned that contains:
       |        ^
Package which this enhances but not available for checking: ‘glmmADMB’
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                ^
checkRd: (-1) Valpha.Rd:15: Lost braces; missing escapes or markup?
    15 |   \item{V}{a numeric vector with (i,j) entry: V[i,j] = P(theta_{i} >= theta[alpha_{j}]|data) }
       |                                                                                   ^
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gpuR’
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) HardThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) SoftThresh.Rd:15: Lost braces; missing escapes or markup?
    15 | \code{x} filtered result (y 1_{|y|>t}).
       |                               ^
checkRd: (-1) dGenWish.Rd:48: Lost braces
    48 |   -df/2*log|L(2*Sigma)L'| -1/2*tr{ (L(2*Sigma)L')^-1 L(-D)L' }
       |                                  ^
checkRd: (-1) get.Q.Rd:9: Lost braces
     9 |   equal to exp{b1*x_1ij + ... + bp*x_pij}, where beta=(b1,b2,...,bp) is
       |               ^
checkRd: (-1) get.Q.Rd:10: Lost braces; missing escapes or markup?
    10 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
checkRd: (-1) mcmc.wish.icar.Rd:73: Lost braces; missing escapes or markup?
    73 |   a vector of log-conductance values of the covariates {x_kij}.  Each
       |                                                        ^
Package suggested but not available for checking: ‘rWCVPdata’
Note: found 16 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Running ‘data_exchange.R’
  Comparing ‘data_exchange.Rout’ to ‘data_exchange.Rout.save’ ...136c136
< 1 2012-12-12 12:12:12 2012-12-12 12:12:12
---
> 1 2012-12-12 12:12:12 2012-12-12 13:12:12
159c159
< 1 2012-12-12 12:12:12 2012-12-12 12:12:12
---
> 1 2012-12-12 12:12:12 2012-12-12 13:12:12
'LazyData' is specified without a 'data' directory
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 12 marked UTF-8 strings
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
checkRd: (-1) wtss_to_ts.Rd:31: Lost braces; missing escapes or markup?
    31 | This period can be either {"month", "week", "day"}, 
       |                           ^
checkRd: (-1) wtss_to_ts.Rd:32: Lost braces; missing escapes or markup?
    32 | {"months", "weeks", "days"} or
       | ^
checkRd: (-1) wtss_to_ts.Rd:33: Lost braces; missing escapes or markup?
    33 | {12, 52, 365}. This function creates a new time series with the required 
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.eff.ridge.Rd:6: Lost braces
     6 |  emph{Single Interior Knot} at the MSE Optimal m-Extent of Shrinkage. The
       |      ^
Specified C++11: please drop specification unless essential
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                   ^
checkRd: (-1) ZigZagLogistic.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{dataX}{Design matrix containing observations of the independent variables x. The i-th row represents the i-th observation with components x_{i,1}, ..., x_{i,d}.}
       |                                                                                                                                                                 ^
checkRd: (-1) ZigZagLogistic.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{dataY}{Vector of length n containing {0, 1}-valued observations of the dependent variable y.}
       |                                            ^
checkRd: (-1) ciReg.Rd:10: Lost braces
    10 | \item{fit}{an object of class{lm}, i.e. the output from \code{\link{lm}}.}
       |                              ^
Specified C++14: please drop specification unless essential
File ‘S7/libs/S7.so’:
  Found non-API calls to R: ‘PRCODE’, ‘SET_PRVALUE’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) BootsChapt.Rd:38: Escaped LaTeX specials: \&
checkRd: (-1) SemiparChangePoint.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) schapt.Rd:44: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘CARBayesdata’ ‘MASS’ ‘nimble’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) sim_setup_preconfigured.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_setup_preconfigured.Rd:31: Lost braces in \itemize; meant \describe ?
Note: found 63 marked Latin-1 strings
Note: found 4 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Note: found 3 marked Latin-1 strings
Note: found 120 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
checkRd: (-1) sf_get_all_jobs_bulk.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_jobs_bulk.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:45-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sf_get_all_query_jobs_bulk.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) valid_metadata_list.Rd:10: Lost braces
    10 | code{list}; contains name and valid inputs for data types
       |     ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) binaryChoice.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:111: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:113: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binaryChoice.Rd:114: Lost braces in \itemize; \value handles \item{}{} directly
Running ‘Mroz87SelectionTest.R’ [8s/15s]
  Comparing ‘Mroz87SelectionTest.Rout’ to ‘Mroz87SelectionTest.Rout.save’ ... OK
  Running ‘binarySelectionOutcome.R’ [23s/38s]
  Comparing ‘binarySelectionOutcome.Rout’ to ‘binarySelectionOutcome.Rout.save’ ... OK
  Running ‘fail.R’
  Comparing ‘fail.Rout’ to ‘fail.Rout.save’ ... OK
  Running ‘heckitIvTest.R’
  Comparing ‘heckitIvTest.Rout’ to ‘heckitIvTest.Rout.save’ ... OK
  Running ‘intervalTest.R’ [28s/48s]
  Comparing ‘intervalTest.Rout’ to ‘intervalTest.Rout.save’ ... OK
  Running ‘invMillsRatioTest.R’ [32s/46s]
  Comparing ‘invMillsRatioTest.Rout’ to ‘invMillsRatioTest.Rout.save’ ...60a61
> 
  Running ‘probit.R’
  Comparing ‘probit.Rout’ to ‘probit.Rout.save’ ... OK
  Running ‘selection.R’ [27s/33s]
  Comparing ‘selection.Rout’ to ‘selection.Rout.save’ ... OK
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) SAM.Rd:67: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:59: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:84: Escaped LaTeX specials: \# \$
checkRd: (-1) samr.Rd:88: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:92: Escaped LaTeX specials: \$
checkRd: (-1) samr.Rd:97: Escaped LaTeX specials: \#
checkRd: (-1) samr.assess.samplesize.plot.Rd:12: Escaped LaTeX specials: \#
Specified C++11: please drop specification unless essential
checkRd: (-1) ModelHMMR-class.Rd:37: Lost braces; missing escapes or markup?
    37 |         class {StatHMMR}).
       |               ^
Package suggested but not available for checking: ‘networkTomography’
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 18 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 4 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) gen.ds.Rd:43-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:50-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) gen.ds.Rd:64-65: Lost braces
    64 |    \item{the dependence parameter \code{dep} or the vector of dependence parameters \code{dep}. When missing, these coefficients are obtained from independent standard uniform sampling.
       |         ^
checkRd: (-1) gen.ds.Rd:66: Lost braces
    66 |    \item{the list \code{asy} of asymmetric weights \eqn{\beta_{i,b}} for \eqn{b \in B}  and \eqn{i \in b}. When missing, these coefficients are obtained from independent standard uniform sampling followed by renormalization in order to satisfy the sum-to-one constraints.}
       |         ^
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) OTC.Rd:42: Lost braces; missing escapes or markup?
    42 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTC.Rd:83: Lost braces; missing escapes or markup?
    83 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) OTHist.Rd:29: Lost braces; missing escapes or markup?
    29 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
checkRd: (-1) dOTC.Rd:72: Lost braces; missing escapes or markup?
    72 | discretizing R^{numbers of variables}. If NULL, it is estimating
       |                ^
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) setData.ReducedRankRegressions.Rd:14-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) setData.ReducedRankRegressions.Rd:17-18: Lost braces in \itemize; meant \describe ?
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Updated help pages with examples
    Updated conjugate model sampler
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Licence stub is invalid DCF.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Specified C++11: please drop specification unless essential
checkRd: (-1) getSigmaR.Rd:13-14: Lost braces
    13 |   \item{digits}{digits}{number of decimal places to use when rounding,
       |                        ^
checkRd: (-1) x.oreo.Rd:48: Escaped LaTeX specials: \_ \_
checkRd: (-1) get.events.Rd:51: Lost braces
    51 |   code{\link[deSolve]{events}}
       |       ^
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) scatterD3.Rd:209: Lost braces; missing escapes or markup?
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       | ^
checkRd: (-1) scatterD3.Rd:209: Lost braces
   209 | {https://github.com/skokenes/D3-Lasso-Plugin}{d3-lasso-plugin} feature}
       |                                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.beta.ks.Rd:30: Lost braces
    30 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust.Rd:33: Lost braces
    33 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{\code{num.bicluster}}: {The number of biclusters estimated by the procedure.}
       |                              ^
checkRd: (-1) PermBiclust.sigclust_stop.Rd:36: Lost braces
    36 | \item{\code{x.residual}}: {The data matrix \code{x} after removing the signals}
       |                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mathjaxr’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) get_profile.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_profile.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) schoRsch.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schoRsch.Rd:45: Lost braces in \itemize; meant \describe ?
Note: found 464 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'conos', 'pagoda2'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘RhpcBLASctl’
  All declared Imports should be used.
checkRd: (-1) reduce_dimensionality.Rd:19: Lost braces
    19 | \item{ndim}{the maximum dimension of the space which the data are to be represented in; must be in {1, 2, \ldots, n-1}.}
       |                                                                                                    ^
checkRd: (-1) ti_scorpius.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{distance_method}{A character string indicating which correlationcoefficient (or covariance) is to be computed. One of "pearson", "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}. Default: spearman. Format: character.}
       |                                                                                                                                                                                   ^
checkRd: (-1) ti_scorpius.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{smoother}{\code{principal_curve} parameter; choice of smoother. Domain: {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format: character.}
       |                                                                               ^
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
File ‘scquantum/libs/scquantum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateSNPs.Rd:46: Escaped LaTeX specials: \& \& \&
checkRd: (-1) simulateSNPs.Rd:80: Escaped LaTeX specials: \& \& \&
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘crayon’ ‘knitr’ ‘methods’
  All declared Imports should be used.
checkRd: (-1) scriptloc.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Get location of script in a fashion analagous to ${BASH_SOURCE[0]}}
       |                                                          ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘untitled_consensus_cluster’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                  ^
checkRd: (-1) cln.Rd:27: Lost braces
    27 |    case for text \code{1} for 1st uppercase, code{2} for lowercase, code{3} for uppercase (optional)
       |                                                                         ^
checkRd: (-1) geom_flat_violin.Rd:7: Lost braces
     7 | url{https://gist.github.com/dgrtwo/eb7750e74997891d7c20}
       |    ^
Note: found 1 marked UTF-8 string
checkRd: (-1) sda.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sda.package.Rd:24: Lost braces in \itemize; meant \describe ?
Note: found 51 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
checkRd: (-1) sdc_extabs.Rd:59: Lost braces
    59 | (including ]code{forcelist} variables) that can be used to form tables.}
       |                 ^
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘sde/libs/sde.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Note: found 5 marked Latin-1 strings
  Note: found 51869 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) msdpd.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:77: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpd.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpd.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) msdpdth.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) msdpdth.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hyperpar.Rd:17: Lost braces
    17 | \item{c}{denotes the expected range of eqn{f} .}
       |                                           ^
'LazyData' is specified without a 'data' directory
Running examples in ‘sdpt3r-Ex.R’ failed
The error most likely occurred in:

> ### Name: doptimal
> ### Title: D-Optimal Experimental Design
> ### Aliases: doptimal
> 
> ### ** Examples
> 
> data(DoptDesign)
> 
> out <- doptimal(DoptDesign)
Error in unique.default(x) : unique() applies only to vectors
Calls: doptimal ... detect_ublk -> intersect -> unique -> unique.default
Execution halted
checkRd: (-1) seas.check.Rd:48-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) seas.check.Rd:58: Lost braces in \itemize; meant \describe ?
Note: found 3 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) seedCCA.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{u}{numeric, maximum number of projections. The default is 10. This is used for \code{type="seed1"}, \code{type="seed2"} and {tyepe="pls"}.}
       |                                                                                                                                   ^
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘testit’
  All declared Imports should be used.
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘webp’
  All declared Imports should be used.
Running examples in ‘seminr-Ex.R’ failed
The error most likely occurred in:

> ### Name: PLSc
> ### Title: seminr PLSc Function
> ### Aliases: PLSc
> 
> ### ** Examples
> 
> mobi <- mobi
> 
> #seminr syntax for creating measurement model
> mobi_mm <- constructs(
+              reflective("Image",        multi_items("IMAG", 1:5)),
+              reflective("Expectation",  multi_items("CUEX", 1:3)),
+              reflective("Quality",      multi_items("PERQ", 1:7)),
+              reflective("Value",        multi_items("PERV", 1:2)),
+              reflective("Satisfaction", multi_items("CUSA", 1:3)),
+              reflective("Complaints",   single_item("CUSCO")),
+              reflective("Loyalty",      multi_items("CUSL", 1:3))
+            )
> #seminr syntax for creating structural model
> mobi_sm <- relationships(
+   paths(from = "Image",        to = c("Expectation", "Satisfaction", "Loyalty")),
+   paths(from = "Expectation",  to = c("Quality", "Value", "Satisfaction")),
+   paths(from = "Quality",      to = c("Value", "Satisfaction")),
+   paths(from = "Value",        to = c("Satisfaction")),
+   paths(from = "Satisfaction", to = c("Complaints", "Loyalty")),
+   paths(from = "Complaints",   to = "Loyalty")
+ )
> 
> seminr_model <- estimate_pls(data = mobi,
+                              measurement_model = mobi_mm,
+                              structural_model = mobi_sm)
Generating the seminr model
All 250 observations are valid.
Error in stats::cor(seminr_model$construct_scores)/adjustment : 
  non-conformable arrays
Calls: estimate_pls -> model_consistent -> PLSc
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SEMinR.Rmd’ using rmarkdown

Quitting from lines 458-459 [unnamed-chunk-27] (SEMinR.Rmd)
Error: processing vignette 'SEMinR.Rmd' failed with diagnostics:
replacement diagonal has wrong length
--- failed re-building ‘SEMinR.Rmd’

SUMMARY: processing the following file failed:
  ‘SEMinR.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘editData’ ‘miniUI’
  All declared Imports should be used.
checkRd: (-1) convert2snafu.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert2snafu.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) correct.changes.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) correct.changes.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) textcleaner.Rd:100-101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:116: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:119: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) textcleaner.Rd:133: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) append.dictionary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:44-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:89-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) append.dictionary.Rd:113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) NRW.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bootSemNeT.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_nets.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.compareShiny.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) test.bootSemNeT.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) PAVranking.Rd:77-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:80-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:83-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PAVranking.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
checkRd: (-1) sendmail_options.Rd:32-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendmail_options.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) match_dataphy.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:39-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) match_dataphy.Rd:42-44: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 836 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
Note: found 3128 marked UTF-8 strings
Note: found 182 marked UTF-8 strings
Note: found 52 marked UTF-8 strings
Specified C++14: please drop specification unless essential
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) process,HybridSequenceClassifier-method.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                               ^
checkRd: (-1) SeqDesignInference.Rd:319: Lost braces; missing escapes or markup?
   319 | (a) difference in means estimator i.e. [ybar_T - ybar_C +/- t_{alpha/2, n_T + n_C - 2} s_{ybar_T - ybar_C}] or
       |                                                                                          ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                              ^
checkRd: (-1) SeqDesignInference.Rd:320: Lost braces; missing escapes or markup?
   320 | (b) the OLS estimator i.e. [beta_hat_T +/- t_{alpha/2, n + p - 2} s_{beta_hat_T}]
       |                                                                     ^
Found the following files/directories:
  ‘assocpointpair_result.csv’ ‘foundereffectfinder_result.csv’
  ‘getfreqs_result.csv’ ‘getfreqs_result.png’ ‘orPlot.pdf1_1.pdf’
  ‘orPlot.pdf2_1.pdf’ ‘orPlot.pdf3_1.pdf’ ‘orPlot.pdf4_1.pdf’
  ‘orPlot.pdf5_1.pdf’ ‘orPlot.pdf6_1.pdf’ ‘orPlot.pdf7_1.pdf’
  ‘orPlot.pdf8_1.pdf’ ‘q-values_result.csv’ ‘rewritetuple_result.csv’
  ‘tartan_plot.pdf’ ‘vispair_plot.pdf’ ‘vispairfeat_plot.pdf’
  ‘volcano_plot.pdf’
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘seqtrie/libs/seqtrie.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) SEset_to_network.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) network_to_SEset.Rd:72: Escaped LaTeX specials: \&
checkRd: (-1) network_to_path.Rd:50: Escaped LaTeX specials: \&
checkRd: (-1) path_to_network.Rd:29: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘BPCells’
Packages suggested but not available for checking:
  'BPCells', 'monocle', 'presto'
Running ‘sfacross.R’ [10s/10s]
  Comparing ‘sfacross.Rout’ to ‘sfacross.Rout.save’ ...9c9
< * For any questions, suggestions, or comments on the 'sfaR' package, you can contact directly the authors or visit:
---
> * For any questions, suggestions, or comments on the 'sfaR' package, please make use of Tracker facilities at:
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘sfheaders/libs/sfheaders.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) bisee.Rd:127: Lost braces
   127 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) hisee.Rd:101: Lost braces
   101 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) isee.Rd:116: Lost braces
   116 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
checkRd: (-1) see.Rd:98: Lost braces
    98 | values including \code{x}, \code{y}, code{family}, \code{clusterID},
       |                                          ^
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                   ^
checkRd: (-1) sgt.Rd:55: Lost braces
    55 |   \code{sigma <= 0}, \code{lambda <= -1}, \code{lambda >= 1}, \code{p <= 0}, and \code{q <= 0} are errors and return \code{NaN}. Also, if \code{mean.cent} is \code{TRUE} but code{p*q <= 1}, the result is an error and \code{NaNs} are produced. Similarly, if \code{var.adj} is \code{TRUE} but code{p*q <= 2}, the result is an error and \code{NaNs} are produced.
       |                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) changept.Rd:17-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) changept.Rd:22: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
checkRd: (-1) powerShape.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShape.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) powerShapeNA.Rd:32-33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rCOSA’
Package suggested but not available for checking: ‘hydromad’
checkRd: (-1) age_corr.Rd:15: Lost braces
    15 | \item{plot}{Should the results be plotted? (/code{TRUE/FALSE})}
       |                                                  ^
checkRd: (-1) age_corr.Rd:17: Lost braces
    17 | \item{agecorrection}{Correct for jumps in age (/code{TRUE}) or
       |                                                     ^
checkRd: (-1) age_corr.Rd:18: Lost braces
    18 | only for starting time (/code{FALSE})}
       |                              ^
Note: found 14 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiftrPrepare.Rd:37: Lost braces
    37 |     See code{\link{shiftrPermBinary}} function and the respective example.
       |             ^
Found the following HTML validation problems:
get_arg_help.html:43:1 (get_arg_help.Rd:13): Warning: trimming empty <dt>
get_desc_help.html:43:1 (get_desc_help.Rd:13): Warning: trimming empty <dt>
get_usage_help.html:43:1 (get_usage_help.Rd:13): Warning: trimming empty <dt>
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘billboarder’ ‘glue’ ‘scrypt’ ‘yaml’
  All declared Imports should be used.
Found the following files/directories:
  ‘Crashpad’
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) js_calls.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) js_calls.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pickCheckboxNamesAndLabels.Rd:14: Lost braces
    14 | \item{choices}{link{pickCheckboxInput} choices list.}
       |                    ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) display.Rd:17: Lost braces; missing escapes or markup?
    17 | div which wraps your message to display it in the {position} corner of your shiny app.
       |                                                   ^
checkRd: (-1) info_value.Rd:15: Lost braces; missing escapes or markup?
    15 | div which wraps rendered value to display it in the {position} corner of your shiny app.
       |                                                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) shinyjs-defunct.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shinyjs-defunct.Rd:20: Lost braces in \itemize; meant \describe ?
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) store_googledrive.Rd:19: Lost braces; missing escapes or markup?
    19 | See the {gargle} package to manage authentication, and especially
       |         ^
checkRd: (-1) store_googledrive.Rd:20: Lost braces; missing escapes or markup?
    20 | \href{https://gargle.r-lib.org/articles/articles/managing-tokens-securely.html}{this vignette from {gargle} package} to manage the process.
       |                                                                                                    ^
checkRd: (-1) custom-labels.Rd:7: Lost braces; missing escapes or markup?
     7 | \title{Modify {shinymanager} labels to use custom text}
       |               ^
checkRd: (-1) use_language.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Use {shinymanager} labels}
       |            ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘uchardet’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) shiny_pivot_table.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) shiny_pivot_table.Rd:64: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) addValidationSuffix.Rd:13: Lost braces; missing escapes or markup?
    13 | A string `"{tagId}-shinyreforms-validation"`.
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.shiny_run’ ‘shinyShortcut.desktop’
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘cmdstanr’
checkRd: (-1) add_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for adding a CSS class used in {shinysurveys}.
       |                                                ^
checkRd: (-1) disable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) enable_element.Rd:16: Lost braces; missing escapes or markup?
    16 | Custom function for disabling an HTML element in {shinysurveys}.
       |                                                  ^
checkRd: (-1) extendInputType.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{extension}{A shiny input type not natively supported by {shinysurveys}. See the examples section for more information.}
       |                                                               ^
checkRd: (-1) getSurveyData.Rd:15: Lost braces; missing escapes or markup?
    15 | default, and the built-in {shinysurveys} userID will be used.}
       |                           ^
checkRd: (-1) radioMatrixInput.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{...}{Additional arguments specific to {shinysurveys} required questions.}
       |                                             ^
checkRd: (-1) remove_class.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for removing a CSS class used in {shinysurveys}.
       |                                                  ^
checkRd: (-1) toggle_element.Rd:18: Lost braces; missing escapes or markup?
    18 | Custom function for toggling enable/disable state of HTML element in {shinysurveys}.
       |                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) run_shinytitle_example.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) run_shinytitle_example.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MrBayes.Rd:24: Lost braces
    24 | \item{contype}{A character string; the type of consensus tree calculated from the posterior distribution of trees}{either "halfcompat" (majority-rule consensus tree) or "allcombat" (strict consensus tree)}
       |                                                                                                                   ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) shutterplot.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.'
       |                       ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                  ^
checkRd: (-1) pop.dist.Rd:41: Lost braces; missing escapes or markup?
    41 | where \emph{dist(i,j)} represents the distance between populations \emph{i} and \emph{j}, \emph{m} and \emph{n} are the number of sequences in populations \emph{i} and \emph{j}, respectively, and \emph{dist(H_{ki},H_{lj})} is the distance between the \emph{k-th} sequence found in population \emph{i} and the \emph{l-th} sequence found in population \emph{j}. 
       |                                                                                                                                                                                                                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) drr.Rd:36: Lost braces; missing escapes or markup?
    36 |   \code{drr} {is Rosin - Rammler probability density function}\cr
       |              ^
checkRd: (-1) drr.Rd:37: Lost braces; missing escapes or markup?
    37 |   \code{urr} {is Rosin - Rammler cumulative distribution function (CDF) representing undersize mass fraction}\cr
       |              ^
checkRd: (-1) drr.Rd:38: Lost braces
    38 |   \code{orr} {is Rosin - Rammler complementary CDF representing oversize mass fraction ie. relative remainder on the sieve with the mesh size \code{x}}\cr
       |              ^
Specified C++11: please drop specification unless essential
Note: found 1231 marked UTF-8 strings
Note: found 28 marked UTF-8 strings
checkRd: (-1) add_k_mer_state.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add_k_mer_state.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) duration_viterbi.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
checkRd: (-1) sig.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sig_report.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘ExportFigtree1.tre’
checkRd: (-1) siland.Rd:64: Lost braces; missing escapes or markup?
    64 | \item x_{l,i}, local variable l,
       |         ^
checkRd: (-1) siland.Rd:70: Lost braces; missing escapes or markup?
    70 | \item d_{r,i} the distance between the center of pixel r and the observation at site i.
       |         ^
checkRd: (-1) inlandwaters.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) inlandwaters.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim_Y_Binary_X.Rd:51: Lost braces
    51 |     \item \code{dist = "binomial"} is drawn from eqn{Bin(XB, XB(1-XB))}
       |                                                     ^
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘Sim.DiffProc/libs/Sim.DiffProc.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespaces in Imports field not imported from:
  ‘pedtools’ ‘readr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_modelDF.Rd:25-38: Lost braces
    25 | convert_xlsx_to_csv<-function(xlsx_file){
       |                                         ^
checkRd: (-1) create_modelDF.Rd:33-36: Lost braces
    33 |   for (i in Sheetnames) {
       |                         ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘database.csv’ ‘output.csv’ ‘output_clst.csv’
checkRd: (-1) internal.statistics.one.lm.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) internal.statistics.one.lm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.logistic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.prop2.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simstudy.t2.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res_mutation.tsv’ ‘res_mutationCounts.txt’
  ‘res_processContribution.txt’ ‘res_processes.txt’
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
checkRd: (-1) coxsimSpline.Rd:93: Lost braces; missing escapes or markup?
    93 | {FD(h[i](t)) = (exp(g(x[j]) - g(x[l])) - 1) * 100}
       | ^
checkRd: (-1) simPH.Rd:16-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:20-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:25-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:31-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:34-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:44-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simPH.Rd:50-53: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    simpleCache [0.0.1]
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) SimDataDist-class.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SimDataDist-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createData.Rd:7: Lost braces
     7 |         This function can be used to create data from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function is used internally to create data, and is available publicly for accessibility and debugging.
       |                                                                                                                         ^
checkRd: (-1) exportData.Rd:7: Lost braces
     7 |         This function can be used to export data created from a set of parameters created from \code{\link{draw}}, called a code{paramSet}. This function can export data to be analyzed with either Mplus or LISREL.
       |                                                                                                                                 ^
Specified C++14: please drop specification unless essential
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Version (Date)
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
checkRd: (-1) make_one_dataset.Rd:67: Lost braces; missing escapes or markup?
    67 |  \code{within.SD} to be extremely small (e.g., $1 * 10^{-7}$) and all corresponding correlations in matrix
       |                                                        ^
checkRd: (-1) add_bold.Rd:15: Lost braces; missing escapes or markup?
    15 | For example, in latex it would take "2" and output "{\\bf 2}"; in html
       |                                                     ^
checkRd: (-1) sim.bdh.age.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.age.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:71: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.gsa.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sim.bdh.taxa.ssa.Rd:70: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sitar-package.Rd:27: Lost braces; missing escapes or markup?
    27 | individual curves, adjusted for {abcd} to lie on top of (i.e. be
       |                                 ^
checkRd: (-1) sitar.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{\link{nlme}}) (default {nlmeControl(returnObject = TRUE)}).}
       |                              ^
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
checkRd: (-1) rawCCD.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{distr.type}{school district type (constructed for illustration purposes; (values={"A", "B", "C", "D"})).}
       |                                                                                          ^
checkRd: (-1) selectMatch.Rd:61: Lost braces; missing escapes or markup?
    61 | \item{replacementUnitsFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "replacementUnits.csv"}
       |                                                                    ^
checkRd: (-1) selectMatch.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{subUnitTableFilename}{character; csv filename for saving {unit:replacement} directory when writeOut == TRUE; default = "subUnitTable.csv"}
       |                                                                ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                  ^
checkRd: (-1) selectMatch.Rd:66: Lost braces; missing escapes or markup?
    66 | list with: 1) table of the form: {selected unit i: (unit i replacements)}, 2) table of the form: {potential unit i:(unit i sub-units)}, 3) balance diagnostics.
       |                                                                                                  ^
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘Crashpad’
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) ss.cc.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ss.ci.Rd:26: Lost braces
    26 | \item{alpha}{The eqn{\\alpha} error used to compute the \eqn{100*(1-\\alpha)\%} confidence interval}
       |                     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |     ^
checkRd: (-1) ss.rr.Rd:84: Lost braces; missing escapes or markup?
    84 | $MS_{factor}/MS_{interaction}$, e.g. in appendix A of AIAG MSA manual, 
       |                 ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                            ^
checkRd: (-1) ss.rr.Rd:87: Lost braces; missing escapes or markup?
    87 | F test is performed as $MS_{factor}/MS_{equipment}$, i.e., repeatability.
       |                                        ^
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Package which this enhances but not available for checking: ‘kmndirs’
GNU make is a SystemRequirements.
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘numDeriv’ ‘png’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘RcppArmadillo’
  All declared Imports should be used.
checkRd: (-1) outliers.hdts.Rd:44: Lost braces; missing escapes or markup?
    44 |   \item I.cov.rob - The matrix (V'GnV)^{-1} used to compute the statistics to detect the idiosyncratic outliers.
       |                                        ^
Note: found 23 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘captioner’
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) nba_team_logo.Rd:22: Lost braces; missing escapes or markup?
    22 | https://i.cdn.turner.com/nba/nba/.element/img/4.0/global/logos/512x512/bg.white/svg/{team_short_name}.svg
       |                                                                                     ^
File ‘slider/libs/slider.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) fit_slim.Rd:24: Lost braces; missing escapes or markup?
    24 | sum(x' V^{-1} (y - x beta)) = 0 as the covariance V tends from V[, , 1] +
       |          ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 2 marked Latin-1 strings
checkRd: (-1) slp-package.Rd:38: Escaped LaTeX specials: \&
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Found the following HTML validation problems:
print.spscan.html:49:1 (print.spscan.Rd:15): Warning: trimming empty <dt>
summary.spscan.html:48:1 (summary.spscan.Rd:15): Warning: trimming empty <dt>
Package suggested but not available for checking: ‘gurobi’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
checkRd: (-1) cities_lon_lat.Rd:6: Lost braces
     6 | A subset of world.cities{maps}. Extracted in order to shink number of dependencies. 
       |                         ^
Note: found 1122 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
checkRd: (-1) customerRetentionDemographics.Rd:10: Escaped LaTeX specials: \$
checkRd: (-1) customerRetentionDemographics.Rd:11: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:12: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:13: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:14: Escaped LaTeX specials: \$ \$
checkRd: (-1) customerRetentionDemographics.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) trlong.Rd:17: Lost braces
    17 |     \item{\code{resp}}{a factor indicating the transport mode choice, and \code{B} denotes taking the bus, code{D} denotes driving one's own vehicle, \code{F} denotes getting a ride with a friend, \code{O} denotes other, and \code{W} denotes walking}
       |                                                                                                                ^
checkRd: (-1) smdocker_log.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:35-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) smdocker_log.Rd:19: Lost braces in \itemize; meant \describe ?
Found the following HTML validation problems:
summary.smerc_cluster.html:48:1 (summary.smerc_cluster.Rd:15): Warning: trimming empty <dt>
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                  ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                            ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                          ^
checkRd: (-1) SimModel1.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{beta}{the \eqn{\beta} matrix, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},...}
       |                                                                                    ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                              ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                        ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                      ^
checkRd: (-1) SimModel2.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{beta_0}{the initial beta, iqx+ip*ik, y_{1,t-1},y_{1,t-2},...,y_{2,t-1},y_{2,t-2},....}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) SMMA.Rd:115: Lost braces
   115 |  is the empirical explained variance from \cite{Meinshausen and B{u}hlmann, 2015}.  See \cite{Lund et al., 2020} for more details and references.
       |                                                                  ^
checkRd: (-1) SMMA.Rd:170: Lost braces
   170 | Meinshausen, N and P. B{u}hlmann (2015). Maximin effects in inhomogeneous large-scale data.
       |                        ^
Specified C++11: please drop specification unless essential
checkRd: (-1) estimMk.Rd:44: Lost braces; missing escapes or markup?
    44 | estimMk returns the transition probability matrix of size (S^{k})xS (with S = length(E)) 
       |                                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getKernel.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getKernel.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getGlobalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) getLocalOptimum.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) smoof_function.Rd:10: Lost braces
    10 | or code{smoof_multi_objective_function}. Both single- and multi-objective functions share the following attributes.
       |        ^
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) hoods2dsmooth.Rd:69: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dmeitsjer.Rd:75: Escaped LaTeX specials: \&
checkRd: (-1) kernel2dsmooth.Rd:42: Escaped LaTeX specials: \&
checkRd: (-1) smoothie-package.Rd:42: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |          ^
checkRd: (-1) smoothtail-package.Rd:63: Lost braces
    63 | Kaspar Ru{f}{i}bach (maintainer), \email{kaspar.rufibach@gmail.com} , \cr \url{http://www.kasparrufibach.ch}
       |             ^
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘lseq’
Found the following files/directories:
  ‘my_new_social_media_plot.png’
checkRd: (-1) SnakesAndLaddersGame.Rd:25: Lost braces; missing escapes or markup?
    25 | {Hector Haffenden} {haffendenh@cardiff.ac.uk}
       |                    ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                  ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                           ^
checkRd: (-1) sk_GLS.Rd:34: Lost braces; missing escapes or markup?
    34 | The GLS solution is: b = ( X^T V^{-1} X )^{-1} X^T V^{-1} z,
       |                                                      ^
checkRd: (-1) sk_GLS.Rd:40: Lost braces; missing escapes or markup?
    40 | Operations with V^{-1} are computed using the factorization \code{fac} (see \code{sk_var}), or
       |                   ^
checkRd: (-1) sk_LL.Rd:37: Lost braces; missing escapes or markup?
    37 | \code{quad_form} is z^T V^{-1} z, for the observed response vector z, which is constructed
       |                           ^
checkRd: (-1) sk_var.Rd:41: Lost braces; missing escapes or markup?
    41 | returns the quadratic form X^T V^{-1} X.
       |                                  ^
checkRd: (-1) sk_var.Rd:33: Lost braces; missing escapes or markup?
    33 | either matrix \code{V}, or X^T V^{-1} X, or a factorization ('chol' or 'eigen')
       |                                  ^
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
checkRd: (-1) knockoffGenotypes.Rd:32: Lost braces; missing escapes or markup?
    32 | This function efficiently constructs group-knockoffs of {0,1,2} variables distributed
       |                                                         ^
checkRd: (-1) knockoffGenotypes.Rd:11: Lost braces; missing escapes or markup?
    11 | \item{X}{a {0,1,2} matrix of size n-by-p containing the original variables.}
       |            ^
checkRd: (-1) knockoffGenotypes.Rd:29: Lost braces; missing escapes or markup?
    29 | A {0,1,2} matrix of size n-by-p containing the knockoff variables.
       |   ^
checkRd: (-1) maize.line.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maize.line.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) raw.data.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{call.rate}{\code{numeric}. Threshold for removing marker by missing genotype rate. SNP with \code{call rate} below threshold are removed from dataset. Must be between {0, 1}}
       |                                                                                                                                                                              ^
checkRd: (-1) raw.data.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{maf}{Threshold for removing SNP by minor allele frequency. Must be between {0, 1}}
       |                                                                                  ^
checkRd: (-1) plot.selm.Rd:101: Lost braces
   101 | data. Default value for code{which} is \code{2:4} if \code{p>1}, otherwise
       |                             ^
Namespace in Imports field not imported from: ‘backports’
  All declared Imports should be used.
Found the following files/directories:
  ‘.R_Test’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘flextable’ ‘htmlTable’ ‘stringr’
  All declared Imports should be used.
checkRd: (-1) map.active.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.add.Rd:99: Lost braces
    99 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.csa.mca.Rd:35: Lost braces
    35 | \link{soc.csa}, \link{map.csa.all}, link{map.csa.mca.array}
       |                                         ^
checkRd: (-1) map.ctr.Rd:85: Lost braces
    85 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.ind.Rd:80: Lost braces
    80 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.mod.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
checkRd: (-1) map.sup.Rd:82: Lost braces
    82 | \link{guides}, \link{theme} and link{guide_legend} functions from the
       |                                     ^
Note: found 938 marked UTF-8 strings
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                          ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                        ^
checkRd: (-1) preg2.Rd:8: Lost braces
     8 | An object of class \\code{tbl_df} (inherits from \\code{tbl}, \\code{data.frame}) with 2 rows and 4 columns.
       |                                                                     ^
checkRd: (-1) s_soda_pred.Rd:8: Lost braces; missing escapes or markup?
     8 | S-SODA assumes within each slice the X vector follow multivariate normal distribution. This function predicts the response y by reverting the P(X | slice(y)) to P(slice(y) | X), and estimates the E(y|X) as sum_{h} E(y | slice(y)=h, X) P (slice(y)=h | X)
       |                                                                                                                                                                                                                   ^
checkRd: (-1) db_compact.Rd:41: Lost braces; missing escapes or markup?
    41 | database structure will be set to true. See GET /{db}. You can also obtain a list of
       |                                                  ^
'LazyData' is specified without a 'data' directory
Running ‘tests.R’
  Comparing ‘tests.Rout’ to ‘tests.Rout.save’ ...4c4
< Package arrayhelpers, version 1.1-0
---
> Package arrayhelpers, version 1.0-20160527
28,36d27
< test(nsamples)        OK    
< test(dev)             OK    
< test(and)             OK    
< test(harden)          OK    
< test(postproc)        OK    
< test(factor2matrix)   OK    
< test(hard)            OK    
< test(wRMAE)           OK    
< test(prd)             OK    
38,39d28
< test(weak)            OK    
< test(hardclasses)     OK    
41d29
< test(npv)             OK    
42a31
> test(prd)             OK    
44,46c33
< test(luk)             OK    
< test(wMAE)            OK    
< test(strong)          OK    
---
> test(harden)          OK    
47a35,44
> test(wRMAE)           OK    
> test(dev)             OK    
> test(strong)          OK    
> test(npv)             OK    
> test(nsamples)        OK    
> test(and)             OK    
> test(weak)            OK    
> test(postproc)        OK    
> test(factor2matrix)   OK    
> test(luk)             OK    
48a46,48
> test(wMAE)            OK    
> test(hard)            OK    
> test(hardclasses)     OK
checkRd: (-1) llwrPTF.Rd:7: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Note: found 152 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) solr_mlt.Rd:70: Lost braces; missing escapes or markup?
    70 | TermVector DEFAULT_FIELD_NAMES = new String[] {"contents"}
       |                                               ^
checkRd: (-1) solve_pH_from_AT.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) solve_pH_from_AT.Rd:93: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) spe.Rd:101: Lost braces
   101 | code{spe} command; (4) \code{alpha} stores significance level as in
       |     ^
checkRd: (-1) load_sorvi_data.Rd:23: Lost braces in \itemize; meant \describe ?
Note: found 1245 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dbplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘SciencesPo’
'LazyData' is specified without a 'data' directory
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘gridlayout’
Note: found 1562 marked UTF-8 strings
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘NLMR’
Package suggested but not available for checking: ‘NLMR’
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘spaMM/libs/spaMM.so’:
  Found non-API call to R: ‘PRVALUE’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
2423,2426c2423,2424
<   Furrer R, Gerber F, Flury R (2023). _spam: SPArse Matrix_.
<   doi:10.32614/CRAN.package.spam
<   <https://doi.org/10.32614/CRAN.package.spam>, R package version
<   2.10-0, <https://CRAN.R-project.org/package=spam>.
---
>   Furrer R, Gerber F, Flury R (2023). _spam: SPArse Matrix_. R package
>   version 2.10-0, <https://www.math.uzh.ch/pages/spam/>.
2435,2436c2433
<     url = {https://CRAN.R-project.org/package=spam},
<     doi = {10.32614/CRAN.package.spam},
---
>     url = {https://www.math.uzh.ch/pages/spam/},
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) sdf_unnest.Rd:20: Lost braces
    20 | \code{a1, a2, a3}, then code{sdf_explode(df, a)} will produce output with each record replicated
       |                             ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) counterfactual_yhat.Rd:47: Lost braces; missing escapes or markup?
    47 | We want the counterfactual Yhat_{g' <- G} |X=x,G=g (or alternatively
       |                                 ^
checkRd: (-1) counterfactual_yhat.Rd:48: Lost braces; missing escapes or markup?
    48 | Yhat_{g' <- G} |G=g).
       |      ^
checkRd: (-1) counterfactual_yhat.Rd:58: Lost braces; missing escapes or markup?
    58 | To estimate Y'=Yhat_{g' <- G} | G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:65: Lost braces; missing escapes or markup?
    65 | To estimate Y'=Yhat_{g' <- G} |X=x, G=g, we need to
       |                     ^
checkRd: (-1) counterfactual_yhat.Rd:27: Lost braces; missing escapes or markup?
    27 | indices representing sample(s) from counterfactual  Yhat_{g' <- G} |X=x,G=g
       |                                                          ^
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
checkRd: (-1) Coord.to.Pointers.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{triangle=TRUE}{Input \code{rows} and {cols} represent lower
       |                                            ^
checkRd: (-1) Coord.to.Pointers.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{triangle=FALSE}{Input \code{rows} and {cols} represent a full
       |                                             ^
checkRd: (-1) cholsolveAQinvAT.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Solve the equation X = AQ^{-1}t(A) under permutations}
       |                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |    ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |             ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                      ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                   ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                            ^
checkRd: (-1) mu_calc.Rd:32: Lost braces; missing escapes or markup?
    32 | mu_{d} | mu_{d} < mu_{d-1} and mu_{d} | mu_{d} > mu_{d-1} respecitively.
       |                                                     ^
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.sparsereg.Rd:22-23: Lost braces
    22 | \env{main1, main2, main3}{
       |                          ^
checkRd: (-1) plot.sparsereg.Rd:25-27: Lost braces
    25 | \env{xlabel}{
       |             ^
checkRd: (-1) plot.sparsereg.Rd:29-31: Lost braces
    29 | \env{plot.one}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:27-29: Lost braces
    27 | \env{interval}{
       |               ^
checkRd: (-1) summary.sparsereg.Rd:31-33: Lost braces
    31 | \env{ci}{
       |         ^
checkRd: (-1) summary.sparsereg.Rd:35-37: Lost braces
    35 | \env{order}{
       |            ^
checkRd: (-1) summary.sparsereg.Rd:39-41: Lost braces
    39 | \env{normal}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:43-45: Lost braces
    43 | \env{select}{
       |             ^
checkRd: (-1) summary.sparsereg.Rd:47-48: Lost braces
    47 | \env{printit}{
       |              ^
checkRd: (-1) summary.sparsereg.Rd:50-52: Lost braces
    50 | \env{stage}{
       |            ^
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) elasticNetSEMcv.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:71-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:75-82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:83-92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:93: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) elasticNetSEMcv.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
File ‘sparseSVM/libs/sparseSVM.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘base’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) SpatialBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SpatialBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) distSG.Rd:40: Lost braces; missing escapes or markup?
    40 |   matrix and weight matrix (plus a matrix with {eID} identifiers
       |                                                ^
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
Note: found 283 marked UTF-8 strings
Specified C++14: please drop specification unless essential
File ‘spatialwidget/libs/spatialwidget.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet', 'spatstat', 'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.sparse', 'spatstat.univar',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat.linnet', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.sparse',
  'spatstat.geom', 'spatstat.random', 'spatstat.explore',
  'spatstat.model', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'nlme', 'rpart'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'spatstat.data', 'spatstat.univar', 'spatstat.geom',
  'spatstat.random', 'spatstat.explore', 'spatstat.model',
  'spatstat.linnet'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:137: Escaped LaTeX specials: \&
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘spDataLarge’
Note: found 56 marked UTF-8 strings
Note: found 34 marked UTF-8 strings
Package suggested but not available for checking: ‘scRNAseq’
checkRd: (-1) findRef.Rd:39: Lost braces
    39 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
checkRd: (-1) hClustAlign.Rd:70: Lost braces
    70 | Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\`{e}re F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.
       |                                                              ^
Note: found 2 marked UTF-8 strings
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Roadmap of specklestar package
'LazyData' is specified without a 'data' directory
checkRd: (-1) FitAkdParameters.Rd:23: Lost braces; missing escapes or markup?
    23 |       p(y|ens) = 1 / K * sum {dnorm(y, z.i, s)} \cr
       |                              ^
checkRd: (-1) australia.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) australia.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) image.plot.Rd:78: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Note: found 17 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘glue’ ‘httptest’
  All declared Imports should be used.
checkRd: (-1) speech_recompiler.Rd:25: Lost braces; missing escapes or markup?
    25 | The default compilation is that of \ code {speech_build (., compiler = TRUE}).
       |                                           ^
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘.neig’
Specified C++11: please drop specification unless essential
checkRd: (-1) cylinder.counts.Rd:61-62: Lost braces
    61 | nucleotide, so that \code{a.c} represents the set {\code{aac}, \code{acc}, 
       |                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) adaptIntegrateSpherePolar.Rd:14: Lost braces
    14 | code{adaptIntegrateBallPolar()} will likely miss these abrupt changes and give
       |     ^
Namespaces in Imports field not imported from:
  ‘sf’ ‘spData’
  All declared Imports should be used.
Note: found 189 marked UTF-8 strings
Found the following files/directories:
  ‘AlphaGA_3.txt’ ‘AlphaML_3.txt’ ‘BetaGA_3.txt’ ‘BetaML_3.txt’
  ‘Performance_GA_ML_ 3 .pdf’ ‘SPIGA_3Pmon.Pm_St1.pdf’
  ‘SPIGA_3Pmon.Pm_St2.pdf’ ‘SPI_AG_3.txt’ ‘SPI_ML_3.txt’
  ‘SPI_ML_3Pm_St1.pdf’ ‘SPI_ML_3Pm_St2.pdf’ ‘SPI_ML_3Pm_St3.pdf’
  ‘SPI_ML_3Pm_St4.pdf’ ‘SPI_PARAM_3.txt’ ‘SPI_PARAM_3Pm_St1.pdf’
  ‘SPI_PARAM_3Pm_St2.pdf’ ‘SPI_PARAM_3Pm_St3.pdf’
  ‘SPI_PARAM_3Pm_St4.pdf’
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) speedtestdata.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) speedtestdata.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ds_aat.Rd:16: Lost braces
    16 | \doi{10.1111/add.14071}{Boffo et al., 2018}. Participants were presented stimuli from a "test"
       |                        ^
checkRd: (-1) ds_gng.Rd:16: Lost braces
    16 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_iat.Rd:19: Lost braces
    19 | \doi{10.1016/j.tate.2019.102887}{Abacioglu and colleagues (2019)}. 
       |                                 ^
checkRd: (-1) ds_rapi.Rd:15: Lost braces
    15 | problems within the last year (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989}).
       |                                                                             ^
checkRd: (-1) ds_sst.Rd:17: Lost braces
    17 | described in detail in \doi{10.1016/j.tate.2019.102887}{Hedge, Powell, and Sumner (2018)}. 
       |                                                        ^
checkRd: (-1) ds_vpt.Rd:22: Lost braces
    22 | \doi{10.1111/acer.12853}{(Pronk, Deursen, Beraha, Larsen, & Wiers, 2015)}.
       |                         ^
checkRd: (-1) splithalfr.Rd:15: Lost braces
    15 |   \item \code{vignette("rapi_sum")} Sum-score for data of the 23-item version of the Rutgers Alcohol Problem Index (\doi{https://doi.org/10.15288/jsa.1989.50.30}{White & Labouvie, 1989})
       |                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) softening.optimized.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) softening.optimized.Rd:44: Lost braces in \itemize; meant \describe ?
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Feature Changes
Package suggested but not available for checking: ‘antaresViz’
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
checkRd: (-1) gbmidwcv.Rd:118: Lost braces
   118 | rfcv{randomForest} and gbm
       |     ^
checkRd: (-1) gbmokgbmidwcv.Rd:108: Lost braces
   108 | variable and anisotropy parameters. see notes vgm{gstat} for details.
       |                                                  ^
Specified C++11: please drop specification unless essential
checkRd: (-1) spnn-package.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) spnn-package.Rd:18: Lost braces in \itemize; meant \describe ?
Suggests orphaned package: ‘taxize’
'LazyData' is specified without a 'data' directory
Note: found 7504 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    updates of 10th May 2021
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Note: found 199 marked UTF-8 strings
Specified C++11: please drop specification unless essential
checkRd: (-1) shpdata1.Rd:7: Lost braces
     7 | \format{An object of class /code{"list"}.}
       |                                 ^
checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
checkRd: (-1) sncFun.01110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                            ^
checkRd: (-1) sncFun.01110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-C1 in insertRef{Streck.2020}{spsh} using eq 21 which can be used
       |                                                         ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                           ^
checkRd: (-1) sncFun.02110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-B in insertRef{Streck.2020}{spsh}
       |                                                        ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                            ^
checkRd: (-1) sncFun.04110.Rd:27: Lost braces
    27 | The function is Eq. Table 1-A  in insertRef{Streck.2020}{spsh}
       |                                                         ^
checkRd: (-1) impactspsur.Rd:42: Lost braces; missing escapes or markup?
    42 | and a matching \code{Qres} list attribute if {Q} was given.
       |                                              ^
checkRd: (-1) spsur3sls.Rd:158: Lost braces; missing escapes or markup?
   158 |   the matrix of regressors, of order \emph{(Nxp_{g})}. Moreover, 
       |                                                 ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                    ^
checkRd: (-1) spsurgs3sls.Rd:67: Lost braces; missing escapes or markup?
    67 | \item{het}{default {FALSE}: if {TRUE} uses the methods 
       |                                ^
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                   ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                              ^
checkRd: (-1) spsOption.Rd:29: Lost braces; missing escapes or markup?
    29 | Some functions in {spsUtil}, {spsComps} and {systempPipeShiny} will behave
       |                                             ^
checkRd: (-1) vol.m3.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vol.m3.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sqldf.Rd:248: Lost braces
   248 | and code{port} arguments of sqldf.
       |         ^
Namespaces in Imports field not imported from:
  ‘DBI’ ‘RSQLite’ ‘dbplyr’ ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{ - a small, positive scalar that determines when iterations 
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{ - an integer denoting the maximum limit on the number of 
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{ - a logical variable denoting whether some of the intermediate 
       |                 ^
checkRd: (-1) fpiter.Rd:67-70: Lost braces
    67 |     \code{intermed}}{ - a logical variable denoting whether the intermediate 
       |                     ^
checkRd: (-1) squarem.Rd:134: Lost braces
   134 |       along with the corresponding log-likelihood value.  When the code{objfn} is not specified it will return the fixed-point residual instead of the objective function values. 
       |                                                                        ^
Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
  All declared Imports should be used.
checkRd: (-1) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^
checkRd: (-1) plot.SRCS.Rd:48-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:52-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:56-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:59-60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:63-64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:65-66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:72-73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:74-75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:77-79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:80-81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:87-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:143-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:146-148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.SRCS.Rd:149: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Note: found 35 marked UTF-8 strings
checkRd: (-1) ssaBSS-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ssaBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sscor.Rd:33: Lost braces; missing escapes or markup?
    33 | Otherwise, if {pdim=TRUE}, the pxp SSCM is computed, and then from the SSCM an estimator of the correlation matrix, which is done by the function \code{\link{SSCM2Shape}}, see there for details.
       |               ^
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) new.distance.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:35-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) new.distance.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:30-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sensitivity.plot.Rd:38-40: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                   ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                              ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                      ^
checkRd: (-1) readratdatafixed.Rd:25: Lost braces; missing escapes or markup?
    25 | number of the set {1, 2, 3}, {1..5}, {1..7} or {1..9}. When there are 10
       |                                                ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) SRanalysis.Rd:100: Lost braces
   100 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
checkRd: (-1) StabilizedRegression.Rd:109: Lost braces
   109 |   P. B{\"u}hlmann (2019). Stabilizing Variable Selection and
       |       ^
Note: found 123 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) stabsel_parameters.Rd:42: Lost braces
    42 |     always use code{"none"}.}
       |                    ^
checkRd: (-1) stabsel_stabsel.Rd:25: Lost braces
    25 |     always use code{"none"}.}
       |                    ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
  All declared Imports should be used.
checkRd: (-1) stackExample.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stackExample.Rd:11: Lost braces in \itemize; meant \describe ?
Note: found 40733 marked UTF-8 strings
checkRd: (-1) stamppFst.Rd:20: Lost braces
    20 | \code{Fsts}{a matrix of pairwise Fst values between populations}
       |            ^
checkRd: (-1) stamppFst.Rd:21: Lost braces
    21 | \code{Pvalues}{a matrix of p-values for each of the pairwise Fst values containined in the 'Fsts' matrix}
       |               ^
checkRd: (-1) stamppFst.Rd:22: Lost braces
    22 | \code{Bootstraps}{a dataframe of each Fst value generated during Bootstrapping and the associated confidence intervals}
       |                  ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                ^
checkRd: (-1) standardize.Rd:94: Lost braces; missing escapes or markup?
    94 | take on values {-0.5, 0, 0.5} rather than {-1, 0, 1}, the standard deviation
       |                                           ^
checkRd: (-1) alertify.Rd:69: Lost braces
    69 | \item{closable}{Logical; if \code{TRUE} (the default), a |code{Close} button is displayed in the header of the dialog.}
       |                                                               ^
checkRd: (-1) notify.Rd:47: Lost braces
    47 | \item{hide}{Logical; if \code{TRUE} (the default), notice is closed after |code{delay} specified in milliseconds.}
       |                                                                                ^
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘httr’ ‘latex2exp’ ‘rstantools’ ‘tibble’ ‘tidyverse’
  ‘utils’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_fields.Rd:27: Lost braces
    27 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) identify_form_fields.Rd:34: Lost braces
    34 | codes, the function will return a warning by default, suggesting setting \code{convert_field_names} to code{TRUE}.
       |                                                                                                            ^
checkRd: (-1) abs_parms.Rd:67: Lost braces; missing escapes or markup?
    67 |    \item $S_{275-295}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:68: Lost braces; missing escapes or markup?
    68 |    \item $S_{350-400}$ slope between 350 and 400 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:69: Lost braces; missing escapes or markup?
    69 |    \item $S_{300-700}$ slope between 275 and 295 nm calculated with nonlinear regression
       |             ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                           ^
checkRd: (-1) abs_parms.Rd:70: Lost braces; missing escapes or markup?
    70 |    \item SR slope ratio, calculated by $S_{275-295}$/$S_{350-400}$
       |                                                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                         ^
checkRd: (-1) abs_parms.Rd:71: Lost braces; missing escapes or markup?
    71 |    \item E2:E3 ratio $a_{250}$/$a_{365}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                         ^
checkRd: (-1) abs_parms.Rd:72: Lost braces; missing escapes or markup?
    72 |    \item E4:E6 ratio $a_{465}$/$a_{665}$
       |                                   ^
checkRd: (-1) abs_parms.Rd:73: Lost braces; missing escapes or markup?
    73 |    \item $a_{254}$ absorbance at 254 nm
       |             ^
checkRd: (-1) abs_parms.Rd:74: Lost braces; missing escapes or markup?
    74 |    \item $a_{300}$ absorbance at 300 nm
       |             ^
checkRd: (-1) stargazer.Rd:229: Lost braces
   229 |   \item{report}{a character string containing only elements of {\code{"v"}, \code{"c"}, \code{"s"},\code{"t"}, \code{"p"}, \code{"*"}} that determines whether, and in which order, variable names (\code{"v"}), coefficients (\code{"c"}), standard errors/confidence intervals (\code{"s"}), test statistics (\code{"t"}) and p-values (\code{"p"}) should be reported in regression tables. If one of the aforementioned letters is followed by an asterisk (\code{"*"}), significance stars will be reported next to the corresponding statistic.}
       |                                                                ^
checkRd: (-1) stargazer.Rd:246: Lost braces
   246 |   \item{table.placement}{a character string containing only elements of {\code{"h"}, \code{"t"},\code{"b"}, \code{"p"}, \code{"!"}, \code{"H"}} that determines the table placement in its LaTeX floating environment.}
       |                                                                         ^
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘starsdata’
Found the following HTML validation problems:
create_symlink.html:55:1 (create_symlink.Rd:17): Warning: trimming empty <dt>
checkRd: (-1) multiCUMSUM.Rd:33: Escaped LaTeX specials: \&
Note: found 14 marked UTF-8 strings
checkRd: (-1) AutoPollution.Rd:16: Lost braces
    16 |     \code{Side} \tab {Side of vehicle: code{1}=right or \code{2}=left}\cr
       |                                            ^
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                        ^
checkRd: (-1) statcan_data.Rd:22: Lost braces; missing escapes or markup?
    22 | \code{statcan_data()} function has 2 arguments to fulfill to get data: {tableNumber} & {lang}.
       |                                                                                        ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                     ^
checkRd: (-1) statcan_search.Rd:18: Lost braces; missing escapes or markup?
    18 | The \code{statcan_search()} function has 2 arguments to fulfill to find a database: {keywords} and {lang}.
       |                                                                                                    ^
Note: found 1 marked Latin-1 string
  Note: found 18 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘statgenGWAS’
  All declared Imports should be used.
checkRd: (-1) plot.QTLMPP.Rd:33-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.QTLMPP.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.gDataMPP.Rd:45-46: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following possibly unsafe calls:
File ‘statnet.common/R/control.utilities.R’:
  unlockBinding("snctrl", environment(snctrl))
  unlockBinding("snctrl", environment(update_my_snctrl))
Package suggested but not available for checking: ‘networksis’
Note: found 57 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sample2indp.pow.Rd:48: Lost braces
    48 | Pooled standard deviation= \code{sp} = sqrt{((n1 - 1) sigma1^2 +(n2 - 1) sigma2^2) / (n1 + n2 - 2)}
       |                                            ^
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DDoutlier’ ‘car’ ‘corrplot’ ‘data.table’ ‘energy’ ‘ggplot2’
  ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘readr’ ‘reshape2’ ‘rmarkdown’
  ‘shinydisconnect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                        ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                  ^
checkRd: (-1) rankSTB.Rd:31: Lost braces; missing escapes or markup?
    31 | are transformed to min. rank-values. In step 6) the "N_{k-1}-(1-alpha)*N largest" elements of "d_{l}^{theta}" have to
       |                                                                                                      ^
checkRd: (-1) stb.default.Rd:43: Lost braces
    43 | sampling from the standard normal distribution. Another example is defining func=function(n){rchisq(n=n, df=3, ncp=2)}
       |                                                                                             ^
checkRd: (-1) stdGlm.Rd:93: Escaped LaTeX specials: \&
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) keypoints.Rd:35-36: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:37-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:40-44: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:45-48: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:49-50: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:63-65: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) keypoints.Rd:66-67: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) STEPCAM_ABC.Rd:19: Lost braces
    19 |   \code{rows}{ every row corresponds to a different plot or community} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:20: Lost braces
    20 |   \code{columns}{ every column corresponds to a different species.} \cr
       |                 ^
checkRd: (-1) STEPCAM_ABC.Rd:25: Lost braces
    25 |   \code{rows}{ every row corresponds to a different species} \cr
       |              ^
checkRd: (-1) STEPCAM_ABC.Rd:26: Lost braces
    26 |   \code{columns}{ the first column contains the name of the species, every consecutive column corresponds to a different trait} \cr
       |                 ^
checkRd: (-1) plotSTEPCAM.Rd:16: Lost braces
    16 |             - \code{DA}{ a vector containing the posterior distribution for the parameter dispersal assembly} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:17: Lost braces
    17 |             - \code{HF}{ a vector containing the posterior distribution for the parameter habitat filtering} \cr
       |                        ^
checkRd: (-1) plotSTEPCAM.Rd:18: Lost braces
    18 |             - \code{LS}{ a vector containing the posterior distribution for the parameter limiting similarity} \cr
       |                        ^
checkRd: (-1) tuneParam.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
checkRd: (-1) tuneParamCL2.Rd:28: Lost braces; missing escapes or markup?
    28 | It supports the BFGS optimization method ('QN') from the optim {stats} function, the Hooke-Jeeves derivative-free
       |                                                                ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) landmarkMatrixToList.Rd:10: Lost braces
    10 |   \item{semilandmark.pattern}{a regular expression pattern passed to \code{sub()} for identifying and grouping curve points. The default is landmark names ending in one or more numbers. To disable grouping, set to code{''}.}
       |                                                                                                                                                                                                                           ^
Note: found 534 marked UTF-8 strings
checkRd: (-1) docker_config_collection.Rd:11: Lost braces; missing escapes or markup?
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("config")}
       | ^
checkRd: (-1) docker_container.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_container")}
       | ^
checkRd: (-1) docker_image_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("image")}
       | ^
checkRd: (-1) docker_plugin_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("plugin")}
       | ^
checkRd: (-1) docker_service_collection.Rd:11: Lost braces
    11 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("service")}
       | ^
checkRd: (-1) docker_task.Rd:13: Lost braces
    13 | \Sexpr[results=rd,stage=render]{stevedore:::generate_help("docker_task")}
       | ^
Note: found 240 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Found the following files/directories:
  ‘corrviz.html’
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Note: found 22806 marked UTF-8 strings
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
Note: found 1725 marked UTF-8 strings
Package suggested but not available for checking: ‘rsgeo’
checkRd: (-1) powderymildew.Rd:14-16: Lost braces
    14 | \code{$demographic.coord}{
       |                          ^
checkRd: (-1) powderymildew.Rd:18-20: Lost braces
    18 | \code{$genetic.coord}{
       |                      ^
checkRd: (-1) powderymildew.Rd:22-24: Lost braces
    22 | \code{$demographic.measures}{
       |                             ^
checkRd: (-1) powderymildew.Rd:26-28: Lost braces
    26 | \code{$genetic.frequencies}{
       |                            ^
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘myNewStrat.R’
Package suggested but not available for checking: ‘StrathE2E2examples’
checkRd: (-1) StrathE2E2-package.Rd:70: Lost braces; missing escapes or markup?
    70 | {Basic model operations:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:79: Lost braces; missing escapes or markup?
    79 | {Parameter estimation:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:88: Lost braces; missing escapes or markup?
    88 | {Sensitivity and Monte Carlo analyses:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:98: Lost braces; missing escapes or markup?
    98 | {Compare model runs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:105: Lost braces; missing escapes or markup?
   105 | {Fishery yield analysis:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:111: Lost braces; missing escapes or markup?
   111 | {Visualize model inputs:} \cr
       | ^
checkRd: (-1) StrathE2E2-package.Rd:117: Lost braces; missing escapes or markup?
   117 | {Visualize model outputs:} \cr
       | ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                   ^
checkRd: (-1) isle.Rd:38: Lost braces
    38 | \code{\link[streamDAG]{stream.order}}, \code{\link[igraph]{delete.vertices}}, code{\link[igraph]{add.vertices}}, code{\link[igraph]{add.edges}}
       |                                                                                                                      ^
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘stringfish/libs/stringfish.so’:
  Found non-API calls to R: ‘LEVELS’, ‘STDVEC_DATAPTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
File ‘stringi/libs/stringi.so’:
  Found non-API calls to R: ‘LEVELS’, ‘NAMED’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘stringmagic/libs/stringmagic.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘STRaitRazoR’
Note: found 705 marked UTF-8 strings
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
checkRd: (-1) Grossarl.Rd:53: Lost braces
    53 | \emph{Festschrift 50 Jahre \"{O}sterreichische Statistische Gesellschaft}, 133-146,
       |                              ^
checkRd: (-1) Grossarl.Rd:54: Lost braces
    54 | \"{O}sterreichische Statistische Gesellschaft.
       |   ^
checkRd: (-1) SP2001.Rd:3: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) SP2001.Rd:12: Escaped LaTeX specials: \&
checkRd: (-1) breakpoints.Rd:223: Lost braces
   223 | Zeileis A., Kleiber C., Kr\"{a}mer W., Hornik K. (2003), Testing and Dating of
       |                             ^
checkRd: (-1) efp.Rd:109: Lost braces
   109 | Kr\"{a}mer W., Ploberger W., Alt R. (1988), Testing for structural change in
       |     ^
checkRd: (-1) efp.Rd:119: Lost braces
   119 | Ploberger W., Kr\"{a}mer W. (1992), The CUSUM test with OLS residuals,
       |                   ^
checkRd: (-1) calculateStatistics.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{quant}{numeric quantile to calculate {0,1}, default 0.95.}
       |                                            ^
Note: found 83 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                            ^
checkRd: (-1) cmss.Rd:21: Lost braces
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                        ^
checkRd: (-1) cmss.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{sim.fn}{Optional function to be used as similarity measure for accept/reject step. Default function is: |cor( bar{x}^{(r)}|,~ bar{x}_{target} ) |}
       |                                                                                                                                            ^
'LazyData' is specified without a 'data' directory
Note: found 7 marked UTF-8 strings
checkRd: (-1) subdetect-package.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) subdetect-package.Rd:12: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyjs’
  All declared Imports should be used.
checkRd: (-1) P3C.Rd:18: Lost braces; missing escapes or markup?
    18 |  used for this will be 1.00*10^{-PoissonThreshold}.}
       |                                ^
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
checkRd: (-1) fp19.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:12-13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fp19.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) suggests.Rd:14: Lost braces; missing escapes or markup?
    14 | {suggests} aims to make that workflow as minimal and painless as possible,
       | ^
'LazyData' is specified without a 'data' directory
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 78 marked UTF-8 strings
File ‘sumR/libs/sumR.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) sunburst.Rd:30: Lost braces; missing escapes or markup?
    30 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{csvdata}
       |                                ^
checkRd: (-1) sunburst.Rd:88: Lost braces; missing escapes or markup?
    88 | \item{jsondata}{\code{deprecated} use data argument instead; data in nested d3 JSON hierarchy with `{name:...,  children:[];}`}
       |                                                                                                     ^
checkRd: (-1) sund2b.Rd:22: Lost braces; missing escapes or markup?
    22 | nested d3 JSON hierarchy with `{name:...,  children:[];}`.  \code{list}, \code{character},
       |                                ^
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
checkRd: (-1) BiclustSet-class.Rd:19: Lost braces
    19 |     \item{\code{Number}:}{code{"numeric"}, number of biclusters in the set}
       |                               ^
Package suggested but not available for checking: ‘velocyto.R’
checkRd: (-1) plot.Rd:42: Lost braces; missing escapes or markup?
    42 |  \item{color.off}{color code; specifying the color for set(s) which are "{absent}" for an intersection.}
       |                                                                          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘extraTrees’
Found the following files/directories:
  ‘JMRData’
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
checkRd: (-1) getFittedProbs.Rd:6-8: Lost braces
     6 | getFittedValues <- function(object) {
       |                                     ^
checkRd: (-1) getFittedProbs.Rd:14-16: Lost braces
    14 | getFittedValues <- function(object) {
       |                                     ^
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘optimx’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘gurobi’
Packages suggested but not available for checking:
  'survHEinla', 'survHEhmc'
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
checkRd: (-1) tprob.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:142: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tprob.Rd:146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coxph_mpl_dc.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{mpl_h0t}{MPL estimates of the baseline hazard for T, i.e. h_{0T}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{mpl_h0c}{MPL estimates of the baseline hazard for C, i.e. h_{0C}(x_i)}
       |                                                                   ^
checkRd: (-1) coxph_mpl_dc.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{mpl_H0t}{MPL estimates of the baseline cumulative hazard for T, i.e. H_{0T}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{mpl_H0c}{MPL estimates of the baseline cumulative hazard for C, i.e. H_{0c}(x_i)}
       |                                                                              ^
checkRd: (-1) coxph_mpl_dc.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{mpl_S0t}{MPL estimates of the baseline survival for T, i.e. S_{0T}(x_i)}
       |                                                                     ^
checkRd: (-1) coxph_mpl_dc.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{mpl_S0c}{MPL estimates of the baseline survival for C, i.e. S_{0C}(x_i)}
       |                                                                     ^
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Note: found 607 marked UTF-8 strings
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) sf.Rd:66: Lost braces; missing escapes or markup?
    66 | A {data.table} which is stored as an attribute of
       |   ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
checkRd: (-1) coxDT.Rd:76: Lost braces; missing escapes or markup?
    76 | The estimation procedure here is performed using coxph {survival} and inserting these estimated
       |                                                        ^
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘readr’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: Obsolescent feature: Old-style character length at (1)
See ‘/data/gannet/ripley/R/packages/tests-devel/svd.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) koInstall.Rd:24: Lost braces; missing escapes or markup?
    24 | set, svKomodo loads {svSocket}, starts the socket server listening to the
       |                     ^
checkRd: (-1) svKomodo-package.Rd:18: Lost braces; missing escapes or markup?
    18 | Komodo and (2) the present {svKomodo} R package that work hand in hand to
       |                            ^
checkRd: (-1) svKomodo-package.Rd:28: Lost braces; missing escapes or markup?
    28 | Nevertheless, the SciViews-K Komodo addin and the {svKomodo} R package
       |                                                   ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                          ^
checkRd: (-1) svKomodo-package.Rd:31: Lost braces; missing escapes or markup?
    31 | communication protocols developed in the {svSocket} and {svHttp} R packages.
       |                                                         ^
checkRd: (-1) svKomodo-package.Rd:37: Lost braces; missing escapes or markup?
    37 | Both SciViews-K and {svKomodo} should be considered archived items. I keep
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) eff_n.Rd:32: Lost braces; missing escapes or markup?
    32 | \code{\link[survey:surveysummary]{survey::svymean()}} and related functions from the {survey}
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) swDsn.Rd:28: Lost braces
    28 | numeric (scalar or vector): Relative treatment effect upon crossing over from control. Note that this is not the treatment effect (the treatment effect is specified in the call to other functions such as \code{swPwr} or \code{swSim})!  If \code{tx.effect.frac} is set to a scalar with value of 1, the standard SW CRT treatment effect will be presumed. If code{tx.effect.frac} is set to a scalar with a fractional value between 0 and 1, then only the first time point upon crossing over from control will have fractional relative treatment effect; the remaining exposure times will have a relative treatment effect of 1. If a vector of fractional treatment effect is specified, each element of the vector corresponds to the (fractional) treatment effect upon crossing over from control; if the length of the vector is less than total number of exposure times, the remaining time points will have a relative treatment effect value of 1; if the length of the vector is greater than total number of time points after crossing over, not all elements of \code{tx.effect.frac} will be used. The default value is (scalar) 1.
       |                                                                                                                                                                                                                                                                                                                                                                        ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyquant’ ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
Package suggested but not available for checking: ‘swephRdata’
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Additional functions and data sets
    Amendments to functions
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    pre-release switchboard (2020 - 2021)
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘prettymapr’
  All declared Imports should be used.
Note: found 77 marked UTF-8 strings
checkRd: (-1) hyph.support.en.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hyph.support.en.Rd:20: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
checkRd: (-1) kRp.hyphen-methods.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) kRp.hyphen-methods.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) manage.hyph.pat.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) elliptical.ts.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{epsilon}{positive convergence tolerance \emph{e}; the iterations converge when |fit - fit_{old}|/|fit| < \emph{e}. Default is \emph{e=1e-04}.}
       |                                                                                                   ^
Namespaces in Imports field not imported from:
  ‘htmltools’ ‘markdown’ ‘nextGenShinyApps’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘odeintr’
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) coord2dist.Rd:14: Lost braces; missing escapes or markup?
    14 | \code{n} x 4 matrix of coordinates consisting of {lat or y, lon or x} pairs for each each site
       |                                                  ^
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
  ‘randomForest’
  All declared Imports should be used.
checkRd: (-1) create_synthetic_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) create_synthetic_example.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) initial_estimates_example.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) robCov.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) robCov.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) slice.Rd:28: Lost braces
    28 | before plotting {ex: \code{trans = c(s = "exp", d = "exp")}}/}
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘test.csv’
'LazyData' is specified without a 'data' directory
Note: found 38 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 551 marked UTF-8 strings
checkRd: (-1) tmCtypes.Rd:22: Escaped LaTeX specials: \#
checkRd: (-1) tabmulti.Rd:68: Lost braces
    68 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
checkRd: (-1) tabmulti.svy.Rd:67: Lost braces
    67 | \\code{yvarlabels = list(race = "Race/ethnicity", age_yrs = "Age (years)")}.}
       |       ^
Note: found 81 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |   ^
checkRd: (-1) parse_logs.Rd:38: Lost braces
    38 |  '{{ip ip_address}} [{{date access_date}}]...'.
       |                      ^
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) SKPar.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) SKPar.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tapnet-package.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) TAQ-functions.Rd:119: Lost braces
   119 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
checkRd: (-1) TAQ-package.Rd:59: Lost braces
    59 | Brownlees, C. T., and Gallo, G. M. (2006). Financial Econometric Analysis at Ultra{--}High Frequency: Data Handling Concerns, \emph{Computational Statistics and Data Analysis} \bold{51}, 2232--2245.
       |                                                                                   ^
Specified C++11: please drop specification unless essential
Note: found 301 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘tau/libs/tau.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package suggested but not available for checking: ‘bold’
bold_search: no visible global function definition for ‘bold_tax_name’
bold_search: no visible global function definition for ‘bold_tax_id’
check_boldid: no visible global function definition for ‘bold_tax_id’
Undefined global functions or variables:
  bold_tax_id bold_tax_name
Note: found 137 marked UTF-8 strings
Note: found 36 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) mean_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
checkRd: (-1) median_ci.Rd:24: Lost braces
    24 | \item{na.rm}{logical code{TRUE/FALSE}. Remove NAs from the dataset. Defaults
       |                          ^
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
checkRd: (-1) tca.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{C1.map}{An \code{p1} by \code{k} matrix of 0/1 values, indicating for each of the \code{p1} covariates in \code{C1} whether to consider its potential effects on the values of each of the \code{k} sources (e.g., if position \code{i,j} in \code{C1.map} is 1 then the potential effect of the \code{i}-th covariate in \code{C1} on the {j}-th source will be considered). If \code{C1.map == NULL} then effects for all covariates in \code{C1} will be considered in each of the sources. Note that \code{C1.map} is available only if \code{constrain_mu == TRUE}.}
       |                                                                                                                                                                                                                                                                                                                                                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘reshape2’ ‘truncnorm’ ‘xtable’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) windows/tk2reg.Rd:17: Escaped LaTeX specials: \_
checkRd: (-1) windows/tk2reg.Rd:18: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) windows/tk2reg.Rd:51: Escaped LaTeX specials: \_
checkRd: (-1) windows/tk2reg.Rd:52: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:53: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:57: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:58: Escaped LaTeX specials: \_ \_
checkRd: (-1) windows/tk2reg.Rd:60: Escaped LaTeX specials: \_
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Package which this enhances but not available for checking: ‘R2wd’
checkRd: (-1) crossEntropy.Rd:32: Lost braces
    32 | link{squaredError}
       |     ^
Found the following files/directories:
  ‘Crashpad’
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) sendChatAction.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sendChatAction.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Note: found 3271 marked UTF-8 strings
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
checkRd: (-1) Tendril.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tendril.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:427: Lost braces; missing escapes or markup?
   427 |       \item  Changes to \code{simulate.stergm} parameters: addition of \code{duration.dependent} parameter: {Logical: Whether the model terms in formula or model are duration dependent. E.g., if a duration-dependent term  is used in estimation/simulation model, the probability of forming or dissolving a tie may dependent on the age the dyad status. If TRUE, the matrix of tie ages will be allocated.}
       |                                                                                                             ^
checkRd: (-1) discordBDStratTNT-ergmProposal-9267ec8b.Rd:18: Lost braces
    18 | code{\link[ergm:blocks-ergmConstraint]{blocks}} constraints and
       |     ^
checkRd: (-1) discordTNT-ergmProposal-bc75dff0.Rd:9: Lost braces
     9 | code{discordance_fraction} of proposed toggles being made on the set of discordant dyads,
       |     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) MC_CRUDE.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) MC_IS.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) PROB_BASEVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) PROB_DETVAR-class.Rd:14: Lost braces
    14 | \item{\code{Id}}{Place in vector of objective functional expression function(x){x[id]}}
       |                                                                                ^
checkRd: (-1) SORM.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{lsf}{objective function with limit state function in form of function(x) {x[1]+x[2]...}}
       |                                                                                ^
checkRd: (-1) SYS_LSF-class.Rd:16: Lost braces
    16 | \item{\code{func}}{prepared for objective functions like SYS_LSF$func <- function(x){return(x[1] + x[2])}}
       |                                                                                     ^
checkRd: (-1) lognormConstCVCI.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) lognormConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) normConstCVCI.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) testassay.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
Found the following files/directories:
  ‘par-7269706c6579’
Package suggested but not available for checking: ‘gurobi’
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
File ‘testthat/libs/testthat.so’:
  Found non-API calls to R: ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_FORMALS’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
checkRd: (-1) permucycle.Rd:37: Lost braces; missing escapes or markup?
    37 |  {The 2 in the first row means there are two cycles;}
       |  ^
checkRd: (-1) permucycle.Rd:38: Lost braces; missing escapes or markup?
    38 |   {The second row means there is a cycle of length 2, with members  (1,3);}
       |   ^
checkRd: (-1) permucycle.Rd:39: Lost braces; missing escapes or markup?
    39 |  {The third row means  there is a cycle of length 1, with member  (2);}
       |  ^
checkRd: (-1) permucycle.Rd:40: Lost braces; missing escapes or markup?
    40 |  {The fourth row is redundant for this specific case.}
       |  ^
checkRd: (-1) permucycle.Rd:41: Lost braces; missing escapes or markup?
    41 |  {One can read from the output of permucycle() to obtain cycle notation (13)(2) of the permutation, and other information.}
       |  ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |               ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                  ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                    ^
checkRd: (-1) patch_table_env.Rd:25: Lost braces
    25 | \\renewcommand{\\multicolumnx}[3]{\\multicolumn{#1}{c}{#3}}
       |                                                       ^
Note: found 37 marked UTF-8 strings
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
checkRd: (-1) infer_Z.Rd:16: Lost braces; missing escapes or markup?
    16 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variatioanl approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp.Rd:26: Lost braces
    26 | It is recommended to use link{sibp_param_search} instead of this function to search over multiple configurations of the most important parameters.  So long as only the training data is used, the analyst can freely experimient with as many parameter configurations as he likes without corrupting his causal inferences.  Once a parameter configuration is chosen, the user can then use \link{sibp_amce} on the test set to estimate the average marginal component effect (AMCE) for each treatment.}
       |                              ^
checkRd: (-1) sibp.Rd:28: Lost braces; missing escapes or markup?
    28 |   \item{nu}{Informally, the probability that the row document has the column treatment.  Formally, the parameter for the variational approximation of z_{i,k}, which is a Bernoulli distribution.}
       |                                                                                                                                                         ^
checkRd: (-1) sibp_amce.Rd:19: Lost braces
    19 |   \item{sibp.amce}{The table returned by code{sibp_amce}.}
       |                                              ^
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
Note: found 3 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
checkRd: (-1) make.phrase.matrix.Rd:20: Lost braces
    20 |  \\tabular{rrrrr}{
       |           ^
checkRd: (-1) make.phrase.matrix.Rd:20-23: Lost braces
    20 |  \\tabular{rrrrr}{
       |                  ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) tfd_von_mises_fisher.Rd:63: Lost braces; missing escapes or markup?
    63 | NOTE: Currently only n in {2, 3, 4, 5} are supported. For n=5 some numerical
       |                           ^
checkRd: (-1) predict.tfunHDDC.Rd:31-39: Lost braces
    31 | The teigen family. Stat Comput 22:1021{1029. <doi.org/10.1007/
       |                                       ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘doRNG’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
checkRd: (-1) shoulders.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) shoulders.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘base’ ‘graphics’ ‘janitor’ ‘rlang’ ‘testthat’ ‘utils’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 197527 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CPdimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) CPdimensionalityplot.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:15: Escaped LaTeX specials: \&
checkRd: (-1) Kinship.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) T2func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T2funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3dimensionalityplot.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3func.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) T3funcrep.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:26: Escaped LaTeX specials: \& \& \&
checkRd: (-1) TV.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) TV.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) pcamean.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) threewayanova.Rd:24: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘tibble/libs/tibble.so’:
  Found non-API call to R: ‘SET_S4_OBJECT’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
File ‘tibblify/libs/tibblify.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘PRENV’, ‘PRVALUE’,
    ‘R_PromiseExpr’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’, ‘SET_BODY’,
    ‘SET_CLOENV’, ‘SET_FORMALS’, ‘SET_GROWABLE_BIT’, ‘SET_TRUELENGTH’,
    ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘badger’ ‘ggplot2’ ‘lubridate’ ‘scales’ ‘xgboost’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘Ckmeans.1d.dp’ ‘autostats’ ‘badger’ ‘framecleaner’ ‘presenter’
  ‘tidybins’ ‘validata’
  All declared Imports should be used.
Note: found 325 marked UTF-8 strings
Note: found 4546 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Initial Release (v0.1.0)
'LazyData' is specified without a 'data' directory
Note: found 60 marked UTF-8 strings
Note: found 4 marked UTF-8 strings
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                    ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                           ^
checkRd: (-1) json_schema.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item object  -> {"name": <type>} e.g., {"age": 32} -> {"age": "number"}
       |                                                          ^
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Minor changes:
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
checkRd: (-1) single_imputation.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) single_imputation.Rd:23-27: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
checkRd: (-1) get_tidysq_options.Rd:37: Lost braces
    37 | \item tidysq_pillar_max_width [code{integer(1)}]\cr
       |                                    ^
checkRd: (-1) read_fasta.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_fasta.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 113 marked UTF-8 strings
Note: found 34206 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
generate_control.html:87:1 (generate_control.Rd:36): Warning: trimming empty <li>
generate_control.html:86:1 (generate_control.Rd:36): Warning: trimming empty <ol>
generate_weights.html:220:1 (generate_weights.Rd:102): Warning: trimming empty <li>
generate_weights.html:219:1 (generate_weights.Rd:102): Warning: trimming empty <ol>
Note: found 4581 marked UTF-8 strings
Package suggested but not available for checking: ‘rrelaxiv’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
checkRd: (-1) compare.Rd:46: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) setup_sql_functions.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Functions}
       |                ^
checkRd: (-1) setup_sql_functions.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs functions needed to operated {timeseriesdb} in
       |                                       ^
checkRd: (-1) setup_sql_grant_rights.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Grant execute on {timeseriesdb} functions}
       |                         ^
checkRd: (-1) setup_sql_grant_rights.Rd:17: Lost braces; missing escapes or markup?
    17 | Grant execute on {timeseriesdb} functions
       |                  ^
checkRd: (-1) setup_sql_tables.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} System Tables}
       |                ^
checkRd: (-1) setup_sql_tables.Rd:17: Lost braces; missing escapes or markup?
    17 | Installs tables needed to operated {timeseriesdb} in
       |                                    ^
checkRd: (-1) setup_sql_triggers.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Install {timeseriesdb} Triggers}
       |                ^
Note: found 2750 marked UTF-8 strings
checkRd: (-1) POSIXst-class.Rd:247: Lost braces
   247 |   do any conversion on the POSIX{l,c}t objects).
       |                                 ^
checkRd: (-1) alcohol.Rd:16-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) alcohol.Rd:22-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) add_md.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{body}{an XML object generated via {tinkr}}
       |                                         ^
checkRd: (-1) md_ns.Rd:13: Lost braces; missing escapes or markup?
    13 | The {commonmark} package is used to translate markdown to XML, but it does
       |     ^
checkRd: (-1) md_ns.Rd:14: Lost braces; missing escapes or markup?
    14 | not assign a namespace prefix, which means that {xml2} will auto-assign a
       |                                                 ^
checkRd: (-1) stylesheet.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{The {tinkr} stylesheet}
       |            ^
checkRd: (-1) stylesheet.Rd:14: Lost braces; missing escapes or markup?
    14 | This function returns the path to the {tinkr} stylesheet
       |                                       ^
checkRd: (-1) stylesheet.Rd:11: Lost braces; missing escapes or markup?
    11 | stylesheet used by {tinkr}.
       |                    ^
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) partition_undirected_graph.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{cutoff}{Numeric. The value max(0, g_{i,j} - cutoff) so that there are <\code{.num_components}> components in the graph.}
       |                                           ^
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
checkRd: (-1) tierChart.Rd:332: Lost braces
   332 |   If the input argument code{boxes} is \code{F}, the \code{lBox},
       |                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Specified C++14: please drop specification unless essential
checkRd: (-1) pmvn.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvn.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pmvt.Rd:25: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 134043 marked UTF-8 strings
checkRd: (-1) tv_episode_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the episode_id value found in the change entries.
       |                                                 ^
checkRd: (-1) tv_season_changes.Rd:29: Lost braces; missing escapes or markup?
    29 | This method is used in conjunction with the /tv/{id}/changes method. This method uses the season_id value found in the change entries.
       |                                                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) pvalEffectPlot.Rd:90: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:93: Lost braces in \itemize; meant \describe ?
checkRd: (-1) pvalEffectPlot.Rd:94: Lost braces in \itemize; meant \describe ?
Note: found 1 marked UTF-8 string
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
'LazyData' is specified without a 'data' directory
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
checkRd: (-1) jsonStr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Format data as a JSON object (like this: {"x": "120"}).}
       |                                                 ^
checkRd: (-1) jsonStr.Rd:18: Lost braces; missing escapes or markup?
    18 | Format data as a JSON object (like this: {"x": "120"}).
       |                                          ^
checkRd: (-1) fixed_width_no_modeling.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fixed_width_no_modeling.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data.Rd:17: Lost braces in \itemize; meant \describe ?
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) TopDom.Rd:21: Lost braces; missing escapes or markup?
    21 | Recommended range is in {5, ..., 20}.}
       |                         ^
checkRd: (-1) getSegsExtra.Rd:14: Lost braces
    14 | \item{data}{data.table returned from function /code{tdtr}}
       |                                                    ^
checkRd: (-1) ETM.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ETM.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
Note: found 91 marked UTF-8 strings
Packages suggested but not available for checking:
  'RGtk2', 'gWidgets2RGtk2'
Package suggested but not available for checking: ‘gurobi’
File ‘torch/libs/torch.so’:
  Found non-API calls to R: ‘PRCODE’, ‘PRENV’, ‘Rf_findVarInFrame3’
File ‘torch/libs/torchpkg.so’:
  Found non-API calls to R: ‘PRCODE’, ‘PRENV’, ‘Rf_findVarInFrame3’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Package suggested but not available for checking: ‘toscaData’
Namespace in Imports field not imported from: ‘hdi’
  All declared Imports should be used.
Note: found 4490 marked UTF-8 strings
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Note: found 23 marked UTF-8 strings
checkRd: (-1) parse_beast_output_files.Rd:23: Lost braces
    23 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:24-28: Lost braces
    24 |     item{
       |         ^
checkRd: (-1) parse_beast_output_files.Rd:29-31: Lost braces
    29 |     item{\code{operators}: the BEAST2 MCMC operator
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:28: Lost braces
    28 |     item{\code{estimates}: parameter estimates}
       |         ^
checkRd: (-1) parse_beast_posterior.Rd:29-33: Lost braces
    29 |     item{
       |         ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
checkRd: (-1) Sim-Functions.Rd:99: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:100-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:109-110: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:111-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:114-116: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Requires orphaned package: ‘taxize’
checkRd: (-1) trait_missing.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trait_missing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
Package suggested but not available for checking: ‘taxidata’
Error(s) in re-building vignettes:
--- re-building ‘tampolining.Rmd’ using rmarkdown

Quitting from lines 43-44 [blow_up] (tampolining.Rmd)
Error: processing vignette 'tampolining.Rmd' failed with diagnostics:
evaluation nested too deeply: infinite recursion / options(expressions=)?
--- failed re-building ‘tampolining.Rmd’

SUMMARY: processing the following file failed:
  ‘tampolining.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 827 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) Blavet.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Blavet.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Oudon.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |        ^
checkRd: (-1) trans.Rd:46: Lost braces; missing escapes or markup?
    46 | "Found {trans("file", .n = n_files)} in {trans("directory", .n = n_dirs)}".
       |                                         ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: ‘fwelnet’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘Capr’
checkRd: (-1) trtsel.Rd:69: Lost braces; missing escapes or markup?
    69 | numeric with two values {0,1} and gaussian(link = "identity") otherwise.
       |                         ^
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
Specified C++11: please drop specification unless essential
Note: found 3 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Note: found 2 marked UTF-8 strings
checkRd: (-1) coef.tridim_transformation.Rd:31: Lost braces
    31 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) coef.tridim_transformation.Rd:32: Lost braces; missing escapes or markup?
    32 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) predict.tridim_transformation.Rd:24: Lost braces
    24 | If summary=TRUE, a data.frame with columns "dv{index}" with mean for each dependent
       |                                               ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                        ^
checkRd: (-1) predict.tridim_transformation.Rd:25: Lost braces; missing escapes or markup?
    25 | variable plus optional quantiles columns with names "dv{index}_{quantile}".
       |                                                                ^
checkRd: (-1) variable_summary.Rd:18: Lost braces; missing escapes or markup?
    18 | data.frame with "{var_name}" column for the mean and
       |                  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |  ^
checkRd: (-1) variable_summary.Rd:19: Lost braces; missing escapes or markup?
    19 | "{var_name}_{prob}" columns for each probability.
       |             ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Running ‘testthat.R’ [13s/31s]
  Comparing ‘testthat.Rout’ to ‘testthat.Rout.save’ ...39,41c39
< [ FAIL 0 | WARN 1 | SKIP 0 | PASS 43 ]
< 
< [ FAIL 0 | WARN 1 | SKIP 0 | PASS 43 ]
---
> [ FAIL 0 | WARN 0 | SKIP 0 | PASS 43 ]
Found the following significant warnings:
  Warning: 'dasinh' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL. [-Wintrinsic-shadow]
  Warning: 'dacosh' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL. [-Wintrinsic-shadow]
See ‘/data/gannet/ripley/R/packages/tests-devel/tripack.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
Packages suggested but not available for checking: 'rrelaxiv', 'gurobi'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 192 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
ypr_sel.html:113:1 (ypr_sel.Rd:31): Warning: trimming empty <li>
ypr_sel.html:112:1 (ypr_sel.Rd:31): Warning: trimming empty <ul>
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘log2console’
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
checkRd: (-1) summary.armasubsets.Rd:16: Lost braces
    16 | \item{matrix.logical}{With matrix=TRUE, the matrix is logical TRUE/FALSE or string "*"/code{" "}}
       |                                                                                            ^
checkRd: (-1) tsBSS-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tsBSS-package.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) diss.AR.LPC.CEPS.Rd:39: Lost braces; missing escapes or markup?
    39 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model.
       |                      ^
checkRd: (-1) diss.AR.PIC.Rd:31: Lost braces; missing escapes or markup?
    31 | If \code{order.x} or {order.y} are \code{NULL}, their respective series will be fitted automatically using a AR model. If \code{permissive} is \code{TRUE} and no AR order is found automatically, an AR order of 1 will be imposed, if this case fails, then no order can be found and the function produces an error.
       |                      ^
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) example.database2.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database2.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) example.database3.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binary_transform.Rd:16: Lost braces; missing escapes or markup?
    16 | Converts any variable with two possible values to a {0,1} binary
       |                                                     ^
checkRd: (-1) binary_transform.Rd:13: Lost braces; missing escapes or markup?
    13 | A vector with values in {0,1}.
       |                         ^
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
File ‘tseriesTARMA/libs/tseriesTARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
checkRd: (-1) repr_dwt.Rd:28: Lost braces; missing escapes or markup?
    28 | The final representation has length equal to floor(n / 2^{level}), where n is a length of original time series.
       |                                                          ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Note: found 1080 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
checkRd: (-1) tweedie-internal.Rd:74: Lost braces
    74 |         doi{10.1093/biomet/74.2.221}
       |            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) fit_stm.Rd:25: Lost braces
    25 | \item{xcov}{Either a \[stats]{formula} with an empty left-hand side specifying external covariates
       |                              ^
Note: found 34 marked Latin-1 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
checkRd: (-1) twosigmag.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:91: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:92: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:95: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twosigmag.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |     ^
checkRd: (-1) twoway.Rd:66: Lost braces
    66 | code{\link{twoway.formula}}, code{\link[stats]{medpolish}}
       |                                  ^
Package which this enhances but not available for checking: ‘sl3’
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |  ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |               ^
checkRd: (-1) est_g_exp.Rd:55: Lost braces; missing escapes or markup?
    55 |  {A - delta}, {A + delta}, and {A + 2 * delta}).
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File ‘typetracer/libs/typetracer.so’:
  Found non-API call to R: ‘SET_BODY’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
checkRd: (-1) cambodia.Rd:47: Lost braces
    47 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) microdata.Rd:33: Lost braces
    33 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
checkRd: (-1) u5mr_cohort.Rd:111: Lost braces
   111 | (\doi{10.1371/journal.pmed.1000253}{10.1371/journal.pmed.1000253})
       |                                    ^
Problems with news in ‘NEWS.md’:
No news entries found.
GNU make is a SystemRequirements.
Note: found 2 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    uktrans_get is fixed when start_date is used (#2)
    Extra layer of of NULL returns to fail gracefully with an informative message.
    Removed travis & appveyor and using gh_actions instead.
    Using gh-pages to create the pkgdown website.
    Create an app as vignette page to search with the help of uklr.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘foreign’ ‘psychTools’ ‘pwr’ ‘rmarkdown’
  All declared Imports should be used.
Note: found 312859 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 468 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
checkRd: (-1) reg_1d.Rd:42: Lost braces; missing escapes or markup?
    42 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
checkRd: (-1) reg_2d.Rd:33: Lost braces; missing escapes or markup?
    33 |         \item Metric input is not in {1,2,3}: Metric does not exist
       |                                      ^
Specified C++11: please drop specification unless essential
Note: found 548 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) simRedCard.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simRedCard.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
checkRd: (-1) mllogitnorm.Rd:45: Lost braces
    45 | link[dlogitnorm]{dlogitnorm}for the normal density.
       |                 ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
File ‘unnest/libs/unnest.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) UNPaC_Copula.Rd:59: Lost braces; missing escapes or markup?
    59 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}
       |                                  ^
checkRd: (-1) UNPaC_Copula.Rd:60: Lost braces; missing escapes or markup?
    60 | \item{\code{sim_CI}}: {vector containing the cluster indices for each generated unimodal reference distribution}
       |                       ^
checkRd: (-1) UNPaC_Copula.Rd:61-62: Lost braces
    61 | \item{\code{pvalue_emp}}: {the empirical p-value:  the proportion of times the cluster index from the reference
       |                           ^
checkRd: (-1) UNPaC_Copula.Rd:63: Lost braces; missing escapes or markup?
    63 | \item{\code{pvalue_norm}}: {the normalized p-value: the simulated p-value based on comparison to a standard normal distribution }
       |                            ^
checkRd: (-1) UNPaC_num_clust.Rd:58-62: Lost braces
    58 | \item{\code{BestK}}: {A matrix with 1 row and 4 columns named: "Max_CI","Max_CI_wi_1SE","Max_scaled_CI" and "Max_logWCSS_wi_1SE".
       |                      ^
checkRd: (-1) UNPaC_num_clust.Rd:63-65: Lost braces
    63 | \item{\code{full_process}}: {A matrix containing the number of clusters, K, evaluated, the CI from the data, the average CI from the null
       |                             ^
checkRd: (-1) UNPaC_num_clust.Rd:66: Lost braces; missing escapes or markup?
    66 | \item{\code{selected_features}}: {A vector of integers indicating the features retained by the feature filtering process.}}
       |                                  ^
Note: found 3347 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 7872 marked UTF-8 strings
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Running ‘logit.R’ [6s/18s]
  Comparing ‘logit.Rout’ to ‘logit.Rout.save’ ...39a40,43
> Deviance Residuals: 
>    Min      1Q  Median      3Q     Max  
> -1.873  -1.232   0.803   1.056   1.587  
> 
137a142,145
> Deviance Residuals: 
>    Min      1Q  Median      3Q     Max  
> -1.899  -1.232   0.789   1.051   1.649  
> 
292a301,304
> 
> Deviance Residuals: 
>    Min      1Q  Median      3Q     Max  
> -1.874  -1.216   0.805   1.067   1.722  
  Running ‘logitEffCat.R’
  Comparing ‘logitEffCat.Rout’ to ‘logitEffCat.Rout.save’ ... OK
  Running ‘logitEffInt.R’
  Comparing ‘logitEffInt.Rout’ to ‘logitEffInt.Rout.save’ ... OK
  Running ‘logitEla.R’
  Comparing ‘logitEla.Rout’ to ‘logitEla.Rout.save’ ... OK
  Running ‘logitElaInt.R’
  Comparing ‘logitElaInt.Rout’ to ‘logitElaInt.Rout.save’ ... OK
  Running ‘lpm.R’ [4s/11s]
  Comparing ‘lpm.Rout’ to ‘lpm.Rout.save’ ... OK
  Running ‘mlogit.R’ [10s/23s]
  Comparing ‘mlogit.Rout’ to ‘mlogit.Rout.save’ ...57c57
< 4 iterations, 0h:0m:1s 
---
> 4 iterations, 0h:0m:0s 
  Running ‘mvprobit.R’ [18s/48s]
  Comparing ‘mvprobit.Rout’ to ‘mvprobit.Rout.save’ ... OK
  Running ‘oprobit.R’ [5s/11s]
  Comparing ‘oprobit.Rout’ to ‘oprobit.Rout.save’ ... OK
  Running ‘probit.R’ [5s/10s]
  Comparing ‘probit.Rout’ to ‘probit.Rout.save’ ...39a40,43
> Deviance Residuals: 
>    Min      1Q  Median      3Q     Max  
> -1.895  -1.234   0.802   1.059   1.589  
> 
137a142,145
> Deviance Residuals: 
>    Min      1Q  Median      3Q     Max  
> -1.927  -1.231   0.785   1.053   1.654  
> 
292a301,304
> 
> Deviance Residuals: 
>    Min      1Q  Median      3Q     Max  
> -1.897  -1.215   0.804   1.069   1.729
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
checkRd: (-1) encoder.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) encoder.Rd:38-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) encoder.Rd:45-48: Lost braces in \itemize; meant \describe ?
Note: found 488 marked UTF-8 strings
Package suggested but not available for checking: ‘USA.state.boundaries.data’
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 9 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
checkRd: (-1) aosat.Rd:20: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) aosat.Rd:21: Escaped LaTeX specials: \_
checkRd: (-1) arctic.oscillations.Rd:19: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) arctic.oscillations.Rd:20: Escaped LaTeX specials: \_
checkRd: (-1) babies.Rd:28: Escaped LaTeX specials: \&
checkRd: (-1) babies.Rd:41: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:25: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:43: Escaped LaTeX specials: \$
checkRd: (-1) cabinet.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) exec.pay.Rd:5: Escaped LaTeX specials: \$
checkRd: (-1) sp500.excess.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) sp500.excess.Rd:6: Escaped LaTeX specials: \&
Note: found 17 marked UTF-8 strings
Note: found 50 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Malformed Title field: should not end in a period.
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
checkRd: (-1) partition_fold.Rd:21-22: Lost braces
    21 |    \code{train}{The mldr dataset with train examples, that includes all
       |                ^
checkRd: (-1) partition_fold.Rd:23-24: Lost braces
    23 |    \code{test}{The mldr dataset with test examples, defined by the
       |               ^
checkRd: (-1) partition_fold.Rd:25-26: Lost braces
    25 |    \code{validation}{Optionally, only if \code{has.validation = TRUE}.
       |                     ^
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘PredValidationPlots.pdf’ ‘RepStructValidationPlots.pdf’
Namespaces in Imports field not imported from:
  ‘BBmisc’ ‘badger’
  All declared Imports should be used.
checkRd: (-1) sendTasks.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sendTasks.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
checkRd: (-1) sample_gen.Rd:18: Lost braces; missing escapes or markup?
    18 | Generate \code{n} random samples from multivariate Gaussian distribution N(0, (L^TL)^{-1})
       |                                                                                      ^
'LazyData' is specified without a 'data' directory
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) vardannual.Rd:97: Lost braces
    97 | \item{ID_level2}{Optional}{variable for unit ID codes. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                           ^
checkRd: (-1) vardannual.Rd:99: Lost braces
    99 | \item{dataset}{Optional}{survey data object convertible to \code{data.table}.}
       |                         ^
checkRd: (-1) vardcrospoor.Rd:122: Lost braces
   122 | \item{ind_gr}{Optional}{variable by which divided independently X matrix of the auxiliary variables for the calibration. One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                        ^
checkRd: (-1) vardcrospoor.Rd:124: Lost braces
   124 | \item{use.estVar}{Logical}{value. If value is \code{TRUE}, then \code{R} function \code{estVar} is used for the  estimation of covariance matrix of the residuals. If value is \code{FALSE}, then \code{R} function \code{estVar} is not used for the estimation of covariance matrix of the residuals.}
       |                           ^
checkRd: (-1) vardom_othstr.Rd:69: Lost braces
    69 | \item{percentratio}{Positive}{numeric value. All linearized variables are multiplied with \code{percentratio} value, by default - 1.}
       |                              ^
checkRd: (-1) varpoord.Rd:121: Lost braces
   121 | \item{month_at_work}{Variable}{for total number of month at work (sum of the number of months spent at full-time work as employee, number of months spent at part-time work as employee, number of months spent at full-time work as self-employed (including family worker), number of months spent at part-time work as self-employed (including family worker)).  One dimensional object convertible to one-column \code{data.table} or variable name as character, column number.}
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) betaburr.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Burr distribution due to Parana\'{i}ba et al. (2011) given by
       |                                                                                                                        ^
checkRd: (-1) betafrechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the beta Fr\'{e}chet distribution due to Barreto-Souza et al. (2011) given by
       |                                                                                           ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                      ^
checkRd: (-1) frechet.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Fr\'{e}chet distribution due to Fr\'{e}chet (1927) given by
       |                                                                                                                      ^
checkRd: (-1) kumburr7.Rd:7: Lost braces
     7 | \description{Computes the pdf, cdf, value at risk and expected shortfall for the Kumaraswamy Burr XII distribution due to Parana\'{i}ba et al. (2013) given by
       |                                                                                                                                   ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) simulateDCSIS.Rd:40: Lost braces
    40 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + exp(2*X22)*e
       |                                ^
checkRd: (-1) simulateDCSIS.Rd:42: Lost braces
    42 |        Y = 6*X1 + 1.5*X2  + 9*1{X12 < 0} + 6*X22 + e
       |                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get.miniseq.sample.files.Rd:15: Lost braces
    15 | \item{file.suffix}{Regex expression for end of file name. For example, `file.suffix = '_S\\d{1,2}_.*_R1_.*'` will match R1 files.1 files.}
       |                                                                                             ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) randomVarImpsRFplot.Rd:97: Escaped LaTeX specials: \&
checkRd: (-1) varSelImpSpecRF.Rd:83: Escaped LaTeX specials: \&
checkRd: (-1) Acoef_sh.Rd:23: Lost braces; missing escapes or markup?
    23 | The function returns the K-by-K matrices {A_1, ..., A_p} as a list object.
       |                                          ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                    ^
checkRd: (-1) VARshrink.Rd:58: Lost braces; missing escapes or markup?
    58 | Consider VAR(p) model: y_t = A_1 y_{t-1} + ... + A_p y_{t-p} + C d_t + e_t,
       |                                                        ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) decomposition.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) decomposition.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |      ^
checkRd: (-1) moving.decomposition.Rd:28: Lost braces
    28 | \item{W2}{nxn matrix of weights. Season is estimated as W2 \%}\% y, if y is the data vector}
       |          ^
checkRd: (-1) moving.estimation.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) moving.estimation.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) datasets.Rd:15: Lost braces
    15 | and dimension information (\code{dim} or code{length}) of each item,
       |                                              ^
GNU make is a SystemRequirements.
File ‘vctrs/libs/vctrs.so’:
  Found non-API calls to R: ‘FRAME’, ‘HASHTAB’, ‘LEVELS’, ‘PRENV’,
    ‘PRVALUE’, ‘R_PromiseExpr’, ‘Rf_findVarInFrame3’, ‘SETLENGTH’,
    ‘SET_BODY’, ‘SET_CLOENV’, ‘SET_ENCLOS’, ‘SET_FORMALS’,
    ‘SET_GROWABLE_BIT’, ‘SET_S4_OBJECT’, ‘SET_TRUELENGTH’,
    ‘STDVEC_DATAPTR’, ‘STRING_PTR’, ‘TRUELENGTH’, ‘UNSET_S4_OBJECT’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  Warning: Obsolescent feature: Old-style character length at (1)
See ‘/data/gannet/ripley/R/packages/tests-devel/Vdgraph.Rcheck/00install.out’ for details.
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 128 marked UTF-8 strings
Note: found 49 marked UTF-8 strings
checkRd: (-1) additiveBeta.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) additiveBeta.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) downloadPBDB.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) multiplicativeBeta.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) predcomp.test.Rd:51: Lost braces; missing escapes or markup?
    51 | S = dbar/sqrt(2*pi*se_{d}(0)/N),
       |                       ^
checkRd: (-1) predcomp.test.Rd:53: Lost braces; missing escapes or markup?
    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                              ^
checkRd: (-1) predcomp.test.Rd:53: Lost braces; missing escapes or markup?
    53 | where d is the loss differential, d = e1 - e2 (e1 = loss(x, xhat1) and e2 = loss(x, xhat2)), dbar is its sample mean, and se_{d}(0) is the standard error for d, which must be estimated, and N is the length of the series investigated.  Let V = 2*pi*se_{d}(0), then V is estimated by
       |                                                                                                                                                                                                                                                            ^
checkRd: (-1) value.Rd:32: Escaped LaTeX specials: \$ \$
'LazyData' is specified without a 'data' directory
File ‘versus/libs/versus.so’:
  Found non-API call to R: ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
checkRd: (-1) ex121.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex124.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex125.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex127.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex32.Rd:18: Escaped LaTeX specials: \&
checkRd: (-1) ex33.Rd:18: Escaped LaTeX specials: \&
File ‘vetr/libs/vetr.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fit.vfp.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:86: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:87: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.vfp.Rd:88: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Note: found 2 marked UTF-8 strings
checkRd: (-1) VirtualArray-single-bracket-method.Rd:6: Lost braces
     6 | \title{Indexing to extract subsets of a 'code{\link[via:XArray-class]{VirtualArray}}'-class object}
       |                                              ^
checkRd: (-1) subset.Rd:20: Lost braces
    20 | \item{drop}{\code{logical} in case the result of subsetting is a single element, should the \\code{\link[via:XArray-class]{VirtualArray}} wrapper be dropped?}
       |                                                                                                   ^
checkRd: (-1) vic_param.Rd:311: Lost braces
   311 | albedo must be supplied in code{forcing_veg}. Default = 1.}
       |                                ^
checkRd: (-1) vic_param.Rd:323: Lost braces
   323 | supplied in code{forcing_veg}. Default = 1.}
       |                 ^
checkRd: (-1) vic_param.Rd:341: Lost braces
   341 | be supplied in code{forcing_veg} Default = 0.}
       |                    ^
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘leaflet’ ‘mapview’
  All declared Imports should be used.
checkRd: (-1) show_query.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) show_query.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vietnamcode_data.Rd:16: Lost braces in \itemize; meant \describe ?
Note: found 60 marked UTF-8 strings
Note: found 468 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) viridis.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:24-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:31-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) viridis.map.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulatePopulation.Rd:75: Lost braces; missing escapes or markup?
    75 |   \item \strong{Pollen productivity}: In each time step the model computes the pollen productivity (in relative values) of the population using the equation \eqn{P_{t} = \sum x_{it} \times max(S_{t}, B)}, where \emph{t} is time (a given simulation time step), \emph{P} is the pollen productivity of the population at a given time, \emph{x_{i}} represents the biomass of every adult individual, \emph{S} is the environmental suitability at the given time, \emph{B} is the contribution of biomass to pollen productivity regardless of environmental suitability (\emph{pollen.control} parameter in the simulation, 0 by default). If \emph{B} equals 1, \emph{P} is equal to the total biomass sum of the adult population, regardless of the environmental suitability. If \emph{B} equals 0, pollen productivity depends entirely on environmental suitability values.
       |                                                                                                                                                                                                                                                                                                                                                    ^
checkRd: (-1) NSpec.DB.Rd:16: Lost braces; missing escapes or markup?
    16 |   ...{currently not used}
       |      ^
checkRd: (-1) wavelength-methods.Rd:32: Lost braces; missing escapes or markup?
    32 | A call to {new} returns a newly allocated object from the class identified by the first argument.
       |           ^
checkRd: (-1) phasePortrait.Rd:350: Lost braces; missing escapes or markup?
   350 |   \code{vMod = xMod^(1/lambda)} and {vArg = xArg^(1/lambda)}\cr\cr
       |                                     ^
checkRd: (-1) compdesc.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) compdesc.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in ‘NEWS.md’:
No news entries found.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
checkRd: (-1) ViSiElse.Rd:101-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:108-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:112-113: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:114-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:116: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:128-134: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:135-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:148-157: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:152-153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSiElse.Rd:154-155: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ViSibook-class.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dim-ViSibook-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dim-ViSibook-methods.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary-ViSigrid-methods.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: found 83 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'LazyData' is specified without a 'data' directory
checkRd: (-1) aminoAcidFun.Rd:37: Lost braces
    37 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the amino acids at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
checkRd: (-1) vlfFun.Rd:36: Lost braces
    36 | \item{ownVLFreduced}{ownVLFMatrix}{A matrix containing only those specimen that have VLFs as well as the nucleotides at the positions that contain VLFs and NAs in all other positions of the sequence.  Only appears if own is not NULL.}
       |                                   ^
Specified C++11: please drop specification unless essential
checkRd: (-1) getTurnType.Rd:38: Lost braces; missing escapes or markup?
    38 | Return one of {Vocalisation, GrpVocalisation, ...} or identifier.
       |               ^
GNU make is a SystemRequirements.
Note: found 4954 marked UTF-8 strings
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    vortexRdata pre-1.0.3
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) compute.means.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) norm.wattfabricius.Rd:5: Escaped LaTeX specials: \&
Problems with news in ‘NEWS.md’:
No news entries found.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
File ‘vroom/libs/vroom.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_TRUELENGTH’,
    ‘STDVEC_DATAPTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
checkRd: (-1) Data-Examples.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Data-Examples.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data-Examples.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Data.trafo.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Toep.estimator.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aquaporin.Rd:10: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
checkRd: (-1) vsts_create_release.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) vsts_create_release.Rd:34: Lost braces in \itemize; meant \describe ?
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following HTML validation problems:
get_logger.html:57:1 (get_logger.Rd:21): Warning: trimming empty <dt>
checkRd: (-1) WACS.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACS.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WACSreadAgroclim.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) WACSreadAgroclim.Rd:16-17: Lost braces in \itemize; \value handles \item{}{} directly
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘warp/libs/warp.so’:
  Found non-API calls to R: ‘Rf_findVarInFrame3’, ‘STRING_PTR’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Found the following significant warnings:
  Warning: Obsolescent feature: Computed GOTO at (1)
See ‘/data/gannet/ripley/R/packages/tests-devel/waveband.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used Fortran compiler: ‘GNU Fortran (GCC) 14.2.0’
'LazyData' is specified without a 'data' directory
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) anchor_points_grey.Rd:9: Lost braces
     9 | Zeeden et al., (2013) and anchored to the code{\link{astrosignal_example}} \cr
       |                                               ^
checkRd: (-1) retrack_wt_MC.Rd:206: Lost braces
   206 | be off in certain intervals. the link[WaverideR]{retrack_wt_MC} mitigates
       |                                                 ^
checkRd: (-1) retrack_wt_MC.Rd:40: Lost braces
    40 | link[WaverideR]{analyze_wavelet} wavelet function
       |                ^
checkRd: (-1) retrack_wt_MC.Rd:41: Lost braces
    41 | To create a list use the link[base]{list} function}
       |                                    ^
checkRd: (-1) retrack_wt_MC.Rd:44: Lost braces
    44 | To create the matrix use the link[base]{cbind} function and only add the
       |                                        ^
Found the following files/directories:
  ‘ReconstructedData.txt’ ‘ReconstructedDataStDev.txt’
  ‘ResampledReconstructions.txt’
  ‘ResampledReconstructionsStandardVariation.txt’
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Note: found 1 marked UTF-8 string
Note: found 3133 marked UTF-8 strings
Note: found 4413 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Note: found 1668 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘prepr’
checkRd: (-1) wdpa_clean.Rd:23: Lost braces
    23 | \item{crs}{\code{character} or code{integer} object representing a
       |                                    ^
Problems with news in ‘NEWS.md’:
No news entries found.
checkRd: (-1) get_cid.Rd:58-59: Lost braces
    58 | <structure search> is assembled as "{\code{substructure} |
       |                                     ^
checkRd: (-1) get_cid.Rd:59-60: Lost braces
    59 | \code{superstructure} | \code{similarity} | \code{identity}} / {\code{smiles}
       |                                                                ^
checkRd: (-1) get_cid.Rd:70-71: Lost braces
    70 | "{\code{fastidentity} | \code{fastsimilarity_2d} | \code{fastsimilarity_3d} |
       |  ^
checkRd: (-1) get_cid.Rd:71-72: Lost braces
    71 | \code{fastsubstructure} | \code{fastsuperstructure}}/{\code{smiles} |
       |                                                      ^
checkRd: (-1) Session.Rd:146: Lost braces
   146 | sQuote{page load} timeout specifies a time to wait for the page loading
       |       ^
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'iptools', 'rgeolocate'
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Note: found 14 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘here’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) busTrace.Rd:15: Lost braces
    15 | /href{https://crawdad.org/coppe-ufrj/RioBuses/20180319/}
       |      ^
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Specified C++11: please drop specification unless essential
File ‘weightedCL/libs/weightedCL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkRd: (-1) WeightedROC.Rd:10: Lost braces; missing escapes or markup?
    10 | integer/numeric with values all in {0=negative,1=positive} or
       |                                    ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       | ^
checkRd: (-1) WeightedROC.Rd:11: Lost braces; missing escapes or markup?
    11 | {1=negative,2=positive} or {-1=negative,1=positive}.}
       |                            ^
checkRd: (-1) CLIC.Rd:149: Lost braces
   149 | Composite likelihood {E}{M} algorithm with applications to
       |                         ^
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  svm.cpp:42:38: warning: argument 1 range [18446744056529682432, 18446744073709551608] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
See ‘/data/gannet/ripley/R/packages/tests-devel/WeightSVM.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc-14 (GCC) 14.2.0’
* used C++ compiler: ‘g++-14 (GCC) 14.2.0’
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
  Cannot extract version info from the following section titles:
    Major changes
    Minor changes
Note: found 4102 marked UTF-8 strings
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_geo_box.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_box.Rd:43-44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) get_geo_entity.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) milakes.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) milakes.Rd:22: Lost braces in \itemize; meant \describe ?
Namespace in Imports field not imported from: ‘webfakes’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
checkRd: (-1) secondDerivative.Rd:14: Lost braces
    14 | This must be a function of the form FUN <- function(x, ...){...}
       |                                                            ^
checkRd: (-1) windAC.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) windAC.Rd:33: Lost braces in \itemize; meant \describe ?
Note: found 1 marked UTF-8 string
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘roxygen2’
  All declared Imports should be used.
Note: found 3881 marked UTF-8 strings
Specified C++11: please drop specification unless essential
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following HTML validation problems:
benefits.html:96:1 (benefits.Rd:39): Warning: trimming empty <h3>
beveridge.html:66:1 (beveridge.Rd:29): Warning: trimming empty <h3>
happiness.html:141:1 (happiness.Rd:54): Warning: trimming empty <h3>
hprice3.html:99:1 (hprice3.Rd:40): Warning: trimming empty <h3>
checkRd: (-1) word2vec_similarity.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) word2vec_similarity.Rd:31: Lost braces in \itemize; meant \describe ?
Note: found 933 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 9378 marked UTF-8 strings
Note: found 154 marked UTF-8 strings
Package suggested but not available for checking: ‘wordnetDicts’
checkRd: (-1) wordpiece_cache_dir.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) wordpiece_cache_dir.Rd:20-21: Lost braces in \itemize; meant \describe ?
Error(s) in re-building vignettes:
--- re-building ‘features.Rmd’ using rmarkdown
Warning in file("", "w+b") :
  cannot open file '/tmp/Rtmpk1Avbl/working_dir/RtmpYM3MuP/Rf25d9b63dfcf578': No such file or directory

Quitting from lines 92-121 [data-sampling-1] (features.Rmd)
Error: processing vignette 'features.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘features.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in file("", "w+b") :
  cannot open file '/tmp/Rtmpk1Avbl/working_dir/RtmpZy1npa/Rf25dec27e643db4': No such file or directory

Quitting from lines 154-170 [model-evaluation-1] (overview.Rmd)
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following files failed:
  ‘features.Rmd’ ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Note: found 4 marked Latin-1 strings
  Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
checkRd: (-1) createDemandSite.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.base.Rd:26: Lost braces
    26 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
checkRd: (-1) createDemandSite.default.Rd:32: Lost braces
    32 |   \item{suppliers}{(optional) A list of object(s) inherited from the folowing classes: \code{\link[WRSS]{createAquifer}}, \code{\link[WRSS]{createRiver}}, \code{\link[WRSS]{createReservoir}}, code{\link[WRSS]{createDiversion}}.}
       |                                                                                                                                                                                                     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘future’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) wtest.Rd:61-64: Lost braces
    61 | {When \code{w.order} =2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) wtest.high.Rd:61-64: Lost braces
    61 | {When \code{w.order} > 2, the \code{wtest()} will automatically calculate the main effect first and then do a pre-filter before calculating interactions.
       | ^
checkRd: (-1) batch_modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) batch_modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_eta3_robust.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ci_wave_variance.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) modwt_wvar_cpp.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wvar_cpp.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) exploreSignatures.Rd:67-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generateData.Rd:47: Lost braces
    47 | \bold{code{data}} \tab the generated data \cr
       |           ^
checkRd: (-1) generateData.Rd:53: Lost braces
    53 | Refer to \bold{\emph{code{\link{retrieveDataFactory}}}} and to
       |                          ^
checkRd: (-1) qualifyFunctionArguments.Rd:14: Lost braces
    14 | A emph{\code{list}} with following names
       |       ^
checkRd: (-1) qualifyFunctionArguments.Rd:26: Lost braces
    26 | \item{code{arguments}}{a \code{pairList} of argument names and values.
       |           ^
checkRd: (-1) completeManualPage.Rd:12: Lost braces
    12 | See \emph{\bold{code{\link{ProcessingContext}}}}. Only
       |                     ^
checkRd: (-1) produceAllManualPagesFromObject.Rd:14: Lost braces
    14 | See \emph{\bold{\\code{\link{ProcessingContext}}}}.}
       |                       ^
checkRd: (-1) xbrlSECdev01.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) xshow.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) xshow.Rd:20: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chemnet.Rd:111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) chemnet.Rd:112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) knecht.Rd:105: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following files/directories:
  ‘xgb.txt’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Problems with news in ‘NEWS.md’:
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) xml_to_df.Rd:144: Lost braces; missing escapes or markup?
   144 | Default {NULL} means the workbook will not be protected with a password}
       |         ^
'LazyData' is specified without a 'data' directory
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: ‘rbokeh’
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Note: found 268 marked UTF-8 strings
Found the following files/directories:
  ‘xtable.html’ ‘xtable.tex’
File ‘xts/libs/xts.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
checkRd: (-1) xwfGridsearch.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{iter}{Number of levels in the adaptive grid search. The resolution in b obtained is 2^{-1-iter}.}
       |                                                                                             ^
checkRd: (-1) cat_sim.Rd:110: Lost braces; missing escapes or markup?
   110 | \code{min} and {max} are mandatory for setting limits on the test length. User-defined
       |                ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
checkRd: (-1) boot.yhat.Rd:3: Lost braces
     3 | \title{Bootstrap metrics produced from /code{calc.yhat}}
       |                                             ^
checkRd: (-1) boot.yhat.Rd:19: Lost braces
    19 |     Ouput of /code{lm}
       |                   ^
checkRd: (-1) boot.yhat.Rd:22: Lost braces
    22 |     Output of /code{calc.yhat}
       |                    ^
checkRd: (-1) booteval.yhat.rd:3: Lost braces
     3 | \title{Evaluate bootstrap metrics produced from /code{calc.yhat}}
       |                                                      ^
checkRd: (-1) booteval.yhat.rd:5: Lost braces
     5 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) combCI.rd:26: Lost braces
    26 |   This function evaluates the bootstrap metrics produced from /code{boot.yhat}.   
       |                                                                    ^
checkRd: (-1) commonality.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) dombin.rd:12: Lost braces
    12 |     Output from /code{dominance}
       |                      ^
checkRd: (-1) dominance.rd:12: Lost braces
    12 |     Output from /code{aps}
       |                      ^
checkRd: (-1) plotCI.yhat.rd:5: Lost braces
     5 |   This function plots CIs that have been produced from /code{booteval.yhat}.
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:32: Lost braces
    32 |   This function plots CIs that have been produced from /code{booteval.yhat}.   
       |                                                             ^
checkRd: (-1) plotCI.yhat.rd:35: Lost braces
    35 | This returns a plot of CIs that have been produced from /code{booteval.yhat}.
       |                                                              ^
'LazyData' is specified without a 'data' directory
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘spelling’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
File ‘yuima/libs/yuima.so’:
  Found non-API call to R: ‘SET_TYPEOF’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
File ‘yyjsonr/libs/yyjsonr.so’:
  Found non-API calls to R: ‘SETLENGTH’, ‘SET_GROWABLE_BIT’,
    ‘SET_TRUELENGTH’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Packages suggested but not available for checking:
  'RNRCS', 'metScanR', 'rnoaa'
'LazyData' is specified without a 'data' directory
Note: found 76 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
checkRd: (-1) glm.cons.Rd:54: Lost braces; missing escapes or markup?
    54 | \item{method}{the method used in fitting the model. The default method "\code{glm.fit.cons}" uses function {nnnpls} from package nnls instead of \code{lm.fit} to impose the sign of the coefficients. As in \code{glm}, the alternative method "\code{model.frame}" returns the model frame and does no fitting.}
       |                                                                                                            ^
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
checkRd: (-1) label_kansuji.Rd:48: Lost braces; missing escapes or markup?
    48 | but if TRUE and installed '{scales}` package, 1.10 will be displayed.}
       |                            ^
Note: found 47 marked UTF-8 strings
Found the following HTML validation problems:
kana.html:65:1 (kana.Rd:33): Warning: trimming empty <dt>
Note: found 5 marked UTF-8 strings
'LazyData' is specified without a 'data' directory
Note: found 146804 marked UTF-8 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘Crashpad’
checkRd: (-1) ZIClass.Rd:87: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:72: Escaped LaTeX specials: \_
checkRd: (-1) ZITrain.Rd:74: Escaped LaTeX specials: \_
checkRd: (-1) zid.Rd:45: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:63: Escaped LaTeX specials: \_
checkRd: (-1) zim.Rd:182: Lost braces
   182 |   dQuote{tab-delimited text file} when you have done and close the spreadsheet
       |         ^
checkRd: (-1) in.zoom.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) in.zoom.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) zm.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_ztable.Rd:75: Lost braces; missing escapes or markup?
    75 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.}
       |                                          ^
checkRd: (-1) ztable_sub.Rd:78: Lost braces; missing escapes or markup?
    78 | must be NULL or contain only elements of {"h","t","b","p","!","H"}.
       |                                          ^
Specified C++11: please drop specification unless essential
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  xtable.A3.Rd: print.xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) abclass.Rd:133: Lost braces; missing escapes or markup?
   133 |     \code{abclass.control()} returns an object of class {abclass.control}
       |                                                         ^
checkRd: (-1) supclass.Rd:109: Lost braces; missing escapes or markup?
   109 | to solve the equivalent linear programming problem via the package {Rglpk}.
       |                                                                    ^
checkRd: (-1) supclass.Rd:110: Lost braces; missing escapes or markup?
   110 | It is recommended to use a recent version of {GLPK}.
       |                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abc.Rd: nnet
  cv4abc.Rd: nnet
  cv4postpr.Rd: nnet
  plot.abc.Rd: nnet
  postpr.Rd: nnet, multinom
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abcrf.Rd: ranger
  covRegAbcrf.Rd: ranger
  densityPlot.Rd: ranger
  err.regAbcrf.Rd: ranger
  plot.regAbcrf.Rd: ranger
  predict.abcrf.Rd: ranger
  predict.regAbcrf.Rd: predict.ranger, ranger
  predictOOB.Rd: predict.ranger, ranger
  regAbcrf.Rd: ranger
  variableImpPlot.Rd: ranger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abctools-package.Rd: abc
  cov.pi.Rd: abc, postpr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abe.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_ex_data.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) get_ex_data.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tidy_results.Rd:30: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      1.9Mb
'LazyData' is specified without a 'data' directory
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    include  12.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bind_tweets.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bind_tweets.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) accelimp.Rd:15: Lost braces
    15 | \item[]{...}
       |        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mice.impute.2l.zip.pmm.Rd: mice
  mice.impute.2l.zipln.Rd: mice
  mice.impute.2l.zipln.pmm.Rd: mice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  acdFit.Rd: solnp
  plotScatterAcd.Rd: stat_smooth
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) overstallwoods.Rd:184-185: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:186-187: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:188-189: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) overstallwoods.Rd:190-191: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doACNE.Rd: AffymetrixCelSet, Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  makeCues.Rd: tuneR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rRegMatch.Rd: daisy, treeClust.dist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
checkRd: (-1) Ehrenfest.Rd:19: Lost braces
    19 | In this experiment there are i balls in Urn I, and remaining 2n-i balls in Urn II. Then at any instance, the probability of selecting a ball from Urn I and placing it in Urn II is i/2n, and the other way of placing a ball from Urn II to Urn I is (2n-i)/2n. At each instant we let the number i of balls in the Urn I to be the state of the system. Thus, the state space is S = { 0, 1, 2, \ldots, 2n }. Then we can pass from state i only to either of the states i-1 or i+1.
       |                                                                                                                                                                                                                                                                                                                                                                                        ^
checkRd: (-1) Ehrenfest.Rd:20: Lost braces
    20 | Here, S = {0, 1, \ldots, 2n}. 
       |           ^
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  adjustIntercept.Rd: cpglm, cpglmm, data.table
  findbars.Rd: mkRespMod, mkReTrms, nlformula, subbars
  plotRE.Rd: ggplot2, ggplot
  weights-actuaRE.Rd: cpglm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoprune.rd: rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) est_S_Plus_Plus_MethodA.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Plus_Plus_MethodB.Rd:31: Lost braces; missing escapes or markup?
    31 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method B}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodA.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{++} using Method A}
       |                                                          ^
checkRd: (-1) est_S_Star_Plus_MethodB.Rd:29: Lost braces; missing escapes or markup?
    29 |   \item{trt_diff}{Estimate of treatment difference for S_{*+} using Method B}
       |                                                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) adana.Rd:25: Lost braces; missing escapes or markup?
    25 |   \item{gatype}{Type of GA. \itemize{\item{"gga": generational GA}  \item{"ssga": steady state GA} } {Default value is "gga"}}
       |                                                                                                      ^
checkRd: (-1) adana.Rd:26: Lost braces; missing escapes or markup?
    26 |   \item{objective}{Type of optimization. \itemize{\item{"min": minimization}  \item{"max": maximization} } {Default value is "max"}}
       |                                                                                                            ^
checkRd: (-1) adana.Rd:34: Lost braces; missing escapes or markup?
    34 |                  {Default value is "initbin"}}
       |                  ^
checkRd: (-1) adana.Rd:56: Lost braces; missing escapes or markup?
    56 |                \itemize{\item{"integer"}  \item{"real"} } {Default value is "real"}}
       |                                                           ^
checkRd: (-1) adana.Rd:185: Lost braces; missing escapes or markup?
   185 |     {Default value is "w"}
       |     ^
'LazyData' is specified without a 'data' directory
File 'adaptivetau/libs/x64/adaptivetau.dll':
  Found non-API call to R: 'STRING_PTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) adapt.Rd:46: Lost braces
    46 | \item{qvals}{a vector of values in [0, 1]U{Inf}. Q-values. See Details}
       |                                           ^
checkRd: (-1) corr_lfdr.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) corr_lfdr.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ctgm_lfdr.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot_2d.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{plot_2d_lfdr} gives the contour plot of local FDR estimates when all p-values are equal to \code{targetp}. It is recommended to run \code{plot_2d_lfdr} for multiple \code{targetp}'s ranging from {0.001, 0.005, 0.01, 0.05}.
       |                                                                                                                                                                                                          ^
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
checkRd: (-1) SVMDECON.Rd:23: Lost braces; missing escapes or markup?
    23 | and the best result from three values of v = {0.25, 0.5, 0.75}
       |                                              ^
checkRd: (-1) ada.Rd:171: Escaped LaTeX specials: \&
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AdbiConnection-class.Rd: DBIConnection-class, DBIDriver-class
  AdbiDriver-class.Rd: dbConnect, DBIDriver-class, DBIConnection-class
  AdbiResult-class.Rd: DBIResult-class, DBIObject-class,
    DBIDriver-class, DBIConnection-class
  AdbiResultArrow-class.Rd: DBIResultArrow-class, DBIResult-class,
    DBIObject-class, DBIDriver-class, DBIConnection-class
  dbConnect.Rd: DBIDriver-class, DBIConnection-class, dbConnect,
    dbDisconnect
  dbFetch.Rd: dbFetch, DBIResult-class
  dbSendQuery.Rd: dbSendQuery, dbGetQuery, DBIConnection-class, dbBind,
    DBIResult-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addScales.Rd: panel.text, xyplot, panel.refline
  panel.addScales.Rd: panel.text, panel.refline
  prepanel.trim.Rd: xyplot, prepanel.default.xyplot
  update.scaledTrellis.Rd: update.trellis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.9Mb
    libs   1.1Mb
checkRd: (-1) varipart.Rd:19: Lost braces
    19 | \item{type}{a character specifying the algorithm which should be used to adjust R-squared (either \code{"simulated"} or \ code{"parametric"}).}
       |                                                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  df2genind.Rd: hierarchy
  pairDist.Rd: dist.dna
  strata-methods.Rd: hierarchy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    adelie   1.2Mb
    libs     4.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abouheif.Rd: phylo4d-class
  adephylo-package.Rd: phylo4d-class, phylo4-class
  bullseye.Rd: phylo4-class, phylo4d-class
  distRoot.Rd: phylo4-class, phylo4d-class
  distTips.Rd: phylo4-class, phylo4d-class
  listDD.Rd: phylo4-class, phylo4d-class
  listTips.Rd: phylo4-class, phylo4d-class
  miscUtils.Rd: phylo4-class
  orthobasis.Rd: phylo4-class, phylo4d-class
  orthogram.Rd: phylo4-class, phylo4d-class
  ppca.Rd: phylo4d-class, phylo4-class
  proxTips.Rd: phylo4-class, phylo4d-class
  sp.tips.Rd: phylo4-class, phylo4d-class
  table.phylo4d.Rd: phylo4d-class
  treePart.Rd: phylo4-class, phylo4d-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
checkRd: (-1) med.groups.Rd:20: Lost braces; missing escapes or markup?
    20 | medication groups using the construction \emph{"{NAME}"}.
       |                                                 ^
checkRd: (-1) med.groups.Rd:26: Lost braces; missing escapes or markup?
    26 | Another example is "NotVita" defined as "(!{Vitamines})", which selects all
       |                                            ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following significant warnings:
  adlift.c:719:15: warning: argument 1 range [18446744071562067968, 18446744073709551614] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
See 'd:/Rcompile/CRANpkg/local/4.5/adlift.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
checkRd: (-1) Amatdual.Rd:15: Lost braces
    15 |   \item{removelist}{a vector of indices into env{X} of the lifted coefficients during the transform (in the order of removal). }
       |                                                 ^
checkRd: (-1) fwtnp.Rd:30: Lost braces
    30 | Given \eqn{n} points on a line, \env{input}, each with a corresponding env{f} value this algorithm computes a lifting transform of the (\env{input},\env{f}) data. If lengths are inputted (\env{inputtype="lengths"}), then the gridpoints are taken to be the left endpoints of the intervals defined by the lengths inputted. 
       |                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  vars2chr.Rd: exprs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kdfun.Rd: divc
  krfun.Rd: divc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) count_cases.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_cases.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:84: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enrich.Rd:88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitaep.Rd:14: Lost braces
    14 | \item A sequence of goodness-of-fit measures consist of Akaike Information Criterion (\code{AIC}), Consistent Akaike Information Criterion (\code{CAIC}), Bayesian Information Criterion (\code{BIC}), Hannan-Quinn information criterion (\code{HQIC}), Anderson-Darling (\code{AD}), Cram\'{e}er-von Misses (\code{CVM}), Kolmogorov-Smirnov (\code{KS}), and log-likelihood (\code{log-likelihood}) statistics.
       |                                                                                                                                                                                                                                                                                              ^
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) estimate.affinity.matrix.Rd:31: Lost braces; missing escapes or markup?
    31 | than \code{Y}, then those variables that appear in \code{X} but no in {Y}
       |                                                                       ^
checkRd: (-1) estimate.affinity.matrix.lowrank.Rd:36: Lost braces; missing escapes or markup?
    36 | \code{Y}, then those variables that appear in \code{X} but no in {Y} should
       |                                                                  ^
checkRd: (-1) show.correlations.Rd:47: Lost braces
    47 | code{ndims} dimensions. Defaults to all dimensions unless the latter are
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) getNetworkGridLayout.Rd:6-11: Lost braces
     6 | getCoordinatesFromVertexId2<-function(AFMImage, vId) {
       |                                                      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AFM.Rd: gstat, fractaldim, rgl
  AFMFractalDimensionAnalyser-getFractalDimensions.Rd: fractaldim
  AFMImageFractalDimensionMethod-class.Rd: fractaldim
  AFMImageNetworksAnalysis-class.Rd: igraph
  AFMImageVariogramAnalysis-evaluateVariogramModels-method.Rd: gstat
  displayHolesIn3D.Rd: rgl
  displayIn3D.Rd: rgl
  exportToSTL.Rd: rgl
  getCircleSpatialPoints.Rd: SpatialPoints
  putImagesFromAnalysisOnDisk.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AccurateGLM-class.Rd: cv.glmnet
  coef.AccurateGLM.Rd: coef.glmnet
  predict.AccurateGLM.Rd: predict.glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'asreml'
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AEHMLE.Rd:42-45: Lost braces
    42 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
checkRd: (-1) AHMLE.Rd:41-43: Lost braces
    41 | \item{basehaz}{: {baseline hazard structure including baseline
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addNoiseAtEventTimes.Rd: data.table
  makeContWeights.Rd: data.table
  weightPredict.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AICcmodavg-package.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AICc_permanova2.Rd: adonis2
  fit_models.Rd: vegdist, adonis2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CalOptimalDecision.Rd:45: Lost braces; missing escapes or markup?
    45 | A \code{data.frame} of (1) the probability that the optimal decision for each observation being d in {0,1,...,k}, (2) expected utility of binary version of judge's decision (g_d), (3) expected utility of binary DMF recommendation, and (4) the difference between (2) and (3). If \code{include.utility.diff.mcmc = TRUE}, returns a list of such \code{data.frame} and a \code{data.frame} that includes the result for mean and quantile of \code{Utility.diff.control.mcmc} and \code{Utility.diff.treated.mcmc} across mcmc samples.
       |                                                                                                      ^
checkRd: (-1) aimPlot.Rd:39: Lost braces; missing escapes or markup?
    39 |  \item \code{Variable} {1st column: The various aims to be completed}
       |                        ^
checkRd: (-1) aimPlot.Rd:40: Lost braces; missing escapes or markup?
    40 |  \item \code{Percentage} {2nd column: The percentage of completeness}
       |                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AIPW.Rd: SuperLearner
  AIPW_base.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CreateInputsPert.Rd:65: Lost braces
    65 | \emph{InputsPert}{[list] object of class \emph{InputsModel} containing the ensembles of perturbed model inputs required to perform data assimilation:}
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  airGRdatassim.Rd: CreateCalibOptions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    ShinyGR   4.3Mb
    doc       3.4Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_airnow_area.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{parameters}{Parameter(s) to return data for. Choices are PM_{2.5}
       |                                                                   ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  keyword_merge.Rd: stem_strings, lemmatize_strings
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.dke.fun.Rd:33: Lost braces; missing escapes or markup?
    33 |   \item{las}{ Numeric in {0,1,2,3}; the style of axis labels. 
       |                          ^
checkRd: (-1) interpp.Rd:119: Lost braces
   119 |   If \code{linear} is \\code{TRUE}, linear
       |                             ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) buildPhylipLineage.Rd:61: Lost braces; missing escapes or markup?
    61 |                                      names with the format {"Inferred1", "Inferred2", ...}.
       |                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gridPlot.Rd: ggplot
  plotAbundanceCurve.Rd: ggplot
  plotDiversityCurve.Rd: ggplot
  plotDiversityTest.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   3.2Mb
checkRd: (-1) ALF.Rd:47: Escaped LaTeX specials: \&
checkRd: (-1) APEXMS.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) APEXMS.Rd:15: Lost braces in \enumerate; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) optimalfrequency.Rd:29: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:30: Escaped LaTeX specials: \$
checkRd: (-1) optimalfrequency.Rd:31: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  amCluster.Rd: dynamicTreeCut, cutreeHybrid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ASBT.Rd:36-37: Lost braces
    36 | \item{method}{Method for aggregating across categories: {"none", "max",
       |                                                         ^
checkRd: (-1) Aggregator.Rd:26: Lost braces; missing escapes or markup?
    26 | {"none", "max", "sum"}. Default: "none".}
       | ^
checkRd: (-1) DGP.Rd:72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DGP.Rd:75: Lost braces in \itemize; meant \describe ?
checkRd: (-1) OLS.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) OLS.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) allestimates.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) allestimates.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compare_cohorts.Rd:36: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cleanse.data.frame.Rd: tbl_df
  split_by.data.frame.Rd: tbl_df
  treatment_corr.Rd: tbl_df
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alphaci.Rd: future.apply
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.ashape3d.Rd: rgl, material3d
  surfaceNormals.Rd: material3d
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) UN1.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) rateprof.Rd:64: Escaped LaTeX specials: \&
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
checkRd: (-1) altopt.ic.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.ic.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) altopt.rc.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'metaboliteIDmapping'
checkRd: (-1) convertCoord.Rd:32: Lost braces
    32 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) convertCoord.individual.Rd:33: Lost braces
    33 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.Rd:39: Lost braces
    39 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
checkRd: (-1) getCoord.individual.Rd:39: Lost braces
    39 | here{https://lbs.amap.com/faq/account/key/72}}
       |     ^
checkRd: (-1) getLocation.Rd:60: Lost braces; missing escapes or markup?
    60 | {https://lbs.amap.com/faq/account/key/72}}
       | ^
checkRd: (-1) getLocation.individual.Rd:60: Lost braces
    60 | Please check here{https://lbs.amap.com/faq/account/key/72}}
       |                  ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write.amelia.Rd: write.dta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  play.Rd: tuneR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ammiBayes.conf.plot.Rd: lattice
  ammiBayes.mean.plot.Rd: lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) aMNLFA.prune.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) aMNLFA.prune.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) AmpliconDuo-package.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:40-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:43-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:47-49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:50-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:53-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AmpliconDuo-package.Rd:56-58: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  amExample1.Rd: allelematch
  amExample2.Rd: allelematch
  amExample3.Rd: allelematch
  amExample4.Rd: allelematch
  amExample5.Rd: allelematch
  amregtest.Rd: allelematch
  artData.Rd: amDataset, allelematch
  artRun.Rd: allelematch
  artVersion.Rd: allelematch-package
  ggSample.Rd: allelematch
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) AncestryMapper2.0-package.Rd:33: Escaped LaTeX specials: \~
checkRd: (-1) AncestryMapper2.0-package.Rd:38: Escaped LaTeX specials: \~
checkRd: (-1) EKF_1d_interp_joint.Rd:55: Lost braces; missing escapes or markup?
    55 | Prior 1x1 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
checkRd: (-1) EKF_interp_joint.Rd:65: Lost braces; missing escapes or markup?
    65 | Prior 2x2 covariance matrix for predicting x_t from x_{t-1}.
       |                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_segments.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) animate.Rd:625-627: Lost braces
   625 | group = function(...) {
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggplot_gtable.Rd: gtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
stat_unique.html:110:1 (stat_unique.Rd:65): Warning: trimming empty <li>
stat_unique.html:109:1 (stat_unique.Rd:65): Warning: trimming empty <ul>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anim.save.Rd: saveGIF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) concat.Rd:35: Lost braces; missing escapes or markup?
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                     ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                               ^
checkRd: (-1) concat.Rd:35: Lost braces
    35 | \item{index_unique}{Whether to make the index unique by using the keys. If provided, this is the delimeter between "{orig_idx}{index_unique}{key}". When \code{NULL}, the original indices are kept.}
       |                                                                                                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  annotate.Rd: htmlwidgets
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PV_post_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_post_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:7: Escaped LaTeX specials: \_ \_
checkRd: (-1) PV_pre_triang_3.Rd:22: Escaped LaTeX specials: \_ \_
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    R  34.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HartiganShapes.Rd: procGPA
  LloydShapes.Rd: procGPA
  archetypesBoundary.Rd: stepArchetypes, archetypes
  archetypoids.Rd: archetypes, stepArchetypes
  shapes3dShapes.Rd: shapes3d
  stepArchetypesRawData.Rd: stepArchetypes, archetypes
  stepArchetypoids.Rd: stepArchetypes, archetypes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) PS-methods.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) PS-methods.Rd:65-67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Sim-Functions.Rd:126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:127-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:138-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Sim-Functions.Rd:141-143: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apcluster-methods.Rd: dgTMatrix-class, Matrix-class
  conversions.Rd: dgTMatrix-class, sparseMatrix-class, Matrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) apc.indiv.est.model.Rd:142: Lost braces
   142 | For model testing: \code{\link{apc.indiv.model.table}}, code{\link{apc.indiv.compare.direct}}, \code{\link{waldtest}}, \code{\link{linearHypothesis}}
       |                                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apc.indiv.compare.direct.Rd: plm
  apc.indiv.est.model.Rd: plm, svyglm, waldtest, linearHypothesis
  apc.indiv.model.table.Rd: plm, waldtest, linearHypothesis
  apc.plot.data.level.Rd: levelplot, lattice
  apc.plot.fit.residuals.Rd: levelplot, lattice
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  multidna2alignment.Rd: as.alignment
  multidna2genind.Rd: genind-class, DNAbin2genind
  multidna2multiphyDat.Rd: DNAbin2genind
  plot-multidna-method.Rd: image.DNAbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) aphylo-class.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) raphylo.Rd:33: Lost braces; missing escapes or markup?
    33 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
checkRd: (-1) sim_fun_on_tree.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{tip.type, node.type}{Integer vectors with values {0,1}. 0 denotes duplication node and 1 speciation node. This is used in \link{LogLike}.}
       |                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aphylo-class.Rd: Ntip, Nnode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
mislabel.html:25:1 (mislabel.Rd:20): Warning: trimming empty <p>
raphylo.html:25:1 (raphylo.Rd:57): Warning: trimming empty <p>
sim_fun_on_tree.html:25:1 (sim_fun_on_tree.Rd:50): Warning: trimming empty <p>
checkRd: (-1) predict_adjust.Rd:77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:78: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) predict_adjust.Rd:80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) print.predict_adjust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) iconplot.Rd:172: Lost braces
   172 |     the height of the area containing the panels and a margin of size code{100 * 0.1} 
       |                                                                           ^
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    documents     2.4Mb
    libs          1.1Mb
    screenshots   1.6Mb
'LazyData' is specified without a 'data' directory
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AQEval.data.Rd: openair, importAURN, importKCL
  find.breaks.Rd: breakpoints
  isolate.signal.Rd: mgcv, gam
  quantify.breaks.Rd: timeAverage, breakpoints, segmented
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.6Mb
    doc    1.8Mb
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                              ^
checkRd: (-1) getages.Rd:11: Lost braces; missing escapes or markup?
    11 | containing the amalgamated $^{40}$Ar$^*$/$^{39}$Ar$_K$-ratios and
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.InfDiag.Rd: ggplot
  plot.Rd: ggplot
  plot.residARpCRM.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'arcgisplaces/libs/x64/arcgisplaces.dll':
  Found non-API calls to R: 'PRCODE', 'PRENV'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Package suggested but not available for checking: 'arcgisbinding'
Package suggested but not available for checking: 'ArchaeoData'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ActivityEvents-class.Rd: TimeSeries-class
  ArchaeoPhases-package.Rd: TimeScale-class
  CumulativeEvents-class.Rd: TimeSeries-class
  activity.Rd: TimeScale-class
  as_events.Rd: TimeScale-class
  as_phases.Rd: TimeScale-class
  bury.Rd: TimeScale-class
  data.frame.Rd: TimeScale-class
  interval_credible.Rd: TimeScale-class
  interval_hdr.Rd: TimeScale-class
  occurrence.Rd: TimeScale-class
  plot_events.Rd: TimeScale-class
  plot_phases.Rd: TimeScale-class
  read_bcal.Rd: TimeScale-class
  read_chronomodel.Rd: TimeScale-class
  read_oxcal.Rd: TimeScale-class
  summary.Rd: TimeScale-class
  tempo.Rd: TimeScale-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.archetypes.Rd: parameters
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  addHooksToPrintGitHub.Rd: Repository, archivist-package, alink,
    addHooksToPrint
  archive.Rd: Repository, saveToLocalRepo, md5hash, alink, aoptions
  archivist-github-integration.Rd: Repository
  createGitHubRepo.Rd: createLocalRepo, Repository, oauth2.0_token,
    Tags
  deleteGitHubRepo.Rd: Repository, oauth2.0_token
  pushGitHubRepo.Rd: Repository
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) estimate_t0.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) estimate_t0.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:73: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fitArCo.Rd:75: Lost braces in \itemize; meant \describe ?
'library' or 'require' call not declared from: 'arcgislayers'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  prune.Rd: rules
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       | ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                 ^
checkRd: (-1) recm.Rd:55: Lost braces; missing escapes or markup?
    55 | {In all cases,} \eqn{x_{j,t-1}} {in} \eqn{ECT} {is replaced by} \eqn{x_{j,t} \;\;\;\;\; \forall \;\; q_{j} = 0}
       |                                                ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |   ^
checkRd: (-1) uecm.Rd:76: Lost braces; missing escapes or markup?
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                  ^
checkRd: (-1) uecm.Rd:76-77: Lost braces
    76 |   {In addition,} \eqn{x_{j,t-1}} {and} \eqn{\Delta x_{j,t}} {cancel out
       |                                                             ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  normGeometry.Rd: st_drivers
  normTable.Rd: reorganise
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arfima.Rd: TrenchMean
  logLik.arfima.Rd: ltsa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  argonDropNavItem.Rd: argonIcon
  argonInfoCard.Rd: argonIcon
  argonSidebarItem.Rd: argonIcon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SmoothMultiarrayModel.Rd: ChromosomalModel,
    CopyNumberSegmentationModel
  byPath.AffymetrixFileSet.Rd: GenericDataFile
  calculateBaseline.ChipEffectSet.Rd: getAverageFile
  doCRMAv1.Rd: Verbose
  doCRMAv2.Rd: Verbose
  doFIRMA.Rd: Verbose
  doGCRMA.Rd: Verbose
  doRMA.Rd: Verbose
  justRMA.Rd: Verbose
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  writeDataFrame.AromaUnitSignalBinaryFile.Rd: TabularTextFile
  writeDataFrame.AromaUnitSignalBinarySet.Rd: TabularTextFileSet
  writeDataFrame.AromaUnitTabularBinaryFile.Rd: TabularTextFile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    R      4.3Mb
    libs  38.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  artfima-package.Rd: ltsa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.art.Rd: Anova
  art.Rd: lmer
  art.con.Rd: contrast, summary.emmGrid, lmer, emmeans
  artlm.Rd: lmer, merMod
  artlm.con.Rd: lmer, merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    bin   11.3Mb
    misc   2.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bvn.plot.rd: wireframe
  plot.pairw.rd: multcompLetters
  pseudo.v.Rd: empinf, boot
  qq.Plot.Rd: boot, envelope
  r.pb.rd: corr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) breast_cancer_clean_features.Rd:45: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  meldCD.Rd: binomMeld.test
  signTest.Rd: mcnemarExactDP, binom.exact
  wmwTest.Rd: wilcox_test
  wsrTest.Rd: wilcoxsign_test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
checkRd: (-1) convertAlgoPerfToWideFormat.Rd:28: Lost braces
    28 | code{NA} means the performance value is not available, possibly because the algorithm run was aborted.
       |     ^
checkRd: (-1) parseASScenario.Rd:40: Lost braces
    40 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:47: Lost braces
    47 |   code{NA} means the cost is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:55: Lost braces
    55 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
checkRd: (-1) parseASScenario.Rd:62: Lost braces
    62 |   code{NA} means the feature is not available, possibly because the feature computation was aborted.
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createCVSplits.Rd: write.arff
  summarizeLlamaExps.Rd: Registry, reduceResultsList
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alignCross.Rd: subset.cross
  heatMap.Rd: plotRF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'asreml'
'LazyData' is specified without a 'data' directory
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                    ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                 ^
checkRd: (-1) assert.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{msg}{A character string containing the error message to display if any of the conditions are not met. The string can include the placeholder {failed_expressions} to insert a list of the failed expressions. The string can also include {?s} and {?is/are} to insert the correct pluralization for the list of failed expressions.}
       |                                                                                                                                                                                                                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.AssetPricing.Rd:199-200: Lost braces
   199 |   yakka. (Note that \code{flap} stands for dQuote{function list
       |                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nmax3.Rd: pmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'asteRiskData'
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.0Mb
checkRd: (-1) readOEM.Rd:34: Lost braces
    34 |   always, the identifier has the format YYYY-NNNP{PP}, where YYYY is the year
       |                                                  ^
checkRd: (-1) readOEM.Rd:36: Lost braces
    36 |   during year YYYY and P{PP} is a part specifier comprising 1 to 3 capital letters
       |                         ^
checkRd: (-1) readOEM.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:76-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) readOEM.Rd:80-86: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hpop.Rd: ode
  readGLONASSNavigationRINEX.Rd: nanotime
  readGPSNavigationRINEX.Rd: nanotime
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pickle.Rd: trust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AsyK-package.Rd: mse
  Laplace.Rd: mse
  RIG.Rd: mse
  plot.Laplace.Rd: mse
  plot.RIG.Rd: mse
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ATA.BoxCoxAttr.Rd: BoxCox, InvBoxCox, BoxCox.lambda
  ATA.Decomposition.Rd: stlplus
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                       ^
checkRd: (-1) ataCoKriging.Rd:52: Lost braces; missing escapes or markup?
    52 | only one contrained condition for all points and all variables, \\sum_{i=1}^n\\lambda_i +\\sum_{j=1}^m\\beta_j =1, assuming expected means of variables known and constant with the study area.
       |                                                                                                ^
checkRd: (-1) simulation_dgp.Rd:14: Lost braces; missing escapes or markup?
    14 | \item{x_discrete}{TRUE if the distribution of the covariate is uniform on {-3.0, -2.9, ..., 3.0} and
       |                                                                           ^
checkRd: (-1) simulation_dgp.Rd:23: Lost braces
    23 | \item{att_oracle}{the sample analog of E[D{Y(1) - Y(0)}|D=1]}
       |                                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) audioSample.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) audioSample.Rd:21: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  auk_country.Rd: countrycode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_candidate_covariates.Rd:50: Lost braces
    50 | \item \code{covars_data}   {The \code{data.frame} that is filtered out of \code{df} with only the selected \code{covars}}. The values of the
       |                            ^
checkRd: (-1) get_candidate_covariates.Rd:53: Lost braces
    53 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
checkRd: (-1) get_prioritised_covariates.Rd:40: Lost braces
    40 | \item \code{multiplicative_bias}{The absolute log of the multiplicative bias term for each of the auto-selected prioritised covariates}
       |                                 ^
checkRd: (-1) get_recurrence_covariates.Rd:34: Lost braces
    34 | \item \code{patientIds}   {The list of patient ids present in the original input \code{df}. This is exactly the same as the input \code{patientIdVector}}
       |                           ^
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rmd_to_forestharp.Rd: get_source_expressions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Autoplotprotein-package.Rd:27: Lost braces
    27 | code{\link{help}}
       |     ^
checkRd: (-1) Autoplotprotein.Rd:25: Lost braces
    25 | code{\link{help}}
       |     ^
checkRd: (-1) data.Rd:22: Lost braces
    22 | code{\link{help}}
       |     ^
checkRd: (-1) domain_data.Rd:29: Lost braces
    29 | code{\link{help}}
       |     ^
checkRd: (-1) length_data.Rd:32: Lost braces
    32 | code{\link{help}}
       |     ^
checkRd: (-1) plotdomain.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotmutagensis.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) plotsite.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
checkRd: (-1) site_data.Rd:30: Lost braces
    30 | code{\link{help}}
       |     ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) noauto_scorecard.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{fit}{See glm {stats}.}
       |                    ^
checkRd: (-1) noauto_scorecard2.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{fit}{See glm {stats}.}
       |                    ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) avar_mo_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_mo_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) avar_to_cpp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:66: Escaped LaTeX specials: \$
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \#
checkRd: (-1) ec2_create_security_group.Rd:79: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_cognitive_service.Rd: az_resource_group
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aci.Rd: az_resource_group
  acr.Rd: az_resource_group
  aks.Rd: az_resource_group
  create_aci.Rd: az_resource
  create_acr.Rd: az_resource
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) cosmos_mongo.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{host}{For \code{cosmos_mongo_endpoint}, the URL of the Cosmos DB MongoDB endpoint. Usually of the form "https://{account-name}.mongo.cosmos.azure.com:443/".}
       |                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  call_batch_endpoint.Rd: AzureToken
  call_graph.Rd: AzureToken
  graph_login.Rd: get_azure_token
  ms_graph.Rd: get_azure_token
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_key_vault.Rd: az_resource_group
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AzureKusto.Rd: dbReadTable, dbWriteTable, dbGetQuery, dbSendStatement
  DBI_query.Rd: dbConnect, dbReadTable, dbWriteTable
  DBI_table.Rd: dbConnect
  az_kusto.Rd: az_resource_group
  copy_to.kusto_database_endpoint.Rd: collect
  kusto-DBI.Rd: dbConnect, dbDisconnect, dbCanConnect, dbExistsTable,
    dbCreateTable, dbRemoveTable, dbReadTable, dbWriteTable,
    dbGetQuery, dbSendQuery, dbFetch, dbSendStatement, dbExecute,
    dbListFields, dbColumnInfo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  queue.Rd: storage_endpoint
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_resource_group.Rd: AzureToken
  az_rm.Rd: AzureToken
  az_subscription.Rd: AzureToken
  azure_login.Rd: AzureToken
  call_azure.Rd: AzureToken
  utils.Rd: AzureToken
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  az_storage.Rd: az_resource_group
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'lixoftConnectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  backbone.suggest.Rd: Matrix, igraph
  disparity.Rd: Matrix, igraph
  fdsm.Rd: Matrix, igraph
  fixedcol.Rd: Matrix, igraph
  fixedfill.Rd: Matrix, igraph
  fixedrow.Rd: Matrix, igraph
  global.Rd: Matrix, igraph
  lans.Rd: Matrix, igraph
  mlf.Rd: Matrix, igraph
  osdsm.Rd: Matrix, igraph
  sdsm.Rd: Matrix, igraph
  sparsify.Rd: Matrix, igraph
  sparsify.with.geometric.Rd: Matrix, igraph
  sparsify.with.gspar.Rd: Matrix, igraph
  sparsify.with.hypergeometric.Rd: Matrix, igraph
  sparsify.with.jaccard.Rd: Matrix, igraph
  sparsify.with.localdegree.Rd: Matrix, igraph
  sparsify.with.lspar.Rd: Matrix, igraph
  sparsify.with.meetmin.Rd: Matrix, igraph
  sparsify.with.quadrilateral.Rd: Matrix, igraph
  sparsify.with.simmelian.Rd: Matrix, igraph
  sparsify.with.skeleton.Rd: Matrix, igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BACprior.lm.Rd: regsubsets
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  baf.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  forest_plot.Rd: forestplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   3.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_lgmr.Rd: stan_model
  infer_data_and_decision_model.Rd: sampling, tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) contour.angmcmc.Rd:48: Lost braces; missing escapes or markup?
    48 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) contour.angmcmc.Rd:51: Lost braces; missing escapes or markup?
    51 | Ignored if {show.data == FALSE}.}
       |            ^
checkRd: (-1) fit_incremental_angmix.Rd:104: Lost braces; missing escapes or markup?
   104 | \item{alpha}{significance level used in the test H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |                                                    ^
checkRd: (-1) fit_incremental_angmix.Rd:148: Lost braces; missing escapes or markup?
   148 | H_{0K}: expected log predictive density (elpd) for the fitted model with  K components >= elpd for the fitted model
       |   ^
checkRd: (-1) fit_incremental_angmix.Rd:163: Lost braces; missing escapes or markup?
   163 | The incremental fitting stops if  H_{0K} cannot be rejected
       |                                     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bridge_sampler.angmcmc.Rd: bridge_sampler
  circ_varcor_model.Rd: sobol
  densityplot.angmcmc.Rd: as.mcmc.list
  fit_angmix.Rd: future_lapply
  fit_incremental_angmix.Rd: bridge_sampler
  fix_label.Rd: label.switching
  loo.angmcmc.Rd: waic, loo
  rvmcos.Rd: sobol
  rwnorm2.Rd: rmvnorm
  rwnorm2mix.Rd: rmvnorm
  waic.angmcmc.Rd: waic
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
rwnorm2.html:111:126 (rwnorm2.Rd:60): Warning: trimming empty <code>
rwnorm2.html:115:73 (rwnorm2.Rd:61): Warning: trimming empty <code>
rwnorm2.html:115:146 (rwnorm2.Rd:61): Warning: trimming empty <code>
rwnorm2.html:115:211 (rwnorm2.Rd:61): Warning: trimming empty <code>
rwnorm2.html:119:126 (rwnorm2.Rd:62): Warning: trimming empty <code>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bamlss-package.Rd: mgcv
  bamlss.Rd: mgcv
  bamlss.frame.Rd: mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'bamlss/libs/x64/bamlss.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Package suggested but not available for checking: 'fdpbandsdata'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BANOVA.run.Rd: rstan
  pairs.BANOVA.Rd: rstan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getBanterModel.Rd: randomForest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) barcode.Rd:52: Escaped LaTeX specials: \&
checkRd: (-1) barcoding.spe.identify2.Rd:27: Lost braces; missing escapes or markup?
    27 | read.dna() from package {ape} was used to obtain DNAbin object for unaligned non-coding barcodes.
       |                         ^
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    java   9.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    help   2.2Mb
File 'base64enc/libs/x64/base64enc.dll':
  Found non-API call to R: 'SETLENGTH'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) bd_collect.Rd:30: Lost braces; missing escapes or markup?
    30 | the {dplyr}'s verbs and thus use it in local memory completely.
       |     ^
checkRd: (-1) bd_write.Rd:52: Lost braces; missing escapes or markup?
    52 | Writes a remote table to disk that was called via {bdplyr}.
       |                                                   ^
checkRd: (-1) bdplyr.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Compatibility with {dplyr} verbs without using SQL language}
       |                           ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Earlier versions
checkRd: (-1) BasicTable.Rd:659: Lost braces; missing escapes or markup?
   659 | `function(v, cell) { if(isTRUE(v>0.8)) return("green") }`.\cr
       |                    ^
checkRd: (-1) TableStyle.Rd:151: Lost braces; missing escapes or markup?
   151 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
checkRd: (-1) TableStyle.Rd:172: Lost braces; missing escapes or markup?
   172 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
checkRd: (-1) TableStyles.Rd:209: Lost braces; missing escapes or markup?
   209 | The CSS style rule, e.g. { text-align: center; color: red; }
       |                          ^
checkRd: (-1) TableStyles.Rd:232: Lost braces; missing escapes or markup?
   232 | The CSS style rule, e.g. cell { text-align: center; color: red; }
       |                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BasicTable.Rd: R6Class
  FlexTableRenderer.Rd: R6Class
  FlexTableStyle.Rd: R6Class
  FlexTableStyles.Rd: R6Class
  TableCell.Rd: R6Class
  TableCellRanges.Rd: R6Class
  TableCells.Rd: R6Class
  TableHtmlRenderer.Rd: R6Class
  TableOpenXlsxRenderer.Rd: R6Class
  TableOpenXlsxStyle.Rd: R6Class
  TableOpenXlsxStyles.Rd: R6Class
  TableStyle.Rd: R6Class
  TableStyles.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) nfiMetrics.Rd:23: Lost braces
    23 | code{(4)} the number of
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  readNFI.Rd: read.dbf, RODBC, mdb.get
  urlToTemp.Rd: timeout
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bubbleplot.Rd: scale_colour_gradient2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'BAS/libs/x64/BAS.dll':
  Found non-API call to R: 'SETLENGTH'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ExperimentJob.Rd:14: Lost braces
    14 |   \item{\code{algo.id} [\code{character(1)}]:}{algo.id}{Algorithm ID.}
       |                                                        ^
checkRd: (-1) getAlgorithmIds.Rd:13: Lost braces
    13 | \item{ids}{[code{integer}]\cr
       |                 ^
checkRd: (-1) getProblemIds.Rd:13: Lost braces
    13 | \item{ids}{[code{integer}]\cr
       |                 ^
checkRd: (-1) makeExperimentRegistry.Rd:28: Lost braces
    28 | Default is dQuote{<name of registry>_files} in current working directory.}
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getExperimentParts.Rd: Job
  reduceResultsExperimentsParallel.Rd: batchMapQuick
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) JobCollection.Rd:41: Lost braces
    41 |  \item{namespaces}{code{character} with required packages to load via \code{\link[base]{requireNamespace}}.}
       |                        ^
checkRd: (-1) addAlgorithm.Rd:31: Lost braces
    31 | Algorithms are functions which get the code{data} part as well as the problem instance (the return value of the
       |                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  JoinTables.Rd: data.table
  Worker.Rd: R6Class
  addExperiments.Rd: data.table
  batchMap.Rd: data.table
  batchMapResults.Rd: data.table
  batchReduce.Rd: data.table
  estimateRuntimes.Rd: data.table
  findJobs.Rd: data.table
  getErrorMessages.Rd: data.table
  getJobTable.Rd: data.table
  grepLogs.Rd: data.table
  killJobs.Rd: data.table
  removeExperiments.Rd: data.table
  resetJobs.Rd: data.table
  runHook.Rd: data.table
  submitJobs.Rd: data.table
  summarizeExperiments.Rd: data.table
  unwrap.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) plotDistributions.Rd:32: Lost braces
    32 | plot{...} functions are generated programmatically so the function calls in
       |     ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pwr_curve.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) coupledMetropolis.Rd:83-85: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:86-88: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:89-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:92-94: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:95-97: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:98-100: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:101-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:104-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:110-112: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:113-115: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:116-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:119-121: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:122-124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) coupledMetropolis.Rd:125-127: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotPost.Rd: hdi
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BayesComm-package.Rd:33: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.bayescomm.Rd: plot.mcmc
  summary.bayescomm.Rd: summary.mcmc
  window.bayescomm.Rd: window.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  binomialBACT.Rd: bdpnormal
  binomial_analysis.Rd: bdpnormal
  historical_binomial.Rd: bdpnormal
  historical_normal.Rd: bdpnormal
  historical_survival.Rd: bdpnormal
  normalBACT.Rd: bdpnormal
  normal_analysis.Rd: bdpnormal
  survivalBACT.Rd: bdpnormal
  survival_analysis.Rd: bdpnormal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dilution.Rd:13: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) dilution.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:15: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:16: Escaped LaTeX specials: \$
checkRd: (-1) personality.Rd:17: Escaped LaTeX specials: \$
checkRd: (-1) bayesDccGarch.Rd:91: Lost braces; missing escapes or markup?
    91 | \item{$H_n1 }{ Bayesian prediction of volatilities and co-volatilities for y_{n+1}.}
       |                                                                              ^
checkRd: (-1) bayesDccGarch.Rd:92: Lost braces; missing escapes or markup?
    92 | \item{$R_n1 }{ Bayesian prediction of coditional correlation for y_{n+1}.}
       |                                                                    ^
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   5.5Mb
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) GroupSingleVoxelFETS.Rd:53: Lost braces
    53 | online trajectories related to the state parameter, the simulated BOLD responses, \mjseqn{\hat{Y}}{ascii}.
       |                                                                                                   ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
    libs      1.2Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    doc   10.8Mb
    libs   1.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  id_activations.posterior.Rd: excursions.inla
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Holt.Rd: auto.arima
  Hw.Rd: auto.arima
  LocalLevel.Rd: auto.arima
  autoplot.ts.Rd: geom_forecast, fortify
  forecast.varstan.Rd: forecast.ts, ets, stlf
  fourier.Rd: seasonaldummy
  garch.Rd: auto.arima
  loo.varstan.Rd: psis, pareto-k-diagnostic, loo_compare
  ssm.Rd: auto.arima
  stan_Holt.Rd: auto.arima
  stan_Hw.Rd: auto.arima
  stan_LocalLevel.Rd: auto.arima
  stan_garch.Rd: auto.arima
  stan_ssm.Rd: auto.arima
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loo_bgam.Rd: pareto-k-diagnostic, psis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following HTML validation problems:
getSamples.html:74:1 (getSamples.Rd:35): Warning: trimming empty <h3>
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) gMLE.bb.Rd:18: Lost braces
    18 |   \item{optim.method}{optimization method in \code{optim()}{stats}.}
       |                                                            ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) bma.bx.cy.Rd:69: Lost braces
    69 | the initial values for parameters in models. For example, inits<-function(){list(alpha=0,beta=0,c=0,var1=0.5,r=1,lamda=0.01)}.
       |                                                                            ^
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    help   1.8Mb
    libs   3.4Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DE.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DE.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) DEzs.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) convert.trajectories.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write.projection.summary.Rd:34: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.bayeslm.fit.Rd:18: Lost braces; missing escapes or markup?
    18 |   \item{X         }{ If call \code{bayeslm} with matrices input \code{x} and {y} but not formula, pass new matrix to predict here. See example for details.}
       |                                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hs_gibbs.Rd: summary.mcmc
  summary.bayeslm.fit.Rd: summary.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LN_hierarchical.Rd: lmer, mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  convolve.Rd: funnel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot-traj.Rd:71: Lost braces; missing escapes or markup?
    71 | the plots are saved into directory {sim.dir}/predictions/migTrajectories.}
       |                                    ^
checkRd: (-1) insert_NAs.Rd:22: Lost braces; missing escapes or markup?
    22 | A data frame where new rows have been inserted to regularize the \code{date} column. This results in values provided for \code{id}, \code{date}, and {dt} while inserting NAs for all other columns. Additionally, observations with duplicate date-times are removed.
       |                                                                                                                                                      ^
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    doc    1.0Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   3.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MCMC-combos.Rd: posterior
  MCMC-diagnostics.Rd: posterior
  MCMC-distributions.Rd: posterior
  MCMC-intervals.Rd: posterior
  MCMC-overview.Rd: posterior
  MCMC-parcoord.Rd: posterior
  MCMC-recover.Rd: posterior
  MCMC-scatterplots.Rd: posterior, ggtitle
  MCMC-traces.Rd: posterior
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  age.specific.migration.Rd: wpp2019
  pop.aggregate.Rd: bayesLife, bayesTFR
  pop.predict.subnat.Rd: bayesTFR, convert.tfr.trajectories
  predict.pop.Rd: bayesLife, convert.e0.trajectories, bayesTFR,
    convert.tfr.trajectories
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) pulse_of_the_nation.Rd:10: Escaped LaTeX specials: \$
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
GNU make is a SystemRequirements.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
checkRd: (-1) BayesTreePrior.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) BayesTreePrior.Rd:41: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stan.Rd: stan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AgeC14_Computation.Rd: rjags
  AgeS_Computation.Rd: rjags, runjags
  Age_Computation.Rd: jags.model, rjags
  Age_OSLC14.Rd: rjags, runjags
  Generate_DataFile-deprecated.Rd: read_BIN2R, Luminescence
  Generate_DataFile_MG-deprecated.Rd: read_BIN2R
  Model_Age.Rd: rjags
  Model_AgeC14.Rd: rjags
  Model_AgeS.Rd: rjags
  Model_Palaeodose.Rd: rjags
  Palaeodose_Computation.Rd: jags.model, rjags
  create_DataFile.Rd: RLum.Analysis-class
  plot_MCMC.Rd: rjags
  plot_Scatterplots.Rd: rjags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) runUI.Rd:11: Lost braces
    11 | Runs a \bold{Shiny} application. This function normally does not return; interrupt bold{R} to stop the application (usually by pressing Ctrl+C or Esc).
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) getOperatingSystem.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getOperatingSystem.Rd:30: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  c3mtc.Rd: c3
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.4Mb
checkRd: (-1) goftype1.Rd:4: Lost braces
     4 | \description{The goodness-of-fit (GOF) measures consist of Anderson-Darling (\code{AD}) and Cram\'{e}er-von Misses (\code{CVM}) statistics for progressive type-I interval censoring scheme are given, respectively, by
       |                                                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcfraildv.Rd: bcfrailph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  shrgamsp.Rd: coxph
  simstdybcf.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BchronDensity.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronDensity.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BchronRSL.Rd:34-41: Lost braces
    34 | itemize{
       |        ^
checkRd: (-1) Glendalough.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) Sluggan.Rd:19: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BchronDensityFast.Rd: densityMclust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcmarg.Rd: gls
  summary.bcmmrm.Rd: glsObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) WindowSweep.Rd:32: Lost braces
    32 | `code{\link{GetVT}}`.   Otherwise, any column (e.g. \code{"Depth"}) in the 
       |      ^
checkRd: (-1) WindowSweep.Rd:36: Lost braces
    36 | \code{T.mid}  from the output of the `code{\link{GetVT}}`.}
       |                                           ^
Package suggested but not available for checking: 'BRugs'
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) gene_s.Rd:17: Lost braces; missing escapes or markup?
    17 | giving the virus access to the cell and thus facilitating the COVID-19 disease. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                                                             ^
checkRd: (-1) sars_cov_2.Rd:16: Lost braces; missing escapes or markup?
    16 | It consists of n = 29903 base pairs. The gene sequence is mapped to the alphabet {0,1,2,3} via the obvious map A->0, C->1, G->2, T->3.
       |                                                                                  ^
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.6Mb
    extdata   1.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) bde.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) bde.Rd:56: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gettaxo.Rd: taxize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  default_params_doc.Rd: check_rename_fun
  remove_beastier_folder.Rd: beautier, remove_beautier_folder
  rename_beast2_options_filenames.Rd: check_rename_fun
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bedr.plot.region.Rd: venn.diagram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CIBER.Rd: ggplot2, biAxisDiamondPlot, diamondPlot, gtable
  determinantStructure.Rd: data.tree
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  behavr.Rd: data.table
  bin_apply.Rd: data.table
  meta.Rd: data.table
  rejoin.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sfa.Rd: ucminf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  press.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_model_data.Rd: tibble
  kit_summary_table.Rd: stanfit
  plot_kit_use.Rd: stanfit, ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) sockeye.Rd:13-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sockeye.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) stagnant.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hill.Rd:39: Lost braces; missing escapes or markup?
    39 | \code{a} in {0, 1, 2} (see details))}
       |             ^
checkRd: (-1) read_ambi.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_ambi.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_iti.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_taxa.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_twn.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) read_twn.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  l2array.Rd: abind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) gen.data.Rd:42: Lost braces
    42 | code{cortype = 2} denotes the constant structure, where the \eqn{(i,j)} entry of covariance
       |     ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  functional.betapart.core.Rd: convhulln
  functional.betapart.core.pairwise.Rd: convhulln
  inter_geom.Rd: intersectn
  qhull.opt.Rd: convhulln
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  betategarch-package.Rd: zoo
  tegarchSim.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Malformed Title field: should not end in a period.
checkRd: (-1) BETSsearch.Rd:56: Lost braces
    56 |        \item{To exclude whole expressions from the search, surround them with code{' '} and insert a \code{~} before each of them.
       |                                                                                   ^
checkRd: (-1) dummy.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{date}{a \code{list}. The periods for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                               ^
checkRd: (-1) dummy.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{from}{An \code{integer vector} The starting period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                                                         ^
checkRd: (-1) dummy.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{to}{The ending period of a sequence of perids for which the dummy must be set to one. Periods must be represented as {integer vectors}, as described for \code{start} and \code{end}.}
       |                                                                                                                            ^
'LazyData' is specified without a 'data' directory
788a789
> 
809a811
> 
922a925
> 
943a947
>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CombinePolygons.Rd: st_union
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   1.5Mb
checkRd: (-1) bgmm-package.Rd:23: Escaped LaTeX specials: \&
checkRd: (-1) sp_bgsmtr.Rd:42: Lost braces; missing escapes or markup?
    42 | \item{c.star}{The threshold for computing posterior tail probabilities p_{ij} for Bayesian FDR as defined in Section 3.2 of  Song, Ge et al.(2019). If not specified the default is to set this threshold as the minimum posterior standard deviation, where the minimum is taken over all regression coefficients in the model.}
       |                                                                          ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.3Mb
GNU make is a SystemRequirements.
checkRd: (-1) dotPlot.Rd:56: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bhm-package.Rd: coxph, survival
  bhm.Rd: coxph
  brm.Rd: coxph
  mpl.Rd: coxph
  resboot.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 149.2Mb
  sub-directories of 1Mb or more:
    include  148.1Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) module_calibrationfile_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedplots_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_correctedstats_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_fileupload_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_info_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_log_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_modelselection_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_plotting_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_results_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_settings_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
checkRd: (-1) module_statistics_server.Rd:19: Lost braces; missing escapes or markup?
    19 | expression: input_re = reactive({input})}
       |                                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  detect_keys.Rd: read_rmd
  doi2bib.Rd: cr_cn
  reflist.Rd: write_rmd, render_rmd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Jeffreysbs.Rd:17: Escaped LaTeX specials: \&
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diagnosticTest.Rd: additivityTests
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) BiDimRegression.Rd:29: Lost braces; missing escapes or markup?
    29 | \item \code{euclidean.df1, affine.df1} -  degrees of freedom of the nominator used for the F-statistics propagated by Nakaya (1997); df1 = p-2, with p is the number of elements  needed to calculate the referring model: p=4 for the Euclidean and p=6 for the affine geometry {Nakaya, 1997, Table 1}.
       |                                                                                                                                                                                                                                                                                  ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'ffbase'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  setupX.Rd: cv.ncvreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) bdm.ptsne.Rd:47: Lost braces; missing escapes or markup?
    47 | By default the algorithm is structured in \eqn{\sqrt{n}} epochs of \eqn{\sqrt{z}} iterations each, where \var{n} is the dataset size and \var{z} is the thread-size (\eqn{z=n*layers/threads}). The running time of the algorithm is then determined by \eqn{epochs*iters*t_i+ epochs*t_e} where \var{t_{i}} is the running time of a single iteration and \var{t_{e}} is the inter-epoch running time.
       |                                                                                                                                                                                                                                                                                                                                                                   ^
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'rrelaxiv'
checkRd: (-1) pQF.Rd:30: Lost braces; missing escapes or markup?
    30 | When \code{M} is not square, a randomised estimator for the trace of \code{crossprod(M)^2} is used. This is the sample size. When \code{M} is of \code{"matrixfree"} and does not include the trace of {crossprod(M)} as a component, this sample size will also be used to compute that. See Hutchinson reference. }
       |                                                                                                                                                                                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DBI.Rd: DBIObject-class, DBIDriver-class, DBIConnection-class,
    DBIResult-class
  bigquery.Rd: DBIDriver-class, DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DBI.Rd: DBIResult-class, DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) VARXFit.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXFit.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) VARXLagCons.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
File 'Binarize/libs/x64/Binarize.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compute.sigma.star.Rd: nearPD, phi2tetra, is.positive.definite
  jointly.generate.binary.normal.Rd: nearPD, rmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) binom.confint.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:32-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) binom.confint.Rd:45: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) aa.index.Rd:14: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:15: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:16: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:17: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:18: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:19: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:20-23: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) aa.index.Rd:24: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:33-37: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:38-39: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) example.data.Rd:40-41: Lost braces in \enumerate; meant \describe ?
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read_audio.Rd: Wave
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
checkRd: (-1) ringApply.Rd:9: Lost braces; missing escapes or markup?
     9 |   \item{lv}{{numeric} position, or {character} name, of an
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.modelFrame.Rd: anova.lme
  frametoLme.Rd: lme, nlme, groupedData
  lmeForm.Rd: groupedData
  modelFrame.Rd: lme, nlme, groupedData
  muleMan.Rd: groupedData, mgram, ecodist
  shiftFrame.Rd: groupedData
  summary.modelFrame.Rd: summary.lme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bilat.Rd: intersect.owin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) calc_ed.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_pi.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) calc_si.Rd:14: Lost braces; missing escapes or markup?
    14 | of groups or less than \code{a}. Both \code{a} and {b} must have the the same 
       |                                                    ^
checkRd: (-1) cluster_reg_exp.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) cluster_reg_exp.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DynamicGrowth.Rd: geom_line
  FitDynamicGrowth.Rd: geom_line, geom_point
  FitDynamicGrowthMCMC.Rd: geom_line, geom_point
  FitIsoGrowth.Rd: modFit, geom_line, geom_point
  FitMultipleDynamicGrowth.Rd: geom_line
  FitMultipleGrowthMCMC.Rd: geom_line
  FitSecondaryGrowth.Rd: modFit
  GlobalGrowthFit.Rd: geom_line
  GrowthFit.Rd: geom_line, geom_point
  GrowthPrediction.Rd: geom_line
  GrowthUncertainty.Rd: geom_line, geom_ribbon
  IsothermalGrowth.Rd: geom_line
  StochasticGrowth.Rd: geom_line, geom_ribbon
  TimeDistribution.Rd: geom_histogram
  check_growth_guess.Rd: ggplot
  dBaranyi.Rd: ode
  fit_growth.Rd: modFit, modMCMC
  fit_isothermal_growth.Rd: modFit
  fit_multiple_growth.Rd: modFit
  fit_multiple_growth_MCMC.Rd: modMCMC
  fit_secondary_growth.Rd: modFit
  get_dyna_residuals.Rd: modFit, modCost
  get_multi_dyna_residuals.Rd: modFit
  predict_dynamic_growth.Rd: ode
  predict_growth.Rd: ode
  show_guess_dynamic.Rd: ggplot
  show_guess_primary.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_dynamic_inactivation.Rd: modFit, FME
  fit_inactivation_MCMC.Rd: modMCMC, FME
  get_prediction_cost.Rd: modCost
  predict_inactivation.Rd: ode, deSolve
  sample_IsoFit.Rd: mvrnorm
  sample_dynaFit.Rd: modFit, mvrnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ROC.Rd:55: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:56: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:57: Lost braces in \enumerate; \value handles \item{}{} directly
checkRd: (-1) ROC.Rd:58: Lost braces in \enumerate; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  auxBiom.Rd: glmnet
  biom.options.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'asreml'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  heat_map.Rd: facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    help   2.6Mb
checkRd: (-1) mmds.2D.multi.Rd:118: Lost braces
   118 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
checkRd: (-1) mmds.2D.plot.Rd:134: Lost braces
   134 |   a numeric value in inches indicating the height of graph outfile. Default differs by outfile.type. The resolution for tiff and png figures is 150 dpi. See \code{pdf}, code{tiff}, \code{png}, \code{postscript}.
       |                                                                                                                                                                              ^
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
    libs      1.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  covsum_nested.Rd: mixed
  rm_covsum_nested.Rd: covsum, mixed, outTable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) tocher.Rd:13: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  D2.disc.Rd: lda
  aer.Rd: lda
  confusionmatrix.Rd: lda
  sHe.Rd: levelplot
  samplesize.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/BioVenn.Rcheck/00install.out' for details.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  betalinkr.Rd: vegdist, betadiver
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: Obsolescent feature: DATA statement at (1) after the first executable statement
See 'd:/Rcompile/CRANpkg/local/4.5/BiplotGUI.Rcheck/00install.out' for details.
* used Fortran compiler: 'GNU Fortran (GCC) 13.2.0'
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
checkRd: (-1) FighterAircraft.Rd:32: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bi_scale_color.Rd: geom_sf, scale_color_manual
  bi_scale_fill.Rd: geom_sf, scale_fill_manual
  bi_theme.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  waic.cumhist.Rd: loo-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
File 'BiTrinA/libs/x64/BiTrinA.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bizicount.Rd: DHARMa
  zic.reg.Rd: DHARMa
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxlps.Rd: Surv, coxph
  curelps.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.2Mb
    libs       5.3Mb
    testdata   1.4Mb
GNU make is a SystemRequirements.
checkRd: (-1) posteriorFeasibility.Rd:25: Escaped LaTeX specials: \#
checkRd: (-1) sp500Returns.Rd:4: Escaped LaTeX specials: \&
checkRd: (-1) RLdata500.Rd:8: Lost braces
     8 | A data frame with five variables: \code{fname_c1},\code{lname_c1},  \code{by}, code{bm}, \code{bd}.
       |                                                                                    ^
checkRd: (-1) identity.RLdata500.Rd:15: Lost braces
    15 | format A vector that contains the code{id}
       |                                       ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) durban.Rd:16: Lost braces; missing escapes or markup?
    16 | This data set was obtained from the durban.rowcol {agridat} example in package 'agridat' 
       |                                                   ^
checkRd: (-1) fraction.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:31-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fraction.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_density.Rd:25: Lost braces; missing escapes or markup?
    25 | evenly spaced points between \code{min} and {max}.
       |                                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  build_dir.Rd: render
  html_page.Rd: html_document2, output_format
  hugo_cmd.Rd: server_config
  read_toml.Rd: raw_string
  serve_site.Rd: server_config
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) bluebike.Rd:17: Lost braces
    17 | \item{\code{import_month_data}}\cr {Takes in numeric year/month values and imports data from \href{https://www.bluebikes.com/system-data}{Blue Bikes System Data} for the specified time}
       |                                    ^
checkRd: (-1) bluebike.Rd:18: Lost braces; missing escapes or markup?
    18 | \item{\code{station_distance}}\cr {Returns stations with distance in ascending order given the user's current location}
       |                                   ^
checkRd: (-1) bluebike.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{\code{station_radius}}\cr {Plots the position of the stations within walking distance (500 m), and present the basic information about the stations via leaflet}
       |                                 ^
checkRd: (-1) bluebike.Rd:20: Lost braces; missing escapes or markup?
    20 | \item{\code{trip_distance}}\cr {Computes the geographical distance between the start and end stations}
       |                                ^
checkRd: (-1) bluebike.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{\code{trip_history_sample}} \cr {A sample of 1000 trip data entries from February 2022}
       |                                       ^
checkRd: (-1) bluebike.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{\code{station_data}} \cr {A dataset that includes identification, position, and other basic information about bluebike stations}
       |                                ^
Specified C++11: please drop specification unless essential
Found the following significant warnings:
  Warning: Obsolescent feature: Computed GOTO at (1)
See 'd:/Rcompile/CRANpkg/local/4.5/BMA.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used Fortran compiler: 'GNU Fortran (GCC) 13.2.0'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bmem.Rd: sem
  power.bmem.Rd: model.syntax
  power.curve.Rd: model.syntax
  summary.power.Rd: lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bmem.Rd: sem
  bmem.bs.Rd: sem
  bmem.em.Rd: sem
  bmem.em.boot.Rd: sem
  bmem.em.jack.Rd: sem
  bmem.list.Rd: sem
  bmem.list.boot.Rd: sem
  bmem.list.jack.Rd: sem
  bmem.mi.Rd: sem
  bmem.mi.boot.Rd: sem
  bmem.mi.jack.Rd: sem
  bmem.pair.Rd: sem
  bmem.pair.boot.Rd: sem
  bmem.pair.jack.Rd: sem
  bmem.sobel.Rd: sem
  popPar.Rd: lavaan
  power.basic.Rd: model.syntax
  power.boot.Rd: model.syntax
  power.curve.Rd: model.syntax
  summary.power.Rd: lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
checkRd: (-1) dot-pred_array_to_df.Rd:20: Lost braces; missing escapes or markup?
    20 | Helper function for as.data.frame.{fitted, forecast}. Converts predictive array to data.frame.
       |                                   ^
GNU make is a SystemRequirements.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'cmdstanr'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  summary.bmmfit.Rd: summary.brmsfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BMSC_pareto_k_table.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:60-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:64-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:67-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMSC_pareto_k_table.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Bspatial.Rd: spLM
  Bsptime.Rd: spDynLM, spT.time, spLM
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                           ^
checkRd: (-1) autoplot.tsregime.Rd:20: Lost braces; missing escapes or markup?
    20 | Graph for the stochastic processes of the object \ dQuote {\ code {tsregime}} for: Output process and if they exist for: Threshold process and Covariates process. In the case that there are missing data, a red line is drawn at the indicated time.
       |                                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.Rd: autolayer, ggplot, fortify
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BMTfit.Rd: mledist, fitdist, fitdistrplus, gofstat, plotdist,
    cdfcomp, bootdist, mmedist, qmedist, mgedist
  BMTfit.mge.Rd: mledist, mgedist, fitdistrplus, fitdist
  BMTfit.mle.Rd: mledist, fitdistrplus, fitdist
  BMTfit.mme.Rd: mledist, mmedist, fitdistrplus, fitdist
  BMTfit.mpse.Rd: mledist, fitdistrplus, fitdist
  BMTfit.mqde.Rd: mledist, fitdistrplus, fitdist
  BMTfit.qme.Rd: mledist, qmedist, fitdistrplus, fitdist
  mpsedist.Rd: mledist, fitdistrplus, mmedist, qmedist, mgedist
  mqdedist.Rd: mledist, fitdistrplus, mmedist, qmedist, mgedist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  network.run.Rd: jags.model
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) MvInv.Rd:23-35: Lost braces
    23 | function(eps, u = 0.5, alpha = 1, kappa = 1, gama = 1 / 2, N = 3001) {
       |                                                                      ^
checkRd: (-1) dt_.Rd:19-21: Lost braces
    19 | function(x, df, mean, sd) {
       |                           ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) strength.viewer.Rd:148: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:149: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:151: Lost braces in \itemize; meant \describe ?
checkRd: (-1) strength.viewer.Rd:152: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |               ^
checkRd: (-1) boa.chain.collapse.Rd:20: Lost braces
    20 | \seealso{ code{\link{boa.chain.reset}}, code{\link{boa.chain.subset}} }
       |                                             ^
'LazyData' is specified without a 'data' directory
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
checkRd: (-1) refAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) refAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:11-12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) untreatedAnnots.Rd:13-14: Lost braces in \itemize; meant \describe ?
Packages suggested but not available for checking:
  'adiposerefdata', 'musclerefdata'
checkRd: (-1) Extractor.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Extractor.Rd:19: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  selected_vars.Rd: cv.glmnet, cv.gamlr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following HTML validation problems:
bayes.lin.reg.html:27:32 (bayes.lin.reg.Rd:77): Warning: trimming empty <code>
bayes.lin.reg.html:32:32 (bayes.lin.reg.Rd:79): Warning: trimming empty <code>
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
No news entries found.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/BonEV.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
    libs   1.1Mb
Running 'testthat.R' [42s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(bonsaiforest)
  
  Attaching package: 'bonsaiforest'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("bonsaiforest")
  [ FAIL 1 | WARN 3 | SKIP 12 | PASS 68 ]
  
  ══ Skipped tests (12) ══════════════════════════════════════════════════════════
  • On CRAN (12): 'test-horseshoe.R:58:3', 'test-plot.R:3:3', 'test-plot.R:8:3',
    'test-plot.R:13:3', 'test-plot.R:18:3', 'test-print.R:3:3',
    'test-print.R:8:3', 'test-print.R:13:3', 'test-print.R:18:3',
    'test-simulation.R:16:3', 'test-simulation.R:23:3', 'test-simulation.R:30:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-horseshoe.R:2:3'): horseshoe outputs the right elements for survival ──
  Error in `brms::brmsfamily("cox", bhaz = bhaz)`: unused argument (bhaz = bhaz)
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-horseshoe.R:2:3
   2. │ └─base::withCallingHandlers(...)
   3. └─bonsaiforest::horseshoe(...)
  
  [ FAIL 1 | WARN 3 | SKIP 12 | PASS 68 ]
  Error: Test failures
  Execution halted
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    include  10.5Mb
    lib      29.5Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nnet.Rd: MvnPrior
  suggest.burn.Rd: SuggestBurnLogLikelihood
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> n_00 <- smoking$tc - smoking$qc  # not receive treatement yet not stop smoking
> n_01 <- smoking$qc # not receive treatement but stop smoking
> n_10 <- smoking$tt - smoking$qt # receive treatement but not stop smoking
> n_11 <- smoking$qt # receive treatement and stop smoking
> lnOR <- log(n_11*n_00/n_01/n_10)
> 
> ## Not run: 
> ##D boot.run <- boot.lnOR(n_00, n_01, n_10, n_11, model = 'random', p_cut = 0.05)
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:HSAUR3'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.72 0.08 1.8 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'doMC'
checkRd: (-1) bootSVD.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{Y}{initial data sample, which can be either a matrix or a \code{\link{ff}} matrix. \code{Y} can be either tall (\eqn{p} by \eqn{n}) or wide (\eqn{n} by \eqn{p}). If \code{Y} is entered and \code{V}, \code{d} and \code{U} (see definitions below) are not entered, then \code{bootSVD} will also compute the SVD of \code{Y}. In this case where the SVD is computed, \code{bootSVD} will assume that the larger dimension of \code{Y} is \eqn{p}, and the smaller dimension of code {Y} is \eqn{n} (i.e. \code{bootSVD} assumes that (\eqn{p>n}). This assumption can be overriden by manually entering \code{V}, \code{U} and \code{d}.\cr
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  As2Vs.Rd: ff
  bootSVD.Rd: ff
  fastSVD.Rd: ff
  ffmatrixmult.Rd: ff
  getMomentsAndMomentCI.Rd: ff
  reindexMatricesByK.Rd: ff
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graphoptBbd.Rd: igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getImpExtra.Rd: ranger
  getImpLegacyRf.Rd: ranger
  getImpRf.Rd: ranger
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  legend.grob.Rd: draw.key
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'box/libs/x64/box.dll':
  Found non-API calls to R: 'ENVFLAGS', 'SET_ENVFLAGS'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  box_dir_diff.Rd: digest
  box_upload_new.Rd: httr
  boxr_S3_classes.Rd: as_tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  print.xtable.Rd: xtable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) bp_rats.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) bp_sv.Rd:75: Lost braces; missing escapes or markup?
    75 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) bp_sv.Rd:80: Lost braces; missing escapes or markup?
    80 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:78: Lost braces; missing escapes or markup?
    78 | $$SV = sqrt(sum(x_{i+1} - x_i)^2/n-1)$$
       |                   ^
checkRd: (-1) sv.Rd:82: Lost braces; missing escapes or markup?
    82 | $$SD = sqrt(sum(x_{i+1} - xbar)^2/n-1)$$
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bp_report.Rd: grid.arrange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict.BTm.Rd: predict.glmmPQL
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
calculateIAE: no visible global function definition for 'evalBRAIDrsm'
makeBRAIDreport: no visible global function definition for
  'evalBRAIDrsm'
makeBRAIDreport: no visible global function definition for
  'calcBRAIDconfint'
makeBRAIDreport : <anonymous>: no visible global function definition
  for 'invertBRAIDrsm'
potentiationPlot: no visible global function definition for
  'calcBRAIDconfint'
potentiationPlot : <anonymous>: no visible global function definition
  for 'evalBRAIDrsm'
potentiationPlot: no visible global function definition for
  'evalBRAIDrsm'
Undefined global functions or variables:
  calcBRAIDconfint evalBRAIDrsm invertBRAIDrsm
Missing link or links in Rd file 'braidReports-package.Rd':
  'braidrm-package'

Missing link or links in Rd file 'es8analysis.Rd':
  'es8olatmz' 'runBRAIDanalysis'

Missing link or links in Rd file 'makeBRAIDreport.Rd':
  'runBRAIDanalysis'

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  braidReports-package.Rd: braidrm-package
  es8analysis.Rd: es8olatmz, runBRAIDanalysis
  makeBRAIDreport.Rd: runBRAIDanalysis, scale_fill_gradientn,
    geom_point, geom_line
  potentiationPlot.Rd: geom_ribbon, geom_point, geom_line, geom_hline
  voronoi.Rd: geom_polygon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running examples in 'braidReports-Ex.R' failed
The error most likely occurred in:

> ### Name: calculateIAE
> ### Title: Calculate the Index of Achievable Efficacy
> ### Aliases: calculateIAE
> ### Keywords: misc
> 
> ### ** Examples
> 
> data(es8analysis)
> bfit <- es8analysis$braidFit
> # Modelled effect is base-10 logarithm of cell survival relative to negative controls,
> # so a level of -2 reflects 99% cell killing
> calculateIAE(bfit$fullpar,c(-1,-2),c(1.015*10^-6,5*10^-5))
Error in evalBRAIDrsm(sc1, sc2, parv) : 
  could not find function "evalBRAIDrsm"
Calls: calculateIAE
Execution halted
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_global.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brainR-package.Rd: contour3d, rgl
  makeScene.Rd: contour3d, nifti-class
  write4D.Rd: writeOBJ, writeSTL, contour3d
  write4D.file.Rd: writeOBJ, writeSTL, contour3d
  writeTrianglesSTL.Rd: writeSTL
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brnb.Rd: negbin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) brglm.Rd:173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:174: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:175-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:181-182: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brglm.Rd:183-184: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:54-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) profile.brglm.Rd:58: Lost braces in \itemize; meant \describe ?
Found the following HTML validation problems:
Bridge.html:80:32 (Bridge.Rd:63): Warning: trimming empty <code>
Bridge.html:85:32 (Bridge.Rd:65): Warning: trimming empty <code>
checkRd: (-1) printHands.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) printHands.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) assertall.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) assertall.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) brmsmargins.Rd:129: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:130: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) brmsmargins.Rd:132: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) builders.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) builders.Rd:55: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  builders.Rd: make_standata, as_draws_df
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'cmdstanr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   3.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createBarPrior.Rd: fitCyclopsModel
  createFastBarPrior.Rd: fitCyclopsModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'glmmADMB'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
Running 'test-all.R' [42s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("broom.mixed")
  Loading required package: broom.mixed
  GAMLSS-RS iteration 1: Global Deviance = 4771.925 
  GAMLSS-CG iteration 1: Global Deviance = 4771.013 
  GAMLSS-CG iteration 2: Global Deviance = 4770.994 
  GAMLSS-CG iteration 3: Global Deviance = 4770.994 
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 237 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-rstanarm.R:35:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-alltibbles.R:57:21'): (code run outside of `test_that()`) ──────
  Error in `.requirePackage(package)`: unable to load required package 'rstan'
  Backtrace:
       ▆
    1. └─broom.mixed (local) testf("glance", z) at test-alltibbles.R:62:13
    2.   ├─testthat::expect_is(get(fn_str)(obj), "tbl_df") at test-alltibbles.R:57:21
    3.   │ └─testthat::quasi_label(enquo(object), label, arg = "object")
    4.   │   └─rlang::eval_bare(expr, quo_get_env(quo))
    5.   ├─get(fn_str)(obj)
    6.   └─broom.mixed:::glance.brmsfit(obj)
    7.     └─broom.mixed:::glance_stan(...)
    8.       ├─stats::sigma(x)
    9.       └─broom.mixed:::sigma.brmsfit(x)
   10.         ├─"sigma" %in% brms::variables(object)
   11.         ├─brms::variables(object)
   12.         └─brms:::variables.brmsfit(object)
   13.           └─methods (local) dimnames(x$fit)
   14.             └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
   15.               └─methods:::.findInheritedMethods(classes, fdef, mtable)
   16.                 └─methods::getClass(cl1, where = where, .Force = TRUE)
   17.                   └─methods::getClassDef(Class, where)
   18.                     └─methods:::.requirePackage(package)
  
  [ FAIL 1 | WARN 4 | SKIP 1 | PASS 237 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'broom_mixed_intro.rmd' using rmarkdown

Quitting from lines 65-79 [dwplot1] (broom_mixed_intro.rmd)
Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
unable to load required package 'rstan'
--- failed re-building 'broom_mixed_intro.rmd'

SUMMARY: processing the following file failed:
  'broom_mixed_intro.rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/BRugs.Rcheck/00install.out' for details.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bsitar.Rd: opencl, save_pars, brmsfit_needs_refit
  update_model.bgmfit.Rd: brms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    components   1.0Mb
    fonts        2.9Mb
    lib          4.9Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) bscontrol.Rd:39: Lost braces; missing escapes or markup?
    39 | \item{opt.solver}{a character string in the set {'enum', 'enum_c', 'gurobi', 'cplex', 'lpSolve', 'greedy'} indicating the optimization solver to be used in the program. The choice of 'cplex' requires the package \code{cplexAPI}, 'gurobi' requires the package \code{gurobi}, and 'lpSolve' requires the package \code{lpSolve}. These solver options are only available in the full version at \url{https://github.com/profyliu/bsnsing/}. The default (and the best) is 'enum_c'.}
       |                                                 ^
checkRd: (-1) bscontrol.Rd:45: Lost braces; missing escapes or markup?
    45 | \item{opt.model}{a character string in the set {'gini','error'} indicating the optimization model to solve in the program. The default is 'gini'. The 'error' option is not available in the current version.}
       |                                                ^
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.8Mb
    libs   3.2Mb
'LazyData' is specified without a 'data' directory
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  add.dynamic.regression.Rd: SdPrior
  add.monthly.annual.cycle.Rd: zoo
  bsts.Rd: zoo
  descriptive-plots.Rd: zoo, yearmon
  mbsts.Rd: SpikeSlabPrior
  plot.bsts.mixed.Rd: TimeSeriesBoxplot
  to.posixt.Rd: yearmon
  wide.to.long.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) terms.BTM.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.BTM.Rd:26-32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:25-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) terms.data.frame.Rd:32-38: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BT.Rd: rpart, rpart.control
  BT_Call.Rd: rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
checkRd: (-1) pnbd.mcmc.DrawParameters.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) pnbd.mcmc.DrawParameters.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  abe.mcmc.DrawParameters.Rd: mcmc.list
  pggg.mcmc.DrawParameters.Rd: mcmc.list
  pnbd.mcmc.DrawParameters.Rd: mcmc.list
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) bubbleHMLegends.Rd:42: Lost braces; missing escapes or markup?
    42 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) bubbleHeatmap.Rd:96: Lost braces; missing escapes or markup?
    96 | function. If {sizeBreaks} vector is supplied then this will be ignored and
       |              ^
checkRd: (-1) multiPlotInput.Rd:117: Lost braces; missing escapes or markup?
   117 | \code{unitBase}. This will be supplied to pretty function. If {sizeBreaks} is
       |                                                               ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  read_excel_workbook.Rd: read_excel
  read_gsheets.Rd: read_sheet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  brkpt.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) kink_estimator.Rd:60: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lifecycles.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) depreciation-class.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) depreciation-class.Rd:46-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loan-class.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) model2df-methods.Rd:38-39: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Malformed Description field: should contain one or more complete sentences.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  balancedFolds.Rd: EPSGO
  coef.intsearch.Rd: EPSGO
  plot.summary.int.Rd: EPSGO
  stabpath.Rd: glmnet
  summary.intsearch.Rd: EPSGO
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) deleteZeroComponents.Rd:70: Escaped LaTeX specials: \& \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deleteZeroComponents.Rd: merMod
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File 'Cairo/libs/x64/Cairo.dll':
  Found non-API call to R: 'Rf_gsetVar'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
checkRd: (-1) calcUnique.Rd:24: Lost braces
    24 | functions, and often the /code{cut()} function are relatively slow when working with tens of millions of rows or more.
       |                               ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'ReGenesees'
checkRd: (-1) calibration_bands.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{y}{response variable (in {0,1}).}
       |                                ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) Recording.Rd:112: Lost braces; missing escapes or markup?
   112 | Stop recording images with {camcorder}.
       |                            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BuildGeneSets.Rd: edgeR, org.Hs.eg.db, org.Mm.eg.db
  CAMML.Rd: vamForSeurat
  ChIMP.Rd: vamForSeurat
  GetGeneSets.Rd: org.Hs.eg.db, org.Mm.eg.db
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        2.2Mb
    pictures   4.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_coef-commOccu-method.Rd: fit
  plot_effects-commOccu-method.Rd: fit
  predict-commOccu-method.Rd: fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) macrocaic.Rd:31: Lost braces; missing escapes or markup?
    31 |      {RRD = ln(N_1/N_2)}
       |      ^
checkRd: (-1) macrocaic.Rd:34: Lost braces; missing escapes or markup?
    34 |      {PDI = (N_1/(N_1 + N_2))-0.5}
       |      ^
checkRd: (-1) pd.calc.Rd:33: Lost braces
    33 |   \item{Length of tip branch lengths (TIPS)}{Length of tip branch lengths (TIPS)}{Unlike UEH, this measure does not use the unique paths to each tips on the \strong{subtree} and instead gives the sum of the unique branches leading to the tips on the \strong{complete tree}.}
       |                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  comparative.data.Rd: reorder.phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CalculateGlobalSens.Rd: sensRange
  CalculateLocalSens.Rd: sensFun, sensRange
  DesignSurvey.Rd: svydesign
  PlotLocalSens.Rd: element_text
  SetRanges.Rd: sensRange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    entry_level                 1.7Mb
    virtual_patient_simulator   3.1Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    captr .1.4
    captr .1.3
    captr .1.2
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  persistence.prob.Rd: coxph, survreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.ca.rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ca.rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.mjca.rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) States.Rd:48: Escaped LaTeX specials: \$
checkRd: (-1) fitweibull.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitweibull.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) zipcode.Rd:14: Lost braces; missing escapes or markup?
    14 | This is a dataset from the archived/orphaned {zipcode} package.
       |                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  setup_statevars.Rd: deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) NEWS.Rd:96: Lost braces
    96 |     \item code{train} now removes duplicate models in the tuning grid. Duplicates could occur for models with discrete parameters.
       |               ^
checkRd: (-1) calibration.Rd:46: Lost braces; missing escapes or markup?
    46 | formula. This argument is not used for \code{xyplot.calibration}. For {ggplot.calibration}, \code{data}
       |                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  train.Rd: recipe
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) build_for_cran.Rd:13: Lost braces
    13 | The exit status code{R CMD build}, invisibly.
       |                     ^
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
checkRd: (-1) compareCoefs.Rd:30: Lost braces
    30 | \item{pvals}{If code{TRUE} (the default is \code{FALSE}), print two-sided p-values
       |                     ^
checkRd: (-1) mcPlots.Rd:38: Lost braces; missing escapes or markup?
    38 |   axis.  To plot against a factor, you need to specify the full name of one of the indicator variables that define the factor.  For example, for a factor called \code{type} with levels \code{A}, \code{B} and {C}, using the usual drop-first level parameterization of the factor, the regressors for \code{type} would be \code{typeB} or \code{typeC}.  Similarly, to plot against the regressor \code{log(X4)}, you must specify \code{"log((X4)"}, not \code{"X4"}.
       |                                                                                                                                                                                                                 ^
checkRd: (-1) scatterplot.Rd:137: Lost braces
   137 | For  \code{style="filled"} several subarguments modify the appearance of the region:  code{alpha} is a number between 0 and 1 that specifies opacity with defualt 0.15, \code{border}, \code{TRUE} or \code{FALSE} specifies a border for the envelope, and \code{vertical} either \code{TRUE} or \code{FALSE}, modifies the behavior of the envelope at the edges of the graph.
       |                                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Anova.Rd: anova.coxph
  Boot.Rd: boot, boot.array, boot.ci, plot.boot, empinf
  Ellipses.Rd: cov.trob
  S.Rd: multinom, polr, summary.multinom
  ScatterplotSmoothers.Rd: gam, rqss, qss
  avPlots.Rd: cov.trob
  boxCox.Rd: boxcox
  boxCoxVariable.Rd: boxcox
  hist.boot.Rd: boot, boot.ci
  influence-mixed-models.Rd: lme
  marginalModelPlot.Rd: gam
  poTest.Rd: polr
  scatter3d.Rd: gam
  scatterplot.Rd: cov.trob
  scatterplotMatrix.Rd: cov.trob, gam, rqss
  symbox.Rd: boxcox
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'rnaturalearthhires'
File 'cartographer/libs/x64/cartographer.dll':
  Found non-API call to R: 'PRVALUE'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dotDensityLayer.Rd: st_sample
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    www  12.1Mb
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CreateSpacetimeFolds.Rd: trainControl
  bss.Rd: train, trainControl
  errorProfiles.Rd: rollapply
  ffs.Rd: train, trainControl
  global_validation.Rd: train, postResample, confusionMatrix
  nndm.Rd: trainControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) slpDGCM.Rd:130-133: Lost braces
   130 | \code{x1, x2, x3, \dots}- {input to the model, there must be one column
       |                           ^
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    doc  19.9Mb
checkRd: (-1) catmapdata.Rd:9-14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:15-16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:16-17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:17-18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) catmapdata.Rd:20-21: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  catpredi.Rd: mgcv
  catpredi.survival.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cauphylm.Rd: nloptr
  fitCauchy.Rd: nloptr
  fitCauchy.internal.Rd: nloptr
  fit_function.Rd: nloptr
  hdi.ancestralCauchy.Rd: HDInterval
  printRTreeTest.Rd: ape
  rTraitCauchy.Rd: ape
  simulateTipsCauchy.Rd: ape
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'cauphy/libs/x64/cauphy.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) tpcExample.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) as.mbsts.Rd:71: Lost braces; missing escapes or markup?
    71 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
checkRd: (-1) mcmc.Rd:61: Lost braces; missing escapes or markup?
    61 |   \item{states.samples}{(\code{niter}- \code{burn}) draws from p(alpha_t | Y_{1:T}).}
       |                                                                              ^
Package suggested but not available for checking: 'rkeops'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  make_model.Rd: dagitty
  print.causal_model.Rd: dagitty
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  causalSLSE.Rd: vcovHC.default
  extract-causalslse-method.Rd: extract, texreg
  extract-slseFit-method.Rd: extract, texreg
  predict.Rd: vcovHC.default
  summary.Rd: vcovHC.default
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) cbc_design.Rd:160: Lost braces; missing escapes or markup?
   160 | see \code{?DoE.base::fac.design} as well as the JSS article on the {DoE.base}
       |                                                                    ^
checkRd: (-1) cbc_design.Rd:174: Lost braces; missing escapes or markup?
   174 | well as the JSS article on the {DoE.base} package (Grömping, 2018).
       |                                ^
checkRd: (-1) cbc_design.Rd:197: Lost braces; missing escapes or markup?
   197 | {idefix} package (Traets et al, 2020).
       | ^
checkRd: (-1) cbc_power.Rd:70: Lost braces; missing escapes or markup?
    70 | estimation. See the {logitr} documentation for details about other
       |                     ^
Running 'spelling.R' [0s]
  Comparing 'spelling.Rout' to 'spelling.Rout.save' ...6c6
< NULL
---
> All Done!
  Running 'testthat.R' [3s]
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Rcpp_CONEC-class.Rd: C++Object-class
  Rcpp_CPS-class.Rd: C++Object-class
  Rcpp_CTRL-class.Rd: C++Object-class
  Rcpp_DCP-class.Rd: C++Object-class
  Rcpp_DLP-class.Rd: C++Object-class
  Rcpp_DNL-class.Rd: C++Object-class
  Rcpp_DQP-class.Rd: C++Object-class
  Rcpp_PDV-class.Rd: C++Object-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cchs.Rd: Surv, coxph, coxph.object, coxph.control, cch
  cchsData.Rd: nwtco, cch
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CUR.Rd:25: Lost braces; missing escapes or markup?
    25 | The number of low-dimension of C (J1 < {N,M}).
       |                                        ^
checkRd: (-1) CUR.Rd:29: Lost braces; missing escapes or markup?
    29 | The number of low-dimension of R (J2 < {N,M}).
       |                                        ^
checkRd: (-1) CX.Rd:23: Lost braces; missing escapes or markup?
    23 | The number of low-dimension (J < {N,M}).
       |                                  ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cct-class.Rd: rjags-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) data.dtmr.Rd:57: Lost braces; missing escapes or markup?
    57 | \code{RU}: {Referent units}
       |            ^
checkRd: (-1) data.dtmr.Rd:59: Lost braces; missing escapes or markup?
    59 | \code{PI}: {Partitioning and iterating attribute}
       |            ^
checkRd: (-1) data.dtmr.Rd:61: Lost braces; missing escapes or markup?
    61 | \code{APP}: {Appropriateness attribute}
       |             ^
checkRd: (-1) data.dtmr.Rd:63: Lost braces; missing escapes or markup?
    63 | \code{MC}: {Multiplicative Comparison attribute}
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  G.start.Rd: lsei
  cds.Rd: lsei
  cdstoclue.Rd: cl_agreement
  gen.cop.Rd: copClayton
  group.ALS.Rd: lsei
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
    libs   1.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tobit1.Rd: gam, ziplss
  tobit2.Rd: gam, ziplss
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Unexported objects imported by ':::' calls:
  'copula:::dCdu' 'copula:::fitCopStart'
  See the note in ?`:::` about the use of this operator.
checkRd: (-1) listCensusApis.Rd:10: Lost braces; missing escapes or markup?
    10 | Scrapes {https://api.census.gov/data.json} and returns a dataframe
       |         ^
checkRd: (-1) call_api_once.Rd:36: Lost braces
    36 | A code{data.frame} with the requested variables at the requested
       |       ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) centroid.Rd:22: Lost braces; missing escapes or markup?
    22 | Centroid value C_{cen}(v) for node v defined as:
       |                  ^
checkRd: (-1) clusterrank.Rd:23: Lost braces; missing escapes or markup?
    23 | where the term f(c_{i}) accounts for the effect of i's local clustering and the term '+1' results from the contribution of \eqn{j}{j} itself. \cr
       |                    ^
Error(s) in re-building vignettes:
--- re-building 'typical_usage.Rmd' using rmarkdown

Quitting from lines 24-30 [setup] (typical_usage.Rmd)
Error: processing vignette 'typical_usage.Rmd' failed with diagnostics:
Error : Your API call has errors.  The API message returned is Sorry, the system is currently undergoing maintenance or is busy.  Please try again later..

--- failed re-building 'typical_usage.Rmd'

SUMMARY: processing the following file failed:
  'typical_usage.Rmd'

Error: Vignette re-building failed.
Execution halted
'LazyData' is specified without a 'data' directory
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |   ^
checkRd: (-1) cequre.Rd:31: Lost braces; missing escapes or markup?
    31 |   {epsi}^{# regression coefficients} times the initial value,
       |          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) performParallelNLMERun.Rd:22: Lost braces
    22 | \item{partialJob}{is /code{TRUE} if it is not required to stop the job
       |                           ^
checkRd: (-1) performParallelNLMERun.Rd:25: Lost braces
    25 | \item{allowIntermediateResults}{is /code{TRUE} if intermediate results
       |                                         ^
Problems with news in 'NEWS.md':
No news entries found.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Major refactoring of the code
'LazyData' is specified without a 'data' directory
checkRd: (-1) cfc.tbasis.Rd:23: Lost braces
    23 | Assuming one-dimensional \code{p1} and \code{p2} for clarity, the algorithm calculates cumulative incidence function for cuase 1 using a recursive formula: \code{ci1[n+1] = ci1[n] + dci1[n]}, where \code{dci1[n] = 0.5*(p2[n] + p2[n+1])*(p1[n] - p1[n+1])}. The increment in cumulative incidence function for cause 2 is similarly calculated, \code{dci2[n] = 0.5*(p1[n] + p1[n+1])*(p2[n] - p2[n+1])}. These equations guarantee that \code{dci1[n] + dci2[n] = p1[n]*p2[n] - p1[n+1]*p2[n+1]}. Event-free probability is simply calculated as code{efp[n] = p1[n]*p2[n]}. Taken together, this numerical integration ensures that \code{efp[n+1] - efp[n] + dci1[n] + dci2[n] = 0}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cfda-package.Rd: create.basis
  compute_optimal_encoding.Rd: create.basis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cforward.Rd: Surv, concordancefit, coxph
  estimate_concordance.Rd: Surv, concordancefit, coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.cgaim.Rd: doParallel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 38.7Mb
  sub-directories of 1Mb or more:
    include  38.4Mb
Malformed Title field: should not end in a period.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) comparisonsTable.cgOneFactorFit.Rd:47: Lost braces
    47 |         call (see {\dots } section below.)
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anorexiaFT.Rd: anorexia
  boxplot.cgOneFactorData.Rd: survfit
  comparisonsGraph.cgOneFactorComparisonsTable.Rd: panel.text
  comparisonsTable.cgOneFactorFit.Rd: rlm
  comparisonsTable.cgPairedDifferenceFit.Rd: rlm
  comparisonsgraph.Rd: panel.text
  descriptiveTable.cgOneFactorData.Rd: survfit
  downweightedTable.Rd: rlm
  downweightedTable.cgOneFactorFit.Rd: rlm
  downweightedTable.cgPairedDifferenceFit.Rd: rlm
  fit.cgOneFactorData.Rd: rlm, survreg, gls
  fit.cgPairedDifferenceData.Rd: rlm
  kmGraph.Rd: label
  kmGraph.cgOneFactorData.Rd: label
  prepareCGOneFactorData.Rd: Surv, survreg, logtrans
  print.cgOneFactorComparisonsTable.Rd: rlm
  print.cgOneFactorFit.Rd: rlm
  print.cgOneFactorGlobalTest.Rd: rlm
  print.cgOneFactorGrpSummaryTable.Rd: rlm
  print.cgOneFactorSampleSizeTable.Rd: rlm
  print.cgPairedDifferenceComparisonsTable.Rd: rlm
  print.cgPairedDifferenceFit.Rd: rlm
  summary.cgOneFactorFit.Rd: rlm
  summary.cgPairedDifferenceFit.Rd: rlm
  varianceGraph.cgOneFactorFit.Rd: vgam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cpt.geo-class.Rd: ggplot2
  data.set.Rd: data.set-methods
  data.set_-.Rd: data.set<--methods
  pen.value.Rd: pen.value-methods
  pen.value_-.Rd: pen.value<--methods
  test.stat.Rd: test.stat-methods
  test.stat_-.Rd: test.stat<--methods
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ftse100.Rd:8: Lost braces; missing escapes or markup?
     8 |  This dataset gives the daily returns (c_{t+1}/c_t -1) of the UK FTSE 100 index from 2nd April 1984 until the 13th September 2012.
       |                                          ^
checkRd: (-1) Hausdorff.dist.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{vec1}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) Hausdorff.dist.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{vec2}{A \code{integer} vector forms a subset of {1, 2, ..., n}.}
       |                                                       ^
checkRd: (-1) online.univar.multi.Rd:47-57: Lost braces
    47 | online.univar.one2 = function(y_vec, gamma, tau_gamma, ...){
       |                                                            ^
checkRd: (-1) online.univar.multi.Rd:50-55: Lost braces
    50 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:71-89: Lost braces
    71 | online.univar.one3 = function(y_vec, tau_vec, ...){
       |                                                   ^
checkRd: (-1) online.univar.multi.Rd:72-74: Lost braces
    72 |   if(length(y_vec) != length(tau_vec)){
       |                                       ^
checkRd: (-1) online.univar.multi.Rd:77-87: Lost braces
    77 |   while(FLAG == 0 & t <= length(y_vec)){
       |                                        ^
checkRd: (-1) online.univar.multi.Rd:81-86: Lost braces
    81 |     while(j < J & FLAG == 0){
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  changepointsVar-package.Rd: lars
  jumpointsVar.Rd: lars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) cql.Rd:28: Lost braces; missing escapes or markup?
    28 | {X} \code{<x_var>, <(x_facet)>}: \tab\tab\tab\tab  X-axis variable. May include a second categorical\cr
       | ^
checkRd: (-1) cql.Rd:30: Lost braces; missing escapes or markup?
    30 | {Y} \code{<y_var>}: \tab\tab\tab\tab Y-axis variable. *Not used for \code{hist}.\cr
       | ^
checkRd: (-1) cql.Rd:38: Lost braces; missing escapes or markup?
    38 | {Y_label} \code{'<ylab>'}: \tab\tab\tab\tab  Y-axis custom label. Defaults to <y_var>\cr
       | ^
checkRd: (-1) cql.Rd:39: Lost braces; missing escapes or markup?
    39 | {Legend} \code{'<legend>'}: \tab\tab\tab\tab  Legend custom label. Defaults to <x_category>\cr
       | ^
checkRd: (-1) cql.Rd:40: Lost braces; missing escapes or markup?
    40 | {Colorset} \code{'<clist>'}: \tab\tab\tab\tab  Custom set of colors for <x_category> levels.\cr
       | ^
checkRd: (-1) cql.Rd:42: Lost braces; missing escapes or markup?
    42 | {AggFunc} \code{'<func>'}: \tab\tab\tab\tab Summary function for \code{bar} type.\cr
       | ^
checkRd: (-1) cql.Rd:45: Lost braces; missing escapes or markup?
    45 | {Fit} \code{'<show_se>'}: \tab\tab\tab\tab Valid types: \code{true|false}. Fit quadratic line.\cr
       | ^
checkRd: (-1) cql.Rd:47: Lost braces; missing escapes or markup?
    47 | {ConfInt} \code{'<interval>'}: \tab\tab\tab\tab  Show error bars. Value is confidence interval value. E.g. '.95'
       | ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) create_unit_tests.Rd:17: Lost braces; missing escapes or markup?
    17 | Create `{testthat}` test cases for the code.
       |         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) as.data.frame.checkglobals.Rd:43: Lost braces; missing escapes or markup?
    43 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
checkRd: (-1) as.matrix.checkglobals.Rd:32: Lost braces; missing escapes or markup?
    32 | \item \code{type}, the type of the detected entity, either \code{"global"} or {"import"}.
       |                                                                               ^
File 'checkglobals/libs/x64/checkglobals.dll':
  Found non-API call to R: 'Rf_isValidString'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Package suggested but not available for checking: 'darts'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checkpoint.Rd: pkgdepends
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pipe.Rd: magrittr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hats_alignSpectra2D.Rd: rowDist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aovPCAloadings.Rd: GraphicsOptions
  plot2Loadings.Rd: GraphicsOptions
  plotLoadings.Rd: GraphicsOptions
  plotSpectra.Rd: GraphicsOptions
  reviewAllSpectra.Rd: GraphicsOptions
  sPlotSpectra.Rd: GraphicsOptions
  surveySpectra.Rd: GraphicsOptions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hommelFast.Rd: hommel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Missing link or links in Rd file 'rmpt06.Rd':
  '[tern:estimate_proportions]{tern::estimate_proportions}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'countreg'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chillR-package.Rd: ggplot2
  plot_phenology_trends.Rd: fields, ggplot2
  plot_scenarios.Rd: ggplot2, patchwork
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) C316.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C317.amp.Rd:28-32: Lost braces
    28 |     40 x {
       |          ^
checkRd: (-1) C60.amp.Rd:63-67: Lost braces
    63 |     40 x {
       |          ^
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cmdstanr'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chkpt_brms.Rd: brms
  make_brmsfit.Rd: brms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package unavailable to check Rd xrefs: 'cmdstanr'
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggpng.Rd: ggsave
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'entab'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  insert_chunkwise_into.Rd: tbl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) chunker-methods.Rd:63: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:64: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:69: Lost braces in \enumerate; meant \describe ?
checkRd: (-1) chunker-methods.Rd:70: Lost braces in \enumerate; meant \describe ?
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       5.7Mb
    extdata   2.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) ec.datalag.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{prepares Dy y_1 Dy_1 ... Dy_{nlag-1} for estimation}
       |                                    ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                      ^
checkRd: (-1) ec.datalag.Rd:15: Lost braces; missing escapes or markup?
    15 | ymat contains the folloiwing columns {Dy y_1 Dy_1 ... Dy_{nlag-1}}
       |                                                          ^
checkRd: (-1) lagn.Rd:21: Lost braces; missing escapes or markup?
    21 |              REM: alternative to "lead-lag" {dplyr} which applies to vector y
       |                                             ^
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R         1.8Mb
    extdata   4.3Mb
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'userfriendlyscience'
checkRd: (-1) CIplot.Rd:58: Lost braces; missing escapes or markup?
    58 | \item{las}{numeric in {0,1,2,3}; the style of axis labels.
       |                       ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |     ^
checkRd: (-1) rstable.Rd:42: Lost braces
    42 | Lo\"{g}ae\"{v}e, M. (1977). Probability Theory I. (fourth edition) Springer-Verlag, New York.
       |            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  circ.plot.Rd: eqscplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
checkRd: (-1) doseFind.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) doseFind.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) doseFind.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickInverse.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) quickIsotone.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbExecQuery.Rd: dbSendQuery, dbClearResult, dbGetQuery
  lbsClear.Rd: dbCommit, dbRollback
  lbsDeleteAllAuthorsDocuments.Rd: dbCommit, dbRollback
  lbsTidy.Rd: dbCommit, dbRollback
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator.Rd:93: Lost braces; missing escapes or markup?
    93 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                 ^
checkRd: (-1) data_generator.Rd:95: Lost braces; missing escapes or markup?
    95 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++}, S_{*+}
       |                                                                         ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                     ^
checkRd: (-1) data_generator_loop.Rd:96: Lost braces; missing escapes or markup?
    96 |   \item{estimand_mean}{List of means of the FULL, S_{++}, S_{*+} and
       |                                                             ^
checkRd: (-1) data_generator_loop.Rd:98: Lost braces; missing escapes or markup?
    98 |   \item{estimand_sd}{List of standard deviations of the FULL, S_{++},
       |                                                                 ^
checkRd: (-1) data_generator_loop.Rd:99: Lost braces; missing escapes or markup?
    99 |   S_{*+} and PP estimands}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) ciu.ggplot.col.Rd:41: Lost braces; missing escapes or markup?
    41 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.explain.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.meta.result.new.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
checkRd: (-1) ciu.textual.Rd:38: Lost braces; missing escapes or markup?
    38 | \item{ind.inputs}{Indices of input features to explain (the set {i} in CIU
       |                                                                 ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CivisFuture.Rd: Future
  civis_platform.Rd: future, plan
  write_civis_file.Rd: plan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
checkRd: (-1) get_langs.Rd:13: Lost braces
    13 | character vector listing all the languages that tag API call supports. See \code{\link{tag_images}} and code{\link{tag_image_urls}}
       |                                                                                                             ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  generate_classification_data.Rd: knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) clean.Rd:136: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:141: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clean.Rd:142: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    clhs_0.7-2
    clhs_0.7-0
    clhs_0.6-0
    clhs_0.5-7
    clhs_0.5-6
    clhs_0.5-3
    clhs_0.5-2
    clhs_0.5-1
    clhs_0.5-0
    clhs_0.4-3
    clhs_0.4-2
    clhs_0.4-1
    clhs_0.4-0
    clhs_0.3-2
    clhs_0.3-1
    clhs_0.3-0
    clhs_0.2-1
    clhs_0.2-0
    clhs_0.1-0
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ClickHouseHTTPConnection-class.Rd: dbConnect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fitMarkovChain.Rd: Rsolnp
  frequencies.Rd: transactions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) cf_save_kml.Rd:68: Lost braces
    68 | \code{\link{cf_find_station}} and code{vignette("choose-station")} for
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  liftHurstC.Rd: artificial.levels, Hfrombeta
  liftHurstCC.Rd: artificial.levels, Hfrombeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  thornthwaite.Rd: daylength, geosphere
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    extdata  48.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clinDR-package.Rd: DoseFinding
  emaxsim.Rd: Mods
  emaxsimB.Rd: Mods
  fitEmaxB.Rd: rstan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                   ^
checkRd: (-1) clinsig.Rd:129: Lost braces
   129 |  be calculated with the measures specified in samp{mct} and samp{disp},
       |                                                                 ^
'LazyData' is specified without a 'data' directory
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  knitPrintListObjects.Rd: knitr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) print.clogitL1.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) print.clogitL1.Rd:23: Lost braces in \itemize; meant \describe ?
Problems with news in 'NEWS.md':
No news entries found.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cloudml_train.Rd: flags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cb_participant_count.Rd:13: Lost braces
    13 | \item{query}{A phenotype query defined using the code{\link{phenotype}} function and logic operators (see example below)}
       |                                                      ^
checkRd: (-1) phenotype.Rd:10: Lost braces
    10 | \item{id}{A single phenotype id. Possible phenotyoes can be explored using the code{\link{cb_search_phenotypes}} function}
       |                                                                                    ^
checkRd: (-1) clr.Rd:24: Lost braces
    24 | the sense that its Karhunen-Lo\`{e}ve decomposition has qx terms only.}
       |                                 ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.clusEvol.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.clus_lme.Rd: ggexport
  plot.clus_opt_thres3.Rd: ggexport
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clusterabilitytest.Rd: dip.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aucplot.Rd: lattice, xyplot
  cluscomp.Rd: cluster
  clusterCons-package.Rd: cluster, lattice, apcluster
  dkplot.Rd: lattice, xyplot
  expressionPlot.Rd: lattice, xyplot
  membBoxPlot.Rd: lattice, bwplot
  wrappers.Rd: cluster, agnes, pam, diana, apclusterK
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dissmutmatrix.Rd: dissplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |      ^
checkRd: (-1) HTKmeans.Rd:62: Lost braces
    62 | \item{centers }{A matrix of cluster centres.}
       |                ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |      ^
checkRd: (-1) HTKmeans.Rd:63: Lost braces
    63 | \item{cluster }{A vector of integers (from 1:\code{k}) indicating the cluster to which each point is allocated.}
       |                ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |      ^
checkRd: (-1) HTKmeans.Rd:64: Lost braces
    64 | \item{itnb }{The number of iterations executed until convergence}
       |             ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |      ^
checkRd: (-1) HTKmeans.Rd:65: Lost braces
    65 | \item{converged }{Whether the algorithm stopped by converging or through reaching the maximum number of itertions.}
       |                  ^
'LazyData' is specified without a 'data' directory
Running 'agnes-ex.R' [2s]
  Comparing 'agnes-ex.Rout' to 'agnes-ex.Rout.save' ... OK
  Running 'clara-NAs.R' [0s]
  Comparing 'clara-NAs.Rout' to 'clara-NAs.Rout.save' ... OK
  Running 'clara-ex.R' [2s]
  Comparing 'clara-ex.Rout' to 'clara-ex.Rout.save' ... OK
  Running 'clara-gower.R' [0s]
  Running 'clara.R' [3s]
  Comparing 'clara.Rout' to 'clara.Rout.save' ... OK
  Running 'clusplot-out.R' [1s]
  Comparing 'clusplot-out.Rout' to 'clusplot-out.Rout.save' ... OK
  Running 'daisy-ex.R' [1s]
  Comparing 'daisy-ex.Rout' to 'daisy-ex.Rout.save' ... OK
  Running 'diana-boots.R' [2s]
  Running 'diana-ex.R' [0s]
  Comparing 'diana-ex.Rout' to 'diana-ex.Rout.save' ... OK
  Running 'ellipsoid-ex.R' [0s]
  Comparing 'ellipsoid-ex.Rout' to 'ellipsoid-ex.Rout.save' ... OK
  Running 'fanny-ex.R' [1s]
  Comparing 'fanny-ex.Rout' to 'fanny-ex.Rout.save' ...194c194
< iterations          43
---
> iterations          45
1056c1056
< Converged after 46 iterations,  obj =             2665.982
---
> Converged after 44 iterations,  obj =             2665.982
  Running 'mona.R' [1s]
  Comparing 'mona.Rout' to 'mona.Rout.save' ... OK
  Running 'pam.R' [31s]
  Comparing 'pam.Rout' to 'pam.Rout.save' ... OK
  Running 'silhouette-default.R' [2s]
  Comparing 'silhouette-default.Rout' to 'silhouette-default.Rout.save' ... OK
  Running 'sweep-ex.R' [0s]
checkRd: (-1) dtmvnom.Rd:30: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmeansvar.Rd: splitmix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clustvarsel.Rd: mclustModelNames, hc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clusvisMixmod.Rd: MixmodCluster-class
  clusvisVarSelLCM.Rd: VSLCMresults-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cluster_stability.Rd: agnes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
checkRd: (-1) CMAPSS.Rd:10: Lost braces
    10 | \item \code{train}{ a list of class "hhsmm.data" as the train dataset}
       |                   ^
checkRd: (-1) CMAPSS.Rd:11: Lost braces
    11 | \item \code{test}{ a list of class "hhsmm.data" as the test dataset}
       |                  ^
checkRd: (-1) CMAPSS.Rd:12: Lost braces
    12 | \item \code{subsets}{ a matrix containig the number of units in each subset of the CMAPSS data set (FD001-FD004) for the train and test datasets}
       |                     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) cmb.search.Rd:50: Lost braces; missing escapes or markup?
    50 |   \item{order}{applied conditioning order {length p}}
       |                                           ^
checkRd: (-1) gp.realize.Rd:20: Lost braces; missing escapes or markup?
    20 | The list \code{l.v} is created by \code{makedistlist()} from a {n x p} design matrix on which to generate the unconditional GP realization.  The correlation parameters take on values in \code{(0,1)} and use the Gaussian correlation model, calculated as \code{rho^d(xi,xj)^2}.  This helper function is used to create the demonstration data used in the example for \code{calibrate()}.
       |                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mlsei.Rd: solve.QP
  mlsun.Rd: solve.QP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) bvp.Rd:24: Lost braces
    24 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivp.Rd:38: Lost braces
    38 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) ivpsys.Rd:29: Lost braces
    29 | differential equations.  The code{midptivp} method solves initial
       |                                  ^
checkRd: (-1) plot.predict.crrQR.Rd:18: Escaped LaTeX specials: \#
checkRd: (-1) plot.predict.crrQR.Rd:22: Escaped LaTeX specials: \#
Running 'spelling.R' [0s]
  Comparing 'spelling.Rout' to 'spelling.Rout.save' ...6c6
< NULL
---
> All Done!
Running 'spelling.R' [0s]
  Comparing 'spelling.Rout' to 'spelling.Rout.save' ...6c6
< NULL
---
> All Done!
  Running 'testthat.R' [1s]
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nested_data_plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'tobit1'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cnaOpt.Rd: configTable, rreduce, condTbl, cna
  conCovOpt.Rd: configTable, cna
  conCovOpt_utils.Rd: rreduce, condTbl
  ereduce.Rd: full.ct
  findOutcomes.Rd: configTable, cna, selectCases, full.ct
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) cnlt.reg.Rd:43: Lost braces
    43 | \emph{Technometrics}, bold{60} (1), 48-60, DOI 10.1080/00401706.2017.1281846.\cr\cr
       |                           ^
checkRd: (-1) fwtnppermC.Rd:35: Lost braces
    35 | Given \eqn{n} points on a line, \env{x}, each with a corresponding env{f} value this function computes
       |                                                                       ^
Specified C++11: please drop specification unless essential
checkRd: (-1) conversion.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:68-69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:70-72: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:72-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conversion.Rd:75-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:103-104: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:105-106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:107-109: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:109-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) tools.Rd:112-113: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
Package suggested but not available for checking: 'PopGenome'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dic.fit.mcmc.Rd: MCMCmetrop1R
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'disttree'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CoClust-class.Rd: copula-class
  CoClust.Rd: fitCopula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'rkward'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  envfit.coca.Rd: vectorfit, factorfit, envfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
2c2
< This is vegan 2.6-8
---
> This is vegan 2.6-4
Package which this enhances but not available for checking: 'rkward'
checkRd: (-1) educFM.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) educFM.Rd:28: Lost braces in \itemize; meant \describe ?
Package suggested but not available for checking: 'userfriendlyscience'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  create_codemeta.Rd: write_json
  write_codemeta.Rd: write_json
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coefplot.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc   9.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boxesLx.Rd: grViz
  mkratetable.Rd: survival, pyears
  plotcuminc.Rd: survival, pyears
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  subsetPHMM.Rd: derivePHMM
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   2.7Mb
File 'collapse/libs/x64/collapse.dll':
  Found non-API calls to R: 'SETLENGTH', 'SET_TRUELENGTH', 'TRUELENGTH'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
File 'collections/libs/x64/collections.dll':
  Found non-API calls to R: 'PRENV', 'SET_CLOENV'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  roi_select.Rd: imager
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
checkRd: (-1) getHistList.Rd:32: Lost braces; missing escapes or markup?
    32 | ({FALSE})? If a bin is empty, the center of the bin is returned as the
       |  ^
checkRd: (-1) imageClusterPipeline.Rd:82: Lost braces; missing escapes or markup?
    82 | of the bin ({FALSE})? If a bin is empty, the center of the bin is returned
       |             ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_colors_3d.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  InterpolateColorFun.Rd: ggplot2
  OrderDataTSP.Rd: TSP
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   2.0Mb
checkRd: (-1) colour_values.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values.Rd:144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:143: Lost braces in \itemize; meant \describe ?
checkRd: (-1) colour_values_rgb.Rd:144: Lost braces in \itemize; meant \describe ?
Unexported object imported by a ':::' call: 'crayon:::mypaste'
  See the note in ?`:::` about the use of this operator.
Problems with news in 'NEWS.md':
No news entries found.
Malformed Description field: should contain one or more complete sentences.
checkRd: (-1) xsimplex.Rd:6: Lost braces; missing escapes or markup?
     6 |              Generates all points on a {p,n} simplex lattice (i.e. a p-part
       |                                        ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) BMD.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BMD.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) add.risk.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) comire.gibbs.Rd:76: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
checkRd: (-1) count_pairs.Rd:19-20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) count_pairs.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) entropy.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) score_log_nonparam.Rd:36: Lost braces; missing escapes or markup?
    36 | {0, 1}.
       | ^
checkRd: (-1) score_log_semiparam.Rd:40: Lost braces; missing escapes or markup?
    40 | values in {0, 1}.
       |           ^
checkRd: (-1) sort_pairs.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sort_pairs.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   6.7Mb
Specified C++11: please drop specification unless essential
checkRd: (-1) hmm.Rd:47-55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:56-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:63-70: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:71-74: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:75-78: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:79-84: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:85-89: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:95-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:104-107: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:108-111: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:112-118: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:119-129: Lost braces in \itemize; meant \describe ?
checkRd: (-1) hmm.Rd:130-133: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'CAM'
checkRd: (-1) glass.Rd:10: Lost braces
    10 | \item{item}{factor}{200 levels - which item the measurements came from}
       |                    ^
checkRd: (-1) glass.Rd:11-12: Lost braces
    11 | \item{fragment}{factor}{4 levels - which of the four fragments from each item the observations were made
       |                        ^
checkRd: (-1) glass.Rd:13: Lost braces
    13 | \item{logNaO}{numeric}{log of sodium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:14: Lost braces
    14 | \item{logMgO}{numeric}{log of magnesium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:15: Lost braces
    15 | \item{logAlO}{numeric}{log of aluminium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:16: Lost braces
    16 | \item{logSiO}{numeric}{log of silicon concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:17: Lost braces
    17 | \item{logKO}{numeric}{log of potassium concentration to oxygen concentration}
       |                      ^
checkRd: (-1) glass.Rd:18: Lost braces
    18 | \item{logCaO}{numeric}{log of calcium concentration to oxygen concentration}
       |                       ^
checkRd: (-1) glass.Rd:19: Lost braces
    19 | \item{logFeO}{numeric}{log of iron concentration to oxygen concentration}
       |                       ^
checkRd: (-1) atomdeps.Rd:9: Lost braces
     9 |  \item{"tangle"}: {Dihedral angle defined by atoms A-B-C-D as described below. \code{NA}'s represent the free side chain dihedral angles \emph{chi} for that amino acid.}
       |                   ^
checkRd: (-1) atomdeps.Rd:10: Lost braces; missing escapes or markup?
    10 |  \item{"names"}: {The component atoms of the amino acid side chain.  Represents atom D in the dihedral.}
       |                  ^
checkRd: (-1) atomdeps.Rd:11: Lost braces; missing escapes or markup?
    11 |  \item{"matx"}: {The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".}
       |                 ^
checkRd: (-1) atomdeps.Rd:12: Lost braces; missing escapes or markup?
    12 |  \item{"bangle"}: {Planar bond angle formed between B-C-D}
       |                   ^
checkRd: (-1) atomdeps.Rd:13: Lost braces; missing escapes or markup?
    13 |  \item{"blength"}: {Bond length between C-D}
       |                    ^
checkRd: (-1) keener.Rd:82: Lost braces; missing escapes or markup?
    82 | a_{ij} = (S_ij + 1) / (S_ij + S_ji + 2). This step should make comparing
       |   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rlm.Rd: lqs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  confint.Rd: boot.ci
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  codadendrogram.Rd: histogram
  pairwisePlot.Rd: lmrob
  pwlrPlot.Rd: lmrob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
17  sp_018 0.9231127 0.57100180 0.003142932
> 
> w<-trait.sampling(x$final.community,ITV=TRUE,aggregate=TRUE)
> str(w)
'data.frame':	106 obs. of  5 variables:
 $ Site   : chr  "site_002" "site_003" "site_004" "site_005" ...
 $ Species: chr  "sp_001" "sp_001" "sp_001" "sp_001" ...
 $ trait.a: num  0.163 0.163 0.163 0.164 0.163 ...
 $ trait.b: num  0.686 0.686 0.688 0.684 0.685 ...
 $ trait.c: num  0.0942 0.0934 0.0932 0.0934 0.0936 ...
> 
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  9.03 2.89 11.93 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) concstats_hhi.Rd:13: Lost braces; missing escapes or markup?
    13 | value is required. Ranges from {0, 1} and often used for comparison over
       |                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                ^
checkRd: (-1) KCI.Rd:44: Lost braces
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                      ^
checkRd: (-1) KCI.Rd:44: Lost braces; missing escapes or markup?
    44 |  \item \code{testStatistic} the statistic Tr(K_{(ddot{(Y)}|X)} * K_{(E|X)})
       |                                                                    ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cmvnorm.Rd: pmvnorm, dmvnorm, qmvnorm
  condMVN.Rd: pmvnorm, dmvnorm, qmvnorm
  pcmvnorm.Rd: GenzBretz, Miwa, TVPACK, pmvnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pcmvt.Rd: pmvt, GenzBretz
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) babies.Rd:35: Escaped LaTeX specials: \&
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
checkRd: (-1) mya.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) mya.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  loo_conformal.Rd: predictive_interval
  predictive_interval.conformal.Rd: posterior_predict
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  conformal.multidim.full.Rd: future.apply
  conformal.multidim.msplit.Rd: future.apply
  glmnet.funs.Rd: glmnet
  plot_multidim.Rd: ggplot2, gridExtra, hrbrthemes
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  km.outcomes.Rd: survfit
  km.pmf.Rd: survfit
  km.support.Rd: survfit
  km.surv.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) binary_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) binary_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) multi_class_cm.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) NetStats.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) NetStats.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) generate_network.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DBI.Rd: DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Packages suggested but not available for checking: 'conosPanel', 'p2data'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
checkRd: (-1) Univranks.Rd:69: Lost braces; missing escapes or markup?
    69 | To obtain the preference rankings from the paired comparisons the procedure has been the following: the first row of the raw data is [1  3  2   1   2   1  1  2  1   1   1   2   1    1   2]. London is preferred to Paris, St. Gallen, Barcelona Stockholm (LP, LM, LSg, LB and LSt are always equal to 1), and there is no preference between London and Milan (they are tied); Milan is preferred to Paris (PM = 2), St. Gallen, Barcelona and Stockholm; and so on. The first ordering is then <{L M} Sg St B P> corresponding to a ranking [1,5,1,2,4,3], where the columns indicate L  P  M Sg  B St.  
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ^
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Set.Rd: set
  deprecated.Rd: set
  dict.table.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) getConvexHull.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getConvexHull.Rd:30: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  curve_cont.Rd: riskRegression
  plot_surv_3Dsurface.Rd: riskRegression
  plot_surv_animated.Rd: riskRegression, facet_wrap
  plot_surv_area.Rd: riskRegression, facet_wrap
  plot_surv_at_t.Rd: riskRegression, facet_wrap
  plot_surv_contour.Rd: riskRegression, ggplot2, facet_wrap
  plot_surv_heatmap.Rd: riskRegression, facet_wrap
  plot_surv_lines.Rd: riskRegression, facet_wrap
  plot_surv_matrix.Rd: riskRegression, facet_wrap
  plot_surv_quantiles.Rd: riskRegression, facet_wrap
  plot_surv_rmst.Rd: riskRegression, facet_wrap
  plot_surv_rmtl.Rd: riskRegression, facet_wrap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  svylorenz.Rd: oldsvyquantile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CovrgPlot.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{plotCI}{a vector of up to 4 numbers out of the set {1,2,3,4}, corresponding to which
       |                                                          ^
Specified C++11: please drop specification unless essential
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |            ^
checkRd: (-1) copCAR.Rd:40: Lost braces
    40 |        item{\code{maxit}}{the maximum number of iterations to be used by \code{\link{optim}} when optimizing the objective function. Defaults to \code{1000}.}
       |                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                          ^
checkRd: (-1) condQestCopC.Rd:45: Lost braces; missing escapes or markup?
    45 | obtain the conditional qth quantile of Y_{n+1} given {Y1,...,Yn}.
       |                                                      ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                  ^
checkRd: (-1) condQestCopC.Rd:40: Lost braces; missing escapes or markup?
    40 | \code{condQestCopC} returns the conditional tao-th quantile of Y_{n+1} given {Y1,...,Yn}
       |                                                                              ^
checkRd: (-1) ComputeCope.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) ComputeCope.Rd:57-61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DrawContour.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Draws the contour {f=c}.}
       |                          ^
checkRd: (-1) DrawContour.Rd:20: Lost braces; missing escapes or markup?
    20 | Draws the contour {f=c}.
       |                   ^
checkRd: (-1) cope.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) cope.Rd:35: Lost braces in \itemize; meant \describe ?
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.2Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cophe.prepare.dat.susie.Rd: runsusie
  cophe.susie.Rd: check_dataset, runsusie
  cophe.susie.lbf.Rd: runsusie
  cophe_heatmap.Rd: pheatmap
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bcalibrate.Rd: kEstimate, pca
  cal_rv.Rd: kEstimate, pca
  gcalibrate.Rd: kEstimate, pca
  plot_estimates.Rd: theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages suggested but not available for checking:
  'cec2005benchmark', 'cec2013'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  margins.Rd: ptruncnorm, qtruncnorm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   3.2Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CopulaREMADA.Rd: meshgrid
  FactorCopulaREMADA.Rd: meshgrid
  VineCopulaREMADA.Rd: meshgrid
  Vuong.Rd: meshgrid
  hybridCopulaREMADA.Rd: meshgrid
  vineVuong.Rd: meshgrid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  column.Rd: CsparseMatrix-class
  nnzero.Rd: CsparseMatrix-class, RsparseMatrix-class
  submatrix.Rd: CsparseMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CoreCollection.Rd: R6Class
  dot-CoreCollectionClass.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) getSurface.Rd:22: Lost braces
    22 | value \code{getSurface} shortens the output of \code{conv} to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /code{conv} output.
       |                                                                                                                                                                                  ^
checkRd: (-1) cvGen.Rd:29: Lost braces
    29 | The function code{gatherFromList} returns a list with components containing elements of the same name.
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getRpartModel.Rd: rpart.object
  plot.CoreModel.Rd: rpart.plot, rpart.object, plot.rpart, pam
  rfClustering.Rd: pam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) CorMID.Rd:54: Lost braces; missing escapes or markup?
    54 |  individual compound containing 2 carbons and observe a vector of {978,22,0}.
       |                                                                   ^
checkRd: (-1) CorMID.Rd:58: Lost braces; missing escapes or markup?
    58 |  The equivalent corMID vector would be {1,0,0}, indicating that the non-labeled
       |                                        ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bbdml.Rd: trust
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) carstats.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) carstats.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) titanic.Rd:14: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  carstats.Rd: data.table
  rundata.Rd: data.table
  titanic.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) get_policy_scores.Rd:63: Lost braces
    63 | \code{low_estimate}\\code{high_estimate} columns. The \code{SD_estimate} column has the standard deviation of the
       |                          ^
Running examples in 'CoronaNetR-Ex.R' failed
The error most likely occurred in:

> ### Name: get_event
> ### Title: Access CoronaNet Event Data API
> ### Aliases: get_event
> 
> ### ** Examples
> 
> # Grab all data for Saudi Arabia from first 4 months of pandemic
> 
> saudi_data <- get_event(countries = "Saudi Arabia", type = "All",
+ type_sub_cat = "All", from = "2019-12-31", to = "2020-04-30")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve host: postgrest-588174062.us-east-2.elb.amazonaws.com
Calls: get_event ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown

Quitting from lines 55-56 [unnamed-chunk-1] (Introduction.Rmd)
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
Could not resolve host: postgrest-588174062.us-east-2.elb.amazonaws.com
--- failed re-building 'Introduction.Rmd'

SUMMARY: processing the following file failed:
  'Introduction.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(coro)
  > 
  > test_check("coro")
  [ FAIL 3 | WARN 0 | SKIP 5 | PASS 202 ]
  
  ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
  • On CRAN (5): 'test-async.R:25:1', 'test-generator.R:27:3',
    'test-generator.R:34:3', 'test-iterator.R:3:3', 'test-iterator.R:31:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-parser-block.R:63:3'): `{` blocks - nested ─────────────────────
  Error in `node_poke_cdr(prev_refs, nested_refs)`: bad value
  Backtrace:
      ▆
   1. └─coro:::expect_snapshot0(...) at test-parser-block.R:63:3
   2.   ├─rlang::inject(expect_snapshot(!!enquo0(expr), cran = cran)) at D:\RCompile\CRANpkg\local\4.5\coro.Rcheck\tests\testthat\helper-flowery.R:5:5
   3.   └─testthat::expect_snapshot(...)
   4.     └─rlang::cnd_signal(state$error)
  ── Error ('test-parser-block.R:100:3'): `{` blocks - complex nesting ───────────
  Error in `node_poke_cdr(prev_refs, nested_refs)`: bad value
  Backtrace:
      ▆
   1. └─coro:::expect_snapshot0(...) at test-parser-block.R:100:3
   2.   ├─rlang::inject(expect_snapshot(!!enquo0(expr), cran = cran)) at D:\RCompile\CRANpkg\local\4.5\coro.Rcheck\tests\testthat\helper-flowery.R:5:5
   3.   └─testthat::expect_snapshot(...)
   4.     └─rlang::cnd_signal(state$error)
  ── Error ('test-parser-if.R:30:3'): `if` blocks - inner block ──────────────────
  Error in `node_poke_cdr(prev_refs, nested_refs)`: bad value
  Backtrace:
      ▆
   1. └─coro:::expect_snapshot0(...) at test-parser-if.R:30:3
   2.   ├─rlang::inject(expect_snapshot(!!enquo0(expr), cran = cran)) at D:\RCompile\CRANpkg\local\4.5\coro.Rcheck\tests\testthat\helper-flowery.R:5:5
   3.   └─testthat::expect_snapshot(...)
   4.     └─rlang::cnd_signal(state$error)
  
  [ FAIL 3 | WARN 0 | SKIP 5 | PASS 202 ]
  Error: Test failures
  Execution halted
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tCorpus-cash-annotate_rsyntax.Rd: tquery
  tCorpus-cash-subset.Rd: subset.data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrarray.Rd: rcorr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cor_test.Rd: parameters, winsorize
  correlation.Rd: parameters, winsorize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ggbplot.Rd: bplot
  tally.Rd: bplot, calibrate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    extdata  17.7Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrgrapher.Rd: visNetwork
  plot.corrgrapher.Rd: visNetwork
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  polycorr.Rd: polychor
  tetracorr.Rd: polychor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rplot.Rd: geom_point
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
checkRd: (-1) cosmoFns-package.Rd:34: Escaped LaTeX specials: \&
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctmaAllInvFit.Rd: ctStanFit
  ctmaFit.Rd: ctStanFit, ctsem
  ctmaInit.Rd: ctStanFit, ctsem
  ctmaOptimizeFit.Rd: ctStanFit
  ctmaOptimizeInit.Rd: ctStanFit
  ctmaPlotCtsemMod.Rd: ctsem
  ctmaScaleInits.Rd: ctStanFit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) summary_fitlist.Rd:15: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) summary_fitlist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) fasttrakg.Rd:18: Lost braces
    18 |     \item{\code{killip}}{Killip level of cardiac event severity (1-4)age75}{1= Age>75; 0=Age<=75}
       |                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ml.nb1.Rd: glm.nb
  ml.nb2.Rd: glm.nb
  ml.nbc.Rd: glm.nb
  ml.pois.Rd: glm.nb
  modelfit.Rd: glm.nb
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.6Mb
'LazyData' is specified without a 'data' directory
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
File 'covr/libs/x64/covr.dll':
  Found non-API calls to R: 'SET_BODY', 'SET_CLOENV', 'SET_FORMALS'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  axis_canvas.Rd: ggplot2, coord_flip
  background_grid.Rd: theme
  draw_line.Rd: geom_path
  draw_text.Rd: geom_label
  ggsave2.Rd: ggsave
  insert_xaxis_grob.Rd: ggplot2
  save_plot.Rd: ggsave
  theme_minimal_grid.Rd: theme_minimal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxed.Rd: mgcv, rms
  coxed.gam.Rd: mgcv
  coxed.gam.tvc.Rd: mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.9Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) gen_data.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) gen_data.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) plot.coxr.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxr.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) coxph.RT.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) coxph.RT.Rd:59-71: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coxsei-package.Rd: survival
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CPC.Rd: diana, pam, dbscan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cpi.Rd: lrn, create.second_order
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   6.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) sharedat.Rd:23: Lost braces
    23 | \doi{10.7910/DVN/YXMQZM}{Harvard dataverse}
       |                         ^
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
checkRd: (-1) crwPredict.Rd:54-68: Lost braces
    54 | \item("predTime"){
       |                  ^
checkRd: (-1) crwPredict.Rd:59: Lost braces
    59 |  no longer the default (see \item{return.type}). If the original data were 
       |                                  ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> flush(stderr()); flush(stdout())
> 
> ### Name: update_player_meta
> ### Title: Update player_meta
> ### Aliases: update_player_meta
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # Update data to current
> ##D new_player_meta <- update_player_meta()
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.05 0.12 1.17 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
'LazyData' is specified without a 'data' directory
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
checkRd: (-1) normFit.Rd:39: Lost braces; missing escapes or markup?
    39 | {analytes}}
       | ^
checkRd: (-1) normPred.Rd:27: Lost braces
    27 | ode{standards}, \code{analytes}}
       |    ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_multi_silodata.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crossnma.Rd: jags.model
  netconnection.crossnma.Rd: netconnection
  netconnection.crossnma.model.Rd: netconnection
  netgraph.crossnma.Rd: netgraph.netmeta
  netgraph.crossnma.model.Rd: netgraph.netmeta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  body_add_table_list.Rd: body_add_flextable
  body_add_table_section.Rd: body_add_flextable
  ct_compact.Rd: flextable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_slider.Rd: tag, HTML
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CrossVal.Rd: Modeler, Modeler-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Crossword.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the constrained MLEs given beta_{0r}.}
       |                                                                                    ^
checkRd: (-1) confRegCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                   ^
checkRd: (-1) confRegUCRandUCCR.Rd:24: Lost braces; missing escapes or markup?
    24 | of interest, beta_{0r}, and the remaining ones are the unconstrained MLEs given beta_{0r}.}
       |                                                                                      ^
checkRd: (-1) confRegUCRandUCCR.Rd:27: Lost braces; missing escapes or markup?
    27 | beta_{0r} in \code{paramVals}, which are those of interest, usually the ones
       |      ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crrstep.Rd: crr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crsra_anonymize.Rd: digest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
checkRd: (-1) cruts-package.Rd:21: Lost braces
    21 | section{Dependencies}{
       |        ^
checkRd: (-1) cruts-package.Rd:21-24: Lost braces
    21 | section{Dependencies}{
       |                      ^
checkRd: (-1) cruts-package.Rd:26: Lost braces
    26 | section{Citation}{
       |        ^
checkRd: (-1) cruts-package.Rd:26-28: Lost braces
    26 | section{Citation}{
       |                  ^
checkRd: (-1) cruts-package.Rd:30-32: Lost braces
    30 | references{
       |           ^
'LazyData' is specified without a 'data' directory
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc  11.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  alma.Rd: TTR
  assert.Rd: cli
  dema.Rd: TTR
  ema.Rd: TTR
  evwma.Rd: TTR
  fetch.Rd: xts
  get_fgindex.Rd: xts
  get_fundingrate.Rd: xts
  get_lsratio.Rd: xts
  get_openinterest.Rd: xts
  get_quote.Rd: xts
  hma.Rd: TTR
  sma.Rd: TTR
  vwap.Rd: TTR
  wma.Rd: TTR
  zlema.Rd: TTR
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
    16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
       |                                                          ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) calculateEffects.Rd:24: Lost braces; missing escapes or markup?
    24 | equals (I-B)^{-1}Gamma. The indirect effect equals the difference between
       |              ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
checkRd: (-1) csvy.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) csvy.Rd:60: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  csvy.Rd: calibrate, plotpersp, incr, decr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) mcmc.fmove.Rd:81: Lost braces; missing escapes or markup?
    81 |   beta ~ N( 0 , tau^2 * QQ^{-1} )
       |                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  akde.Rd: res
  as.telemetry.Rd: fread
  ctmm-FAQ.Rd: zoom
  projection.Rd: CRS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctpm.fit.Rd: slouch, plot.variogram
  variogram.Rd: plot.variogram
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctqr-package.Rd: pchreg
  ctqr.Rd: Surv, pchreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ctFit.Rd: ctModel
  ctModelFromFit.Rd: ctModel
  ctMultigroupFit.Rd: ctLongToWide, ctModel
  ctPostPredict.Rd: ctPlotArray
  ctRefineTo.Rd: ctModel
  ctsemOMX.Rd: ctModel
  summary.ctsemFit.Rd: ctModel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   7.6Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cubeViewOutput.Rd: shinyWidgetOutput
  cubeview.Rd: levelplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  jumpoints.Rd: lars
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Survcure.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.8Mb
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Misc
checkRd: (-1) abs_d_ppv_npv.Rd:27: Escaped LaTeX specials: \_ \_ \_
Package which this enhances but not available for checking: 'RGtk2'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SparseCCA.Rd: CCA, CCA.permute
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    doc    1.2Mb
    libs   1.2Mb
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simulate_cycloSurv.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  createCyclopsData.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata       1.3Mb
    htmlwidgets   1.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cramer_vonMises.Rd: Copula-class
  Cylcop.Rd: Copula-class
  ccylcop.Rd: Copula-class
  cyl_copula-class.Rd: Copula-class
  cyl_rect_combine-class.Rd: Copula-class
  cyl_rect_combine.Rd: Copula-class
  cyl_rot_combine-class.Rd: Copula-class
  cyl_rot_combine.Rd: Copula-class
  fit_cylcop_ml.Rd: Copula-class, fitCopula
  full2half_circ.Rd: circular
  half2full_circ.Rd: circular
  joint.Rd: Copula-class
  numerical_conditional_cop.Rd: Copula-class
  numerical_inv_conditional_cop.Rd: Copula-class
  plot_cop_surf.Rd: Copula-class
  wasserstein.Rd: Copula-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fit.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) fit.Rd:39: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  geom_fan.Rd: aes, aes_, ggplot, fortify, borders, layer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) CytofTree.Rd:47-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytofTree.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:33-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CytomeTree.Rd:37-38: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:20-21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) RetrievePops.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rnaRaw.Rd: dgCMatrix-class
  rnaVelo.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ConfMatrix.Rd: R6
  D2MCS.Rd: getModelInfo
  GainRatioHeuristic.Rd: gain.ratio
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  StoragehubManager.Rd: R6Class
  d4storagehub4RLogger.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) D4TAlinkTask.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:19-20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:21-22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:23-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) D4TAlinkTask.Rd:25-26: Lost braces in \itemize; meant \describe ?
Found the following HTML validation problems:
saveReportTable.html:80:1 (saveReportTable.Rd:36): Warning: trimming empty <dt>
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DAAGtheme.Rd: theEconomist.theme, standard.theme, simpleTheme,
    custom.theme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fpiter.Rd:55-58: Lost braces
    55 |     \code{tol}{  A small, positive scalar that determines when iterations
       |               ^
checkRd: (-1) fpiter.Rd:60-61: Lost braces
    60 |     \code{maxiter}{  An integer denoting the maximum limit on the number of
       |                   ^
checkRd: (-1) fpiter.Rd:63-65: Lost braces
    63 |     \code{trace}{  A logical variable denoting whether some of the intermediate
       |                 ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  associations.Rd: Assocs
  associations.folder.Rd: Assocs
  kurtosis.folder.Rd: kurtosis
  mdsdd.Rd: Assocs
  plotframes.Rd: xyplot
  skewness.folder.Rd: skewness
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  designGGPlot.Rd: labellers, ggplot, geom_text
  designPlotlabels.Rd: ggplot, geom_text
  interaction.ABC.plot.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) formatScientificTeX.Rd:33: Lost braces; missing escapes or markup?
    33 | function will return  " 3.0\\\\times 10^{2}"
       |                                         ^
Package which this enhances but not available for checking: 'doMC'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DAISIE_ML.Rd: deSolve
  DAISIE_ML1.Rd: deSolve
  DAISIE_ML2.Rd: deSolve
  DAISIE_ML4.Rd: deSolve
  DAISIE_ML_IW.Rd: deSolve
  DAISIE_loglik_integrand.Rd: deSolve
  DAISIE_loglik_integrate.Rd: deSolve
  default_params_doc.Rd: deSolve
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.predict_parts.Rd: break_down, local_attributions,
    local_interactions
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  link_dam_metadata.Rd: data.table
  read_dam_file.Rd: behavr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factload.Rd: polychor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.filter.parent.offspring.Rd: gl.report.rdepth,
    gl.report.reproducibility
  gl.report.parent.offspring.Rd: gl.report.rdepth,
    gl.report.reproducibility
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
checkRd: (-1) gl.filter.maf.Rd:7: Lost braces; missing escapes or markup?
     7 |  {adegenet} object}
       |  ^
checkRd: (-1) gl.pcoa.Rd:68: Lost braces; missing escapes or markup?
    68 | The function is essentially a wrapper for glPca {adegenet} or pcoa \{ape\}
       |                                                 ^
checkRd: (-1) gl.play.history.Rd:17: Lost braces
    17 | code{x2@other$history[c(1,4,5)]}). [optional].}
       |     ^
checkRd: (-1) utils.jackknife.Rd:49: Lost braces
    49 | bold{Note} that when n is very small, jackknife resampling is not recommended.
       |     ^
checkRd: (-1) utils.jackknife.Rd:51: Lost braces
    51 | Parallel computation is implemented. The argument code{n.cores} indicates the 
       |                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.genleastcost.Rd: landgenreport, popgenreport, wassermann, lgrMMRR
  utils.dart2genlight.Rd: adegenet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.diagnostics.sim.Rd: gl.filter.callrate
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gl.spatial.autoCorr.Rd: gl.propShared, gl.dist.ind
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcr_app.Rd: plotly
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) StartEnd.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) StartEnd.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  FillIn.Rd: data.table
  slide.Rd: dplyr
  slideMA.Rd: dplyr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) processFlow.Rd:14: Lost braces
    14 | \item{roundDigits}{Integer. If NA, numerics are not rounded before comparison. If /code{roundDigits} is specified, numerics are 
       |                                                                                        ^
checkRd: (-1) processFlow.Rd:15: Lost braces
    15 | rounded to /code{roundDigits} decimal places using \link[base]{round}.}
       |                 ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) data_edit.Rd:137: Lost braces
   137 | code{data_edit} is a shiny application built on \code{rhandsontable} that is
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  configure_report.Rd: theme
  create_report.Rd: render
  drop_columns.Rd: data.table
  group_category.Rd: data.table
  plotDataExplorer.Rd: theme
  plotDataExplorer.grid.Rd: theme
  plotDataExplorer.multiple.Rd: theme, facet_wrap
  plotDataExplorer.single.Rd: theme
  plot_bar.Rd: geom_bar, theme_gray, theme
  plot_boxplot.Rd: geom_boxplot, geom_jitter, scale_y_continuous,
    theme_gray, theme
  plot_correlation.Rd: geom_text, theme_gray, theme
  plot_density.Rd: geom_density, scale_x_continuous, theme_gray, theme
  plot_histogram.Rd: geom_histogram, scale_x_continuous, theme_gray,
    theme
  plot_intro.Rd: geom_label, theme_gray, theme
  plot_missing.Rd: geom_label, theme_gray, theme
  plot_prcomp.Rd: geom_label, theme_gray, theme
  plot_qq.Rd: geom_qq, geom_qq_line, theme_gray, theme
  plot_scatterplot.Rd: geom_point, geom_jitter, scale_x_continuous,
    scale_y_continuous, theme_gray, theme
  plot_str.Rd: diagonalNetwork, radialNetwork
  set_missing.Rd: data.table
  split_columns.Rd: data.table
  update_columns.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) number_of_rows.Rd:30-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) number_of_rows.Rd:33-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_methods.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) schema_source.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:37-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) special_simulation.Rd:40-43: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  identifyOutliers.Rd: mc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataone-defunct.Rd: getData, getIdentifier, getFormatId,
    setPublicAccess, canRead, addData
  setPublicAccess.Rd: DataObject-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) build_date_factor.Rd:15: Lost braces; missing escapes or markup?
    15 | Map a vector of dates to a factor at one of these levels {"yearmonth", "yearquarter", "quarter", "month"}
       |                                                          ^
checkRd: (-1) build_date_factor.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{type}{One of {"year", "yearquarter", "yearmonth", "quarter", "month"}}
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  aggregate_by_key.Rd: data.table
  build_target_encoding.Rd: data.table
  fast_handle_na.Rd: copy, data.table
  generate_date_diffs.Rd: data.table
  set_col_as_character.Rd: data.table
  set_col_as_date.Rd: data.table
  set_col_as_factor.Rd: data.table
  set_col_as_numeric.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  acc_distributions.Rd: ggplot
  acc_distributions_loc.Rd: ggplot
  acc_distributions_loc_ecdf.Rd: ggplot
  acc_distributions_only.Rd: ggplot
  acc_distributions_only_ecdf.Rd: ggplot
  acc_distributions_prop.Rd: ggplot
  acc_multivariate_outlier.Rd: ggplot2
  acc_robust_univariate_outlier.Rd: ggplot
  acc_shape_or_scale.Rd: ggplot2
  acc_univariate_outlier.Rd: ggplot
  con_contradictions.Rd: ggplot
  con_contradictions_redcap.Rd: ggplot
  con_limit_deviations.Rd: ggplot
  des_scatterplot_matrix.Rd: ggplot
  int_datatype_matrix.Rd: ggplot2
  prep_render_pie_chart_from_summaryclasses_ggplot2.Rd: ggplot2
  pro_applicability_matrix.Rd: ggplot2
  util_heatmap_1th.Rd: ggplot
  util_plot_figure_no_plotly.Rd: ggplot2
  util_plot_figure_plotly.Rd: ggplot2
  util_set_size.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) defaultFactorSummaries.Rd:29: Lost braces
    29 | code{\link{variableType}}, \code{\link{countMissing}}, \code{\link{uniqueValues}},
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  identifyOutliers.Rd: mc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataStepClass.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'data.table/libs/x64/data_table.dll':
  Found non-API calls to R: 'LEVELS', 'NAMED', 'SETLENGTH',
    'SET_GROWABLE_BIT', 'SET_TRUELENGTH', 'STRING_PTR', 'TRUELENGTH'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Running 'S4.R' [0s]
  Running 'autoprint.R' [0s]
  Comparing 'autoprint.Rout' to 'autoprint.Rout.save' ... OK
  Running 'froll.R' [19s]
  Running 'knitr.R' [1s]
  Comparing 'knitr.Rout' to 'knitr.Rout.save' ...28,38d27
< ```
< 
< ```
< ##        x     y     z
< ##    <int> <int> <int>
< ## 1:     1     4     7
< ## 2:     2     5     8
< ## 3:     3     6     9
< ```
< 
< ``` r
52,62d40
< ```
< 
< ```
< ##        x     y     z     a
< ##    <int> <int> <int> <int>
< ## 1:     1     4    10     1
< ## 2:     2     5    11     1
< ## 3:     3     6    12     1
< ```
< 
< ``` r
  Running 'main.R' [12m]
  Running 'nafill.R' [1s]
  Running 'other.R' [0s]
  Running 'programming.R' [1s]
  Running 'types.R' [0s]
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Node.Rd: R6Class
  as.Node.rpart.Rd: rpart, text.rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  stat_pde_density.Rd: aes, aes_, ggplot, fortify, layer, borders
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'SASxport'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbcsp-class.Rd: TSDatabaseDistances, parallelDist
  predict.dbcsp.Rd: predict.lda
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) plot.mleBb.Rd:48: Lost braces
    48 |   \ code{size} is extracted from argument \code{x}.
       |         ^
checkRd: (-1) value_missing_table.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) value_missing_table.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) CI_mc.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{i}{the row index of the interest entry X_{i,j}}
       |                                                ^
checkRd: (-1) CI_mc.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{j}{the row index of the interest entry X_{i,j}}
       |                                                ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arrange.tbl_lazy.Rd: arrange, show_query
  backend-hana.Rd: copy_to
  collapse.tbl_sql.Rd: collapse, compute, collect
  complete.tbl_lazy.Rd: show_query
  copy_inline.Rd: copy_to
  copy_to.src_sql.Rd: copy_to, show_query
  count.tbl_lazy.Rd: count, tally
  db-sql.Rd: copy_to
  dbplyr-slice.Rd: slice_min, slice_max, slice_sample
  distinct.tbl_lazy.Rd: distinct, show_query
  expand.tbl_lazy.Rd: show_query
  filter.tbl_lazy.Rd: show_query
  get_returned_rows.Rd: rows_insert, rows_append, rows_update,
    rows_upsert, rows_delete
  group_by.tbl_lazy.Rd: group_by
  head.tbl_lazy.Rd: show_query
  join.tbl_sql.Rd: join, show_query
  memdb_frame.Rd: !!, !!!, .data, .env
  mutate.tbl_lazy.Rd: mutate, transmute, show_query
  nycflights13.Rd: src_postgres
  pivot_wider.tbl_lazy.Rd: expand
  pull.tbl_sql.Rd: pull
  replace_na.tbl_lazy.Rd: show_query
  rows-db.Rd: rows_insert, rows_append, rows_update, rows_patch,
    rows_upsert, rows_delete, tbl, compute
  select.tbl_lazy.Rd: select, rename, relocate
  summarise.tbl_lazy.Rd: summarise, show_query
  tbl.src_dbi.Rd: compute, collect, show_query, explain, do
  win_over.Rd: group_by, arrange
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbglm.Rd: daisy
  dblm.Rd: daisy
  dbplsr.Rd: plsr, daisy
  disttoD2.rd: daisy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) data.Rd:11: Lost braces
    11 | \doi{10.1007/s40258-021-00647-3}{DOI}
       |                                 ^
Problems with news in 'NEWS.md':
No news entries found.
Package suggested but not available for checking: 'BRugs'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcoptions.Rd: gelman.diag
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CalcStatClusterGivenCenter.Rd:36: Lost braces; missing escapes or markup?
    36 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatClusterGivenCenter.Rd:37: Lost braces; missing escapes or markup?
    37 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) CalcStatsAllClusters.Rd:49: Lost braces; missing escapes or markup?
    49 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) CalcStatsAllClusters.Rd:50: Lost braces; missing escapes or markup?
    50 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) DetectClustersModel.Rd:60: Lost braces; missing escapes or markup?
    60 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) DetectClustersModel.Rd:61: Lost braces; missing escapes or markup?
    61 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
checkRd: (-1) glmAndZIP.iscluster.Rd:34: Lost braces; missing escapes or markup?
    34 | This can be "glm" for generalized linear models (\link{glm} {stats}),
       |                                                             ^
checkRd: (-1) glmAndZIP.iscluster.Rd:35: Lost braces; missing escapes or markup?
    35 | "glmer" for generalized linear mixed model (\link{glmer} {lme4}),
       |                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CalcStatClusterGivenCenter.Rd: glmer
  CalcStatsAllClusters.Rd: glmer
  DetectClustersModel.Rd: glmer, SpatialPolygonsDataFrame, STFDF,
    SpatialPolygons
  glmAndZIP.iscluster.Rd: glmer
  knbinary.Rd: SpatialPolygonsDataFrame
  mergeknclusters.Rd: SpatialPolygonsDataFrame
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcFit-class.Rd: bugs.fit
  gsFit-class.Rd: bugs.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) kernel.assign.Rd:27: Lost braces; missing escapes or markup?
    27 |  {q = [0, 1]}. Kernels are of the Müller-Wang type ("MW"), Müller type ("M")
       |  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dNTD.Rd: plotTensor3D
  dNTF.Rd: plotTensor3D
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CUR.Rd: pcor, spcor
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ddalpha.train.Rd: covMcd, lda, knn, knn.cv
  depth.L2.Rd: covMcd
  depth.Mahalanobis.Rd: covMcd
  depth.betaSkeleton.Rd: covMcd
  depth.potential.Rd: covMcd
  depth.simplicialVolume.Rd: covMcd
  depth.space.Mahalanobis.Rd: covMcd
  depth.space.potential.Rd: covMcd
  depth.space.simplicialVolume.Rd: covMcd
  depth.space.spatial.Rd: covMcd
  depth.spatial.Rd: covMcd
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) detectAgeInterval.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Age}, or code{age}.}
       |                                                                              ^
checkRd: (-1) detectSex.Rd:10: Lost braces
    10 | \item{Dat}{a \code{data.frame} containing a column called \code{Sex}, or code{sex}.}
       |                                                                              ^
checkRd: (-1) ggbgetAgesFit.Rd:28: Lost braces
    28 | code{\link{ggbChooseAges}}
       |     ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.ddpcr_plate.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:138-139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plot.ddpcr_plate.Rd:140-141: Lost braces in \itemize; meant \describe ?
Specified C++11: please drop specification unless essential
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
'LazyData' is specified without a 'data' directory
Specified C++14: please drop specification unless essential
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot_cashflow.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  declare_estimator.Rd: lm_robust, estimatr, glance
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  inst.ratio.Rd: pdfDisplay
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) deconv.Rd:85: Lost braces; missing escapes or markup?
    85 |     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
       |                                                           ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  recode.variables.Rd: recode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dedupe_wide.Rd: data.table
  na_move.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deepforest.Rd: rpart.control
  deeptree.Rd: rpart.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) deepNN-package.Rd:18: Lost braces
    18 | section{Dependencies}{
       |        ^
checkRd: (-1) deepNN-package.Rd:18-21: Lost braces
    18 | section{Dependencies}{
       |                      ^
checkRd: (-1) deepNN-package.Rd:23: Lost braces
    23 | section{Citation}{
       |        ^
checkRd: (-1) deepNN-package.Rd:23-25: Lost braces
    23 | section{Citation}{
       |                  ^
checkRd: (-1) deepNN-package.Rd:27-38: Lost braces
    27 | references{
       |           ^
'LazyData' is specified without a 'data' directory
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    doc    1.8Mb
    help   1.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
checkRd: (-1) deltaPlot.Rd:28: Lost braces
    28 |  \item{purify}{logical: should item purification be performed? (Default is code{FALSE}). See \bold{Details}.}
       |                                                                                ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.1Mb
    help   1.3Mb
checkRd: (-1) kin.Rd:49-50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:53-61: Lost braces
    53 | {\itemize{
       | ^
checkRd: (-1) kin.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:56-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:59-67: Lost braces
    59 | {\itemize{
       | ^
checkRd: (-1) kin2sex.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) kin2sex.Rd:65: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) scramb.Rd:44: Escaped LaTeX specials: \&
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sim.dpp.modal.fast.Rd: spam
  sim.dpp.modal.fast.seq.Rd: spam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
checkRd: (-1) conifersIP.Rd:9: Lost braces; missing escapes or markup?
     9 | \code{conifersIP} {has following variables:}
       |                   ^
checkRd: (-1) conifersIP.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) conifersIP.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sync.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) sync.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dendro.varcov.Rd: varFunc, varIdent, lmeObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DendSer.Rd:50: Escaped LaTeX specials: \&
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.2Mb
    libs   1.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estim_sigma.Rd: estim_ncp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  denseFLMM.Rd: gamm, mgcv, gam, bam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  density_polygons.Rd: sf
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  densregion.Rd: contourplot, levelplot
  densregion.survfit.Rd: survfit
  denstrip.Rd: trellis.par.get
  denstrip.legend.Rd: trellis.par.get
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  start_bot_for_chat.Rd: telegram.bot
  use_ui.Rd: ui_line, ui_todo, ui_done, ui_oops, ui_info,
    ui_code_block, ui_stop, ui_warn, ui_yeah, ui_nope, ui_field,
    ui_value, ui_path, ui_code
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       4.8Mb
    extdata   2.1Mb
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) discrimination.Rd:19: Escaped LaTeX specials: \&
checkRd: (-1) fitdmm.Rd:59: Escaped LaTeX specials: \$
Package suggested but not available for checking: 'Rdonlp2'
checkRd: (-1) responses.Rd:68: Lost braces
    68 |         response.  See code{\link{makeDepmix}} for an example of how to use
       |                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  depmix.fit.Rd: solnp
  response-classes.Rd: nnet
  vcov.Rd: nlme
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) barriers.Rd:127: Escaped LaTeX specials: \$
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.N' '.Nmiss' '.Q1' '.Q3' '.factorN' '.factorNmiss' '.factorQ1'
  '.factorQ3' '.factormax' '.factormean' '.factormedian' '.factormin'
  '.factorsd' '.max' '.mean' '.median' '.min' '.sd'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pander.desctable.Rd: pandoc.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'RDCOMClient'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    1.8Mb
    help   1.7Mb
    libs   1.2Mb
checkRd: (-1) alpha.split.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{r}{vector for the proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                             ^
checkRd: (-1) designCTPB.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{r_set}{the matrix of proportion for each sub-population, r_1 is 1, r_i>r_{i+1}}
       |                                                                                ^
checkRd: (-1) phat.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{r}{vector for the proportion for each sub-population, r_1is 1, r_i>r_{i+1}}
       |                                                                            ^
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data          1.8Mb
    htmlwidgets   3.6Mb
checkRd: (-1) detour-shiny.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{expr}{an expression that generates a {detourr} widget}
       |                                            ^
checkRd: (-1) show_sage.Rd:80: Lost braces; missing escapes or markup?
    80 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter.Rd:67: Lost braces; missing escapes or markup?
    67 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_scatter_internal.Rd:65: Lost braces; missing escapes or markup?
    65 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) show_slice.Rd:76: Lost braces; missing escapes or markup?
    76 | supported using {crosstalk}. The set of interactive controls available are:
       |                 ^
checkRd: (-1) tour_aes.Rd:11: Lost braces; missing escapes or markup?
    11 | Variables are evaluated using {tidyselect} syntax.}
       |                               ^
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DetLTS.Rd: h.alpha.n
  OGKCStep.Rd: h.alpha.n
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.Rd: compiler_flags
  remote-reexports.Rd: ellipsis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MA_estimates.Rd: glmer, lmerControl, glmerControl
  REMB-class.Rd: glmer
  glimem.Rd: glmer, lmerControl, glmerControl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) mtaBin_next.Rd:27: Lost braces
    27 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur,n){0.2}.}
       |                                                                                                                                                                                                                                ^
checkRd: (-1) mtaBin_sim.Rd:30: Lost braces
    30 |   \item{s_1}{A function depending on the number of patients included used for adaptive randomization in plateau determination, only used if the estimation method chosen is "MTA-RA". The default function is function(n_cur){0.2}.}
       |                                                                                                                                                                                                                              ^
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) runContrasts.Rd:79: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:81: Lost braces in \itemize; meant \describe ?
checkRd: (-1) runContrasts.Rd:82: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AIC.dglars.Rd:47: Lost braces
    47 | \item{comp}{the measures of model complexity used to compute the measure of goodness-of-fit. It is equal to \code{npar} when code{complexity = "df"};}
       |                                                                                                                                  ^
checkRd: (-1) dglars.Rd:258: Lost braces
   258 |                 \item{\code{7}}{maximum number of solution points ('code{np}') reached.}
       |                                                                         ^
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) dHSIC-package.Rd:32: Lost braces
    32 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dHSIC-package.Rd:36: Lost braces
    36 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.Rd:84: Lost braces
    84 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.Rd:88: Lost braces
    88 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
checkRd: (-1) dhsic.test.Rd:124: Lost braces
   124 |   Gretton, A., K. Fukumizu, C. H. Teo, L. Song, B. Sch{\"o}lkopf and
       |                                                       ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                    ^
checkRd: (-1) dhsic.test.Rd:128: Lost braces
   128 |   Pfister, N., P. B{\"u}hlmann, B. Sch{\"o}lkopf and J. Peters (2017).
       |                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  class_to_regL1.Rd: rq
  class_to_rq.Rd: rq
  forwardSearch_regL1.Rd: lmsreg, rq, rq.fit.br, rq.fit.fnb
  regL1.Rd: rq, rq.fit.br, rq.fit.fnb
  regL1_het.Rd: rq, rq.fit.br, rq.fit.fnb
  summary.regL1.Rd: summary.rq, boot.rq
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  max_qEI.Rd: genoud
  qEGO.nsteps.Rd: genoud
  sampleFromEI.Rd: km
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) DIconvex.Rd:40: Lost braces; missing escapes or markup?
    40 |  {Paul Schneider <paul.schneider@usi.ch>}{}
       |  ^
checkRd: (-1) define.Rd:16: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:17-18: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) define.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) did_imputation.Rd:74: Lost braces; missing escapes or markup?
    74 | form average treatment effects for groups of {it}.
       |                                              ^
'LazyData' is specified without a 'data' directory
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc  10.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diffChr.Rd: style, num_colors
  diffCsv.Rd: style, num_colors
  diffDeparse.Rd: style, num_colors
  diffFile.Rd: style, num_colors
  diffPrint.Rd: style, num_colors
  diffStr.Rd: style, num_colors
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) sensitivitySamplerManual-DPMech-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual-DPMechNumeric-function-numeric-numeric-numeric-method.Rd:25: Lost braces
    25 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
checkRd: (-1) sensitivitySamplerManual.Rd:22: Lost braces
    22 | \item{k}{order statistic index in {1,...,\code{m}}.}
       |                                   ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  diffr.Rd: createWidget
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'gurobi'
checkRd: (-1) simulate_diff_tables.Rd:72: Lost braces; missing escapes or markup?
    72 |   {The Sharma-Song test} {\code{\link[DiffXTables]{sharma.song.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:74: Lost braces; missing escapes or markup?
    74 |   {The comparative chi-squared test} {\code{\link[DiffXTables]{cp.chisq.test}}}
       |   ^
checkRd: (-1) simulate_diff_tables.Rd:76: Lost braces; missing escapes or markup?
    76 |   {The heterogeneity test} {\code{\link[DiffXTables]{heterogeneity.test}}}
       |   ^
checkRd: (-1) difTID.Rd:185: Lost braces
   185 |  \code{\link[deltaPlotR]{deltaPlot}}, code{\link[deltaPlotR]{diagPlot}}, \code{\link{dichoDif}}
       |                                           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  itemPar1PL.rd: rasch
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DIME.Rd:272: Lost braces; missing escapes or markup?
   272 | \item{name}{the name of the model {"GNG", "iNUDGE","NUDGE"} where
       |                                   ^
checkRd: (-1) DRR-class.Rd:79: Lost braces; missing escapes or markup?
    79 | n^{1/3} up to sacrificing some accuracy, for details see
       |   ^
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'rrelaxiv'
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DirichletRegModel.Rd: update.Formula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  iact.Rd: multiESS
  mcmcdiag.Rd: multiESS
  metropdir.Rd: multiESS
  metropdir.adapt.Rd: multiESS
  msjd.Rd: multiESS
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expectreg.aft.Rd: rb, cdf.qp, cdf.bundle, summary.expectreg,
    plot.expectreg, predict.expectreg, resid.expectreg,
    fitted.expectreg, effects.expectreg
  modreg.Rd: control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) TempDisaggDGP.Rd:79: Escaped LaTeX specials: \&
checkRd: (-1) disaggregate.Rd:56: Escaped LaTeX specials: \&
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nelsonaalen_npdf.Rd: survfit
  npdf_cox.Rd: Surv
  plot.npdf.Rd: survfit.formula, plot.survfit
  survfit_npdf.Rd: survfit.formula
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) app_server.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{input, output, session}{Internal parameters for `{shiny}`.
       |                                                        ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  discrim-package.Rd: discrim_flexible
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) mc_attitudes.Rd:52: Lost braces
    52 | P\'{a}ez, A. (2013). Mapping travelers’ attitudes: does space matter?. Journal of Transport Geography, 26, 117-125. (https://doi.org/10.1016/j.jtrangeo.2012.09.002)
       |    ^
checkRd: (-1) mc_commute.csv.Rd:49: Lost braces
    49 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_long.Rd:74: Lost braces
    74 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_commute_wide.Rd:87: Lost braces
    87 | Whalen, K. E., P\'{a}ez, A., & Carrasco, J. A. (2013). Mode choice of university students commuting to school and the role of active travel. Journal of Transport Geography, 31, 132-142. (https://doi.org/10.1016/j.jtrangeo.2013.06.008)
       |                   ^
checkRd: (-1) mc_modality.Rd:50: Lost braces
    50 | Lavery, T., P\'{a}ez, A., & Kanaroglou, P.S. (2013). Driving out of choices: An investigation of transport modality in a university sample. Transportation Research Part A: Policy and Practice, 57:37-46 (https://doi.org/10.1016/j.tra.2013.09.010)
       |                ^
checkRd: (-1) cIndex.Rd:32: Lost braces; missing escapes or markup?
    32 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) cIndexCompRisks.Rd:31: Lost braces; missing escapes or markup?
    31 | [a_{q-1}, a_q) are available.
       |    ^
checkRd: (-1) dataCensoring.Rd:78: Escaped LaTeX specials: \&
checkRd: (-1) dataLong.Rd:170: Escaped LaTeX specials: \&
checkRd: (-1) dataLongCompRisksTimeDep.Rd:130: Escaped LaTeX specials: \&
checkRd: (-1) dataLongMultiSpell.Rd:123: Escaped LaTeX specials: \&
checkRd: (-1) dataLongTimeDep.Rd:96: Escaped LaTeX specials: \&
checkRd: (-1) estMargProb.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estMargProbCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurv.Rd:23: Lost braces; missing escapes or markup?
    23 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) estSurvCompRisks.Rd:24: Lost braces; missing escapes or markup?
    24 | a_2), ..., [a_{q-1}, a_q), [a_q, Inf).
       |               ^
checkRd: (-1) lifeTable.Rd:21: Lost braces; missing escapes or markup?
    21 | [a_0, a_1), [a_1, a_2), ..., [a_{q-1}, a_q) ("character vector")}
       |                                 ^
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.2Mb
'LazyData' is specified without a 'data' directory
checkRd: (-1) csv_to_disk.frame.Rd:56: Lost braces; missing escapes or markup?
    56 | strings, and you are encouraged to use {fasttime} to convert the strings to
       |                                        ^
checkRd: (-1) purrr_as_mapper.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{.f}{a normal function or purrr syntax function i.e. `~{ ...code...}`}
       |                                                             ^
checkRd: (-1) mess.Rd:28: Lost braces
    28 | Elith J., M. Kearney M., and S. Phillips, 2010. The art of modelling range-shifting species. \doi{10.1111/j.2041-210X.2010.00036.x}{Methods in Ecology and Evolution 1:330-342}.
       |                                                                                                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gbif.Rd: drawExtent, extent
  gmap.Rd: plotRGB
  mess.Rd: writeRaster
  predict.Rd: writeRaster
  randomPoints.Rd: Extent
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) store_in_DB.Rd:89: Lost braces
    89 | link{read_from_DB} function. Those parameters define rows and columns that will be returned.
       |     ^
checkRd: (-1) unite_two_DF.Rd:46: Lost braces; missing escapes or markup?
    46 | \code{data1.shared.var} and {data2.shared.var} must contain unique values within its own data frame.
       |                             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ds.Rd: AIC.ds, plot.ds
  print.summary.dsmodel.Rd: summary.ds
  summary.dsmodel.Rd: summary.ds, dht
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DistatisR-package.Rd: prettyGraphs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'distcomp/libs/x64/distcomp.dll':
  Found non-API call to R: 'NAMED'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
checkRd: (-1) booter.Rd:68: Escaped LaTeX specials: \&
checkRd: (-1) ci.booted.Rd:53: Escaped LaTeX specials: \&
checkRd: (-1) pbooter.Rd:57: Escaped LaTeX specials: \&
GNU make is a SystemRequirements.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dapply.Rd:27-30: Lost braces
    27 | udf <- function(x){
       |                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dists.Rd: betareg
  moments.Rd: betareg, gamlss, bamlss
  plot_dist.Rd: gamlss, bamlss, betareg, ggplot2
  plot_moments.Rd: gamlss, bamlss, betareg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) moranTest.Rd:37: Lost braces; missing escapes or markup?
    37 |   {M(theta)=-(log(y_1-y_0)+log(y_2-y_1)+...+log(y_m-y_m-1))}
       |   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dmrcoef-class.Rd: dgCMatrix-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mock-db-methods.Rd: dbConnect, dbListFields, dbWriteTable,
    dbRemoveTable, dbGetInfo, dbQuoteIdentifier
  mockdb.Rd: dbConnect
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  freqPlot.Rd: geom_violin
  scatterHex.Rd: ggrepel
  scatterPlot.Rd: ggrepel
  yPlot.Rd: geom_violin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) fadlad.Rd:30: Lost braces
    30 | \item{diffbin}{\code{(logical)}: Difference-based duration for discreet time (only applicabble to cases when \code{bin} is provided). If set to \code{TRUE}, single-interval taxa will \code{0} durations. Setting this argument to \code{FALSE} will add code{1} to the durations of all taxa.}
       |                                                                                                                                                                                                                                                               ^
checkRd: (-1) slice.Rd:27: Lost braces
    27 | Due to stratigraphic constraints, we can only process deep time data, when it is sliced to discrete bins. It is suggested that you do this separately for most of your analyses. This function is also used by the code{\link{divDyn}} function when \code{age} entries are provided.
       |                                                                                                                                                                                                                        ^
checkRd: (-1) tabinate.Rd:31: Lost braces
    31 | Setting both \code{bin} If \code{bin=NULL} and code{tax=NULL}, will run \code{FUN} on the entire dataset (no effect). Providing either \code{bin} or \code{tax} and keeping the other \code{NULL} will iterate \code{FUN} for every \code{bin} or \code{tax} entry (whichever is presented).
       |                                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calibrateDepth.Rd: unireg
  labDive-internal.Rd: unireg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  find.mle.Rd: subplex, ace, birthdeath
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'BOLTSSIRR'
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    include  15.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Changes to previous versions
    Minor changes
    Fixes
    Previous Versions
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cr.Rd: smooth.construct.cr.smooth.spec
  ps.Rd: smooth.construct.ps.smooth.spec
  smooth.construct.cb.smooth.spec.Rd: smooth.construct.ps.smooth.spec,
    smooth.construct.cr.smooth.spec,
    smooth.construct.tensor.smooth.spec
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  compare_category.data.frame.Rd: tbl_df
  compare_numeric.data.frame.Rd: tbl_df
  correlate.data.frame.Rd: grouped_df
  describe.data.frame.Rd: tbl_df, grouped_df, group_by
  describe.tbl_dbi.Rd: group_by
  diagnose.data.frame.Rd: tbl_df, grouped_df
  diagnose_category.data.frame.Rd: tbl_df, grouped_df
  diagnose_numeric.data.frame.Rd: tbl_df, grouped_df
  diagnose_outlier.data.frame.Rd: tbl_df, grouped_df
  diagnose_paged_report.data.frame.Rd: tbl_df
  diagnose_report.data.frame.Rd: tbl_df
  diagnose_sparese.data.frame.Rd: tbl_df
  diagnose_web_report.data.frame.Rd: tbl_df
  eda_paged_report.data.frame.Rd: tbl_df
  eda_report.data.frame.Rd: tbl_df
  eda_web_report.data.frame.Rd: tbl_df
  find_na.Rd: tbl_df
  find_outliers.Rd: tbl_df
  find_skewness.Rd: tbl_df
  imputate_na.Rd: tbl_df
  imputate_outlier.Rd: tbl_df
  normality.data.frame.Rd: tbl_df, group_by
  normality.tbl_dbi.Rd: group_by
  overview.Rd: tbl_df
  plot_bar_category.data.frame.Rd: tbl_df, grouped_df
  plot_box_numeric.data.frame.Rd: tbl_df, grouped_df
  plot_correlate.data.frame.Rd: tbl_df
  plot_hist_numeric.data.frame.Rd: tbl_df, grouped_df
  plot_normality.data.frame.Rd: tbl_df
  plot_outlier.data.frame.Rd: tbl_df
  plot_qq_numeric.data.frame.Rd: tbl_df, grouped_df
  target_by.data.frame.Rd: tbl_df, grouped_df
  target_by.tbl_dbi.Rd: grouped_df
  transformation_paged_report.Rd: tbl_df
  transformation_report.Rd: tbl_df
  transformation_web_report.Rd: tbl_df
  univar_category.data.frame.Rd: tbl_df
  univar_numeric.data.frame.Rd: tbl_df
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dma.Rd:47: Lost braces; missing escapes or markup?
    47 | When y_t is controlled, only y_{t-delay-1} and before 
       |                                ^
checkRd: (-1) dma.Rd:64: Lost braces; missing escapes or markup?
    64 |                  estimate of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:66: Lost braces; missing escapes or markup?
    66 |                  variance of theta_{j-1} for model k at t}
       |                                    ^
checkRd: (-1) dma.Rd:68: Lost braces; missing escapes or markup?
    68 |                  estimate of theta_{j-1} at t}
       |                                    ^
checkRd: (-1) dma.Rd:70: Lost braces; missing escapes or markup?
    70 |                  variance of thetahat_{j-1} at t}
       |                                       ^
checkRd: (-1) dca.Rd:24: Lost braces; missing escapes or markup?
    24 | \eqn{neglinks_{ij} = 1} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) dca.Rd:26: Lost braces; missing escapes or markup?
    26 | \eqn{neglinks_{ij} = 0} means chunklet \code{i} and chunklet {j}
       |                                                              ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |            ^
checkRd: (-1) rca.Rd:57: Lost braces; missing escapes or markup?
    57 |       e.g. {1, 3, 7} and {4, 6}, might belong to the
       |                          ^
checkRd: (-1) scale_color_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) scale_fill_dMod.Rd:10: Lost braces
    10 | \item{...}{arguments goint to code{scale_color_manual()}}
       |                                   ^
checkRd: (-1) trust.Rd:103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:104: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:107-108: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:109-110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:115-122: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:123-126: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:127: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:128-131: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:132-133: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:134-135: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:136-138: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) trust.Rd:139-141: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EstimateDMQ.rd: DEoptim
  fn.DEoptim.Rd: DEoptim
  fn.solnp.Rd: solnp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dm_examine_cardinalities.Rd: as_tibble
  dm_examine_constraints.Rd: as_tibble
  dm_from_con.Rd: src
  dm_zoom_to.Rd: nest_join
  json_nest.Rd: tidyr_tidy_select
  json_pack.Rd: tidyr_tidy_select
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  tractography.Rd: rgl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                 ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                             ^
checkRd: (-1) outliers.ranking.Rd:142: Lost braces; missing escapes or markup?
   142 |   max ( 0, ( |g_{y,i}| - |g_{x,i}| ) / ( |g_{y,i}| + |g_{x,i}| ) ),
       |                                                         ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |           ^
checkRd: (-1) outliers.ranking.Rd:143: Lost braces; missing escapes or markup?
   143 |   where g_{y,i} and g_{x,i} are the two groups involved in the merge at
       |                       ^
checkRd: (-1) outliers.ranking.Rd:144: Lost braces; missing escapes or markup?
   144 |   step i, and g_{x,i} is the group which X belongs to. Note that if X
       |                 ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kNN.Rd: knn, knn1, knn.cv
  rpartXse.Rd: rpart, prune.rpart
  rt.prune.Rd: rpart, prune.rpart
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) setCPT.O.Rd:85: Lost braces; missing escapes or markup?
    85 | statespace {0,1,2}, which this is *not* checked anywhere. Thus, if
       |            ^
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
Warning: Some observed peaks are below the given detection threshold and are set to 0
> p <- mixpar(rho = list(30), eta = list(34), xi = list(0.08),
+             phi = list(c(K1 = 0.71, K3 = 0.1, K2 = 0.19)))
> l <- logL(mixHp)
> l(p)
[1] -324.0419
> 
> 
> 
> cleanEx()
> nameEx("map.genotypes")
> ### * map.genotypes
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: map.genotypes
> ### Title: Maximum posterior genotypes of unknown contributors
> ### Aliases: map.genotypes
> 
> ### ** Examples
> 
> data(MC18, USCaucasian, SGMplusDyes)
> mix <- DNAmixture(list(MC18), k = 3, K = "K1", C = list(50), database = USCaucasian)
Warning: Some observed peaks are below the given detection threshold and are set to 0
> p <- mixpar(rho = list(30), eta = list(30), xi = list(0.07),
+             phi = list(c(K1 = 0.7, U1 =0.2, U2 = 0.1)))
> ## Inlude the peak height information
> setPeakInfo(mix, p)
> ## Marginally best genotypes for contributor U1
> mpU1 <- map.genotypes(mix, pmin = 0.01, U = 1, type = "seen", markers = "D16S539")
======== End of example output (where/before crash/hang up occured ?) ========
Specified C++11: please drop specification unless essential
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  deepAFT.Rd: survreg
  deepSurv.Rd: survreg
  dnn-package.Rd: coxph, survival
  print.Rd: survreg
  survfit.deepAFT.Rd: survfit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dnr.Rd:12: Escaped LaTeX specials: \#
checkRd: (-1) beetle.Rd:13: Lost braces; missing escapes or markup?
    13 |     \item{\code{x}}{dose (log base 10 CS2mgl^{-1})}
       |                                              ^
Specified C++11: please drop specification unless essential
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  to_miniature.Rd: image_border, pdf_convert, image_read
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  checks.Rd: rcmdcheck
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs   1.7Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  corrPlot.Rd: levelplot
  fac.design.Rd: factorize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package which this enhances but not available for checking: 'gurobi'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  functionsFromDoEbase.Rd: DoE.base
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) rsmformula.Rd:96: Lost braces
    96 |       URL{http://www.jstatsoft.org/v32/i07/}.
       |          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  rsmformula.Rd: rsm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doFuture.Rd: foreach, future
  grapes-dofuture-grapes.Rd: %dopar%
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  bootAverageDominanceAnalysis.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) py_select_interpreter.Rd:5: Lost braces; missing escapes or markup?
     5 | \title{Tell {reticulate} to use Python Conda version available on Domino Data Lab.}
       |             ^
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    data      1.9Mb
    extdata   2.3Mb
checkRd: (-1) redisWorker.Rd:56: Lost braces; missing escapes or markup?
    56 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
checkRd: (-1) startLocalWorkers.Rd:54: Lost braces; missing escapes or markup?
    54 | You can increase it by including a {timeout=n} argument value.
       |                                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  redisDelete.Rd: hiredis
  redisGet.Rd: hiredis
  redisSet.Rd: hiredis
  registerDoRedis.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    New features
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  doRNG-package.Rd: RNGseq
  grapes-dorng-grapes.Rd: foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'gurobi'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dosresmeta-package.Rd: mvmeta, mvmeta-package, mvmeta.fit, blup
  dosresmeta.Rd: mvmeta.fit, mvmeta
  dosresmeta.control.Rd: mvmeta.control
  dosresmetaObject.Rd: mvmetaObject
  mlprof.fun.Rd: mvmeta.control, mvmeta.fit
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'dotCall64/libs/x64/dotCall64.dll':
  Found non-API call to R: 'NAMED'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) dot.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot_sst.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) PMLE.Weibull.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.Weibull.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.loglogistic.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.loglogistic.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
checkRd: (-1) PMLE.lognormal.Rd:20: Lost braces; missing escapes or markup?
    20 |   \item{D1}{Randomize the intial value if |mu_h-mu_{h+1}|>D1}
       |                                                    ^
checkRd: (-1) PMLE.lognormal.Rd:21: Lost braces; missing escapes or markup?
    21 |   \item{D2}{Randomize the intial value if |sigma_h-sigma_{h+1}|>D2}
       |                                                          ^
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sha_url.Rd: digest
  source_url.Rd: digest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.2Mb
checkRd: (-1) downscale.Rd:9: Lost braces; missing escapes or markup?
     9 | \item{occupancies}{Either a data frame containing two columns or an object of class \code{"upgrain"} from the \code{\link{upgrain}} function. If using a data frame the first column must be the grain sizes (cell area in squared units e.g. km^{2}). The second column is the proportion of occupancies at each grain size.}
       |                                                                                                                                                                                                                                                  ^
checkRd: (-1) ensemble.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
checkRd: (-1) hui.downscale.Rd:13: Lost braces; missing escapes or markup?
    13 | \item{new.areas}{vector of grain sizes as cell area (in same units as cell.width but squared e.g. km^{2}) at fine scales for model prediction.}
       |                                                                                                      ^
checkRd: (-1) predict.downscale.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{new.areas}{vector of grain sizes (in squared units e.g. km^{2}) for which area of occupancy will be predicted.}
       |                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  downscale.Rd: mpfr
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  correlationTest.Rd: phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  chron.ci.Rd: boot, boot.ci
  latexify.Rd: captureOutput
  pass.filt.Rd: butter, cheby1, filtfilt
  rasterPlot.Rd: readPNG
  uuid.gen.Rd: digest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'dplR/libs/x64/dplR.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
File 'dplyr/libs/x64/dplyr.dll':
  Found non-API calls to R: 'LEVELS', 'PRVALUE',
    'R_shallow_duplicate_attr', 'SET_PRCODE', 'SET_PRENV',
    'SET_PRVALUE'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  datapackage_init.Rd: toJSON, export
  datapackage_install.Rd: import
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) confint.dr4pl.Rd:49: Escaped LaTeX specials: \&
checkRd: (-1) gof-dr4pl.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) vcov.dr4pl.Rd:61: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  new_cache.Rd: storr_rds
  recover_cache.Rd: storr_environment
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) EDcomp.Rd:88: Escaped LaTeX specials: \&
checkRd: (-1) LL.4.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) W4.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) algae.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) anova.drc.Rd:40: Escaped LaTeX specials: \&
checkRd: (-1) deguelin.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) gompertz.Rd:55: Escaped LaTeX specials: \&
checkRd: (-1) hatvalues.drc.Rd:43: Lost braces
    43 |   emph{Generalized Linear Models}, 
       |       ^
checkRd: (-1) hatvalues.drc.Rd:44: Escaped LaTeX specials: \&
checkRd: (-1) llogistic.Rd:64: Escaped LaTeX specials: \&
checkRd: (-1) modelFit.Rd:36: Escaped LaTeX specials: \&
checkRd: (-1) weibull1.Rd:67: Escaped LaTeX specials: \&
checkRd: (-1) excalibur.Rd:18: Lost braces; missing escapes or markup?
    18 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
checkRd: (-1) festuca.Rd:16: Lost braces; missing escapes or markup?
    16 |     \item{\code{GR}}{a numeric vector: germination rates in d^{-1}}
       |                                                               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ED.drcte.Rd: drm
  drmte.Rd: LL.4, LL.5, W1.4, getMeanFunctions, drmc
  drmteControl.Rd: drm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) generate_individual_graphs.Rd:11: Lost braces
    11 | code{\link[DrDimont]{compute_correlation_matrices}}}
       |     ^
checkRd: (-1) dreamerplot.Rd:53: Lost braces; missing escapes or markup?
    53 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
checkRd: (-1) posterior.Rd:70: Lost braces; missing escapes or markup?
    70 | a dose returns the plot of pr(trt_dose - trt_{reference_dose} | data).}
       |                                              ^
Specified C++11: please drop specification unless essential
checkRd: (-1) predict.drf.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:34-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:36-37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:38-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:40-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.drf.Rd:44: Lost braces in \itemize; meant \describe ?
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  findRoots.Rd: nleqslv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   3.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  RNAseqdata.Rd: rlog, vst
  itemselect.Rd: lmFit, eBayes, topTable, DESeqDataSetFromMatrix,
    DESeq, results
  microarraydata.Rd: normalizeBetweenArrays
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) popsize.Rd:70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize.Rd:75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) popsize_cond.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dr.weights.Rd: cov.rob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DR.SC.Rd: Seurat
  drscPlot.Rd: DimPlot
  readscRNAseq.Rd: ReadMtx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    appinformation   4.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Survey.LT-class.Rd: make.design
  Survey.PT-class.Rd: make.design
  dsims-package.Rd: make.region, make.design
  make.density.Rd: make.region
  make.ds.analysis.Rd: ds
  make.population.description.Rd: make.region
  make.simulation.Rd: make.design, make.region
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DSLiteConnection-class.Rd: DSConnection-class
  DSLiteDriver-class.Rd: DSDriver-class
  DSLiteResult-class.Rd: DSResult-class
  getDSLiteData.Rd: DSConnection-class
  setupCNSIMTest.Rd: datashield.login
  setupDASIMTest.Rd: datashield.login
  setupDATASETTest.Rd: datashield.login
  setupDISCORDANTTest.Rd: datashield.login
  setupDSLiteServer.Rd: datashield.login
  setupSURVIVALTest.Rd: datashield.login
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'dsBaseClient'
checkRd: (-1) dsm_varprop.Rd:67: Lost braces
    67 | parameter uncertainty. See Wood, Pya & S{\"a}fken (2016) for more
       |                                         ^
checkRd: (-1) dsm_varprop.Rd:100: Lost braces
   100 | Wood, S.N., Pya, N. and S{\"a}fken, B. (2016) Smoothing parameter and model
       |                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  check.cols.Rd: mrds
  dsm.cor.Rd: residuals.gam
  dsm_cor.Rd: residuals.gam
  dsm_varprop.Rd: gamObject
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  OpalConnection-class.Rd: DSConnection-class
  OpalDriver-class.Rd: DSDriver-class
  OpalResult-class.Rd: DSResult-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Voss.density.Rd: dLBA, ddiffusion, dwiener
  estDstarM.Rd: DEoptim.control, DEoptim
  estND.Rd: DEoptim.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Onoue.Friberg.Rd: pomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) DTDAcif.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTDAcif.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) efron.petrosian.Rd:22: Lost braces
    22 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
checkRd: (-1) lynden.Rd:21: Lost braces
    21 |    \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                                ^
checkRd: (-1) shen.Rd:24: Lost braces
    24 |   \item{error}{ Numeric value. Maximum pointwise error when estimating the density associated to X (f) in two consecutive steps. If this is missing, it is $1e{-06}$.}
       |                                                                                                                                                               ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) applied_crm.Rd:64: Lost braces; missing escapes or markup?
    64 | The empiric model is specified as F(d, beta) = d^{exp(beta)}. The logistic model is
       |                                                  ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  arrange.dtplyr_step.Rd: arrange
  count.dtplyr_step.Rd: count
  distinct.dtplyr_step.Rd: distinct
  filter.dtplyr_step.Rd: arrange
  group_by.dtplyr_step.Rd: group_by, ungroup
  group_modify.dtplyr_step.Rd: group_map, group_modify
  intersect.dtplyr_step.Rd: union_all
  lazy_dt.Rd: collect, pull, select
  left_join.dtplyr_step.Rd: left_join, right_join, inner_join,
    full_join, anti_join, semi_join
  mutate.dtplyr_step.Rd: mutate
  relocate.dtplyr_step.Rd: relocate
  rename.dtplyr_step.Rd: rename, rename_with
  select.dtplyr_step.Rd: select
  slice.dtplyr_step.Rd: slice
  summarise.dtplyr_step.Rd: summarise
  transmute.dtplyr_step.Rd: transmute
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Mena.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Mena.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) count_subgroup.Rd:29: Lost braces; missing escapes or markup?
    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
checkRd: (-1) p_count_subgroup.Rd:29: Lost braces; missing escapes or markup?
    29 | {.subgroup} for the subgroup column name and \{.name\} for the subgroup
       | ^
Found the following HTML validation problems:
p_mutate.html:56:1 (p_mutate.Rd:17): Warning: trimming empty <dt>
p_rename.html:56:1 (p_rename.Rd:17): Warning: trimming empty <dt>
p_select.html:56:1 (p_select.Rd:17): Warning: trimming empty <dt>
p_transmute.html:56:1 (p_transmute.Rd:17): Warning: trimming empty <dt>
p_ungroup.html:56:1 (p_ungroup.Rd:21): Warning: trimming empty <dt>
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dataTableOutput.Rd: shinyWidgetOutput
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
checkRd: (-1) DTWUMI_1gap_imputation.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) DTWUMI_1gap_imputation.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DurgaPlot.Rd: RColorBrewer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cfaHB.Rd: lavaan, cfa, model.syntax
  cfaOne.Rd: lavaan, cfa, model.syntax
  equivTest.Rd: lavaan
  exactFit.Rd: lavaan, cfa, model.syntax
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'cmdstanr'
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    data   9.3Mb
Problems with news in 'NEWS.md':
No news entries found.
checkRd: (-1) dyadic_similarity.Rd:27: Lost braces; missing escapes or markup?
    27 |      For example, the order {a, b, c} implies that a > b, a  > c, and b > c.
       |                             ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'lle'
'LazyData' is specified without a 'data' directory
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                          ^
checkRd: (-1) generate_kinetics.Rd:57: Lost braces; missing escapes or markup?
    57 | By default, sampled from {-1, 1} with probabilities {.25, .75}.
       |                                                     ^
checkRd: (-1) new_log_level.Rd:19: Lost braces; missing escapes or markup?
    19 | \item{log_style}{is a {crayon::style()} that will colorize
       |                       ^
checkRd: (-1) new_log_level.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{msg_style}{is a {crayon::style()} style that will gray scale the
       |                       ^
checkRd: (-1) sys_context.Rd:22: Lost braces; missing escapes or markup?
    22 | \item{"sysname"} : {The operating system name.}
       |                    ^
checkRd: (-1) sys_context.Rd:23: Lost braces; missing escapes or markup?
    23 | \item{"release"} : {The OS release.}
       |                    ^
checkRd: (-1) sys_context.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{"version"} : {The OS version.}
       |                    ^
checkRd: (-1) sys_context.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{"nodename"} : {A name by which the machine is known on the network (if any).}
       |                     ^
checkRd: (-1) sys_context.Rd:26: Lost braces; missing escapes or markup?
    26 | \item{"machine"} : {A concise description of the hardware, often the CPU type.}
       |                    ^
checkRd: (-1) sys_context.Rd:27: Lost braces; missing escapes or markup?
    27 | \item{"login"} : {The user's login name, or "unknown" if it cannot be ascertained.}
       |                  ^
checkRd: (-1) sys_context.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{"user"} : {The name of the real user ID, or "unknown" if it cannot be ascertained.}
       |                 ^
checkRd: (-1) sys_context.Rd:29: Lost braces; missing escapes or markup?
    29 | \item{"r-ver"} : {R Version in (major).(minor) format.}
       |                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  new_fmt_layout.Rd: crayon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Produc.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Produc.Rd:22: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:33: Escaped LaTeX specials: \&
checkRd: (-1) NKI-breast-cancer-clinical-data.Rd:37: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:26: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:31: Escaped LaTeX specials: \&
checkRd: (-1) WBC-follow-up-data.Rd:41: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:13: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:14: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:30: Escaped LaTeX specials: \&
checkRd: (-1) WBC-measurements-data.Rd:40: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dynr.cook.Rd: autoplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) dynsim.Rd:48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:50-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dynsim.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dynsimGG.Rd: scale_colour_brewer, discrete_scale
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mapdf.Rd: map
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Specified C++11: please drop specification unless essential
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   1.7Mb
checkRd: (-1) monitor_long_1d.Rd:33: Lost braces
    33 | If \code{side="upward"}{apply control charts that aim to detect upward shifts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:34: Lost braces
    34 | If \code{side="downward"}{apply control charts that aim to detect downward shifts.} \cr
       |                          ^
checkRd: (-1) monitor_long_1d.Rd:35: Lost braces
    35 | If \code{side="both"}{apply control charts that aim to detect shifts in both sides}}
       |                      ^
checkRd: (-1) monitor_long_1d.Rd:38: Lost braces
    38 | If \code{chart="CUSUM"}{apply CUSUM charts.} \cr
       |                        ^
checkRd: (-1) monitor_long_1d.Rd:39: Lost braces
    39 | If \code{chart="EWMA"}{apply EWMA charts.}}
       |                       ^
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
checkRd: (-1) AM.Rd:95-98: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:99-102: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:123-125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:126-133: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:134-135: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:136-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:163-165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:166-173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:174-176: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:177-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AM.Rd:179-180: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:48-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:53-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:55-56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) MHLS.Rd:75: Lost braces; missing escapes or markup?
    75 | From the initial values, \code{B0} and {S0}, \code{\link{MHLS}} draws \code{beta} and \code{subgrad} samples.
       |                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) plot.earlyR.Rd:34-46: Lost braces
    34 | if (require(incidence)) {
       |                         ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) surrogates_ews.Rd:31: Lost braces
    31 | \item{span}{parameter that controls the degree of smoothing (numeric between 0 and 100, Default 25). see more on loess{stats}}
       |                                                                                                                       ^
checkRd: (-1) surrogates_ews.Rd:33: Lost braces
    33 | \item{degree}{the degree of polynomial to be used for when loess fitting is applied, normally 1 or 2 (Default). see more on loess{stats}}
       |                                                                                                                                  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  earth.Rd: rlm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'earth/libs/x64/earth.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_earthtones.Rd: get_map, pam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cens_margin_to.Rd: group_by, summarize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.5/easyDifferentialGeneCoexpression.Rcheck/00install.out' for details.
checkRd: (-1) ArrayToNc.Rd:30-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:39-50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ArrayToNc.Rd:51-76: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EasyData.Rd: SSBtoolsData
  PTwrap.Rd: runArgusBatchFile, createArgusInput
  ProtectTable.Rd: GaussSuppression, protectTable,
    protect_linked_tables, primarySuppression, FindDimLists,
    FindTableGroup, Stack, AutoSplit, runArgusBatchFile,
    createArgusInput
  ProtectTable1.Rd: FindTableGroup, protectTable,
    protect_linked_tables, runArgusBatchFile, primarySuppression,
    makeProblem, HierarchicalGroups, FactorLevCorr, FindDimLists,
    FindCommonCells
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Package which this enhances but not available for checking: 'gurobi'
checkRd: (-1) write_spss.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:32-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:35-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) write_spss.Rd:46: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.Rd: paircomp
  envirosound.Rd: paircomp
  soundquality.Rd: paircomp
  winetaste.Rd: paircomp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cumhaz_splines.Rd: msfit
  ebmstate-package.Rd: survival, mstate
  msfit_generic.Rd: msfit, mstate
  probtrans_ebmstate.Rd: probtrans
  probtrans_fft.Rd: probtrans
  probtrans_mstate.Rd: probtrans, mstate
  unique_paths.Rd: transMat, msprep
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) OCC1950.Rd:64: Lost braces
    64 |     \doi{10.18128/D010.V10.0}{IPUMS USA: Version 10.0 [dataset]. Minneapolis, MN: IPUMS}. 
       |                              ^
checkRd: (-1) Oil.Rd:45: Lost braces
    45 |       code{pt-pt-1} on a constant
       |           ^
checkRd: (-1) breaches.Rd:70-74: Lost braces
    70 |     \code{breach_end}{
       |                      ^
checkRd: (-1) breaches.Rd:75-78: Lost braces
    75 |     \code{year}{
       |                ^
checkRd: (-1) nuclearWeaponStates.Rd:82-92: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:93-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:104-127: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:128-140: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:141-150: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:151-161: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:162-172: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:173-191: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nuclearWeaponStates.Rd:192-219: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  USFinanceIndustry.Rd: readNIPA
  USstateAbbreviations.Rd: readUSstateAbbreviations,
    grepNonStandardCharacters, subNonStandardCharacters
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) BoxCox.Rd:266-269: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:270-275: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:276-284: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) BoxCox.Rd:285-293: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Newdata.Rd:88-91: Lost braces
    88 |   {replace \code{newDat[, x2]}:  
       |   ^
checkRd: (-1) interpPairs.Rd:120: Lost braces
   120 |     environment / list to use with code{object},
       |                                        ^
checkRd: (-1) matchQuote.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:75-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:81-88: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) matchQuote.Rd:89-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate.bic.glm.Rd:81-91: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:92-103: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.bic.glm.Rd:104-108: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:79-83: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:84-95: Lost braces in \itemize; meant \describe ?
checkRd: (-1) simulate.glm.Rd:96-100: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  logVarCor.Rd: pdLogChol
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) e_pictorial.Rd:57-58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) e_pictorial.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) nesting.Rd:48: Lost braces
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |  ^
checkRd: (-1) nesting.Rd:48: Lost braces; missing escapes or markup?
    48 | `{itemStyle: {color: 'red', fontBold: 'bold'}}`.
       |              ^
checkRd: (-1) nesting.Rd:51: Lost braces; missing escapes or markup?
    51 | `{symbolSize: 4}`.
       |  ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  echartsNJSON.Rd: jsonlite
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  navigation.hac.Rd: bearingRhumb, distVincentyEllipsoid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ecipex.Rd: count.elements
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EBVstats.Rd: cellStats
  gaugeIndicator.Rd: list_lsm, calculate_lsm
  plot.EBVstats.Rd: tibble
  plot.Indicator.Rd: tibble
  sampleIndicator.Rd: list_lsm, sample_lsm
  tabuleRaster.Rd: rasterDT
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cgr.Rd: glasso
  plot.cgr.Rd: gplot
  stackedsdm.Rd: mvabund
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs  11.3Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coalesc_abc.Rd: abc
  plot_comm.Rd: ggplot2-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) ecolRxC.Rd:161-166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:167-175: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:176-178: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:179-185: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:186-192: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:193-201: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:202-208: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:209-216: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ecolRxC.Rd:217-221: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  calcres.Rd: ode
  ecosim-package.Rd: calc.stoich.coef, ode
  process-class.Rd: calc.stoich.coef
  system-class.Rd: ode
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  glenan.Rd: envelope
  glomel.Rd: envelope
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  coef.ecpc.Rd: Surv
  cv.ecpc.Rd: Surv
  ecpc.Rd: Surv
  postSelect.Rd: Surv
  predict.ecpc.Rd: Surv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) transformFitness.Rd:25: Lost braces; missing escapes or markup?
    25 | minimization (most others). This function computes a factor from {-1, 1} for
       |                                                                  ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  filter_case_condition.Rd: dplyr_data_masking
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) read.edf.Rd:30: Lost braces
    30 | Kemp B., V\"{a}rri, A., Rosa, A.C., Nielsen, K.D. and Gade, J. (1992).
       |             ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    TODO:
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eval_posterior_eDITH.Rd: aggregate_river
  posterior_pred_sim_eDITH.Rd: aggregate_river, DHARMa
  run_eDITH_BT.Rd: aggregate_river, river_to_AEM, runMCMC,
    createBayesianSetup, dtrunc, MAP, getCredibleIntervals,
    gelmanDiagnostics
  run_eDITH_BT_joint.Rd: aggregate_river, river_to_AEM, runMCMC,
    createBayesianSetup, dtrunc, MAP, getCredibleIntervals,
    gelmanDiagnostics
  run_eDITH_optim.Rd: aggregate_river, river_to_AEM
  run_eDITH_optim_joint.Rd: aggregate_river, river_to_AEM
  run_eDITH_single.Rd: aggregate_river
  sampling_strategy_direct.Rd: aggregate_river
  sampling_strategy_eDNA.Rd: paths_river
  wigger.Rd: extract_river
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.lp.mip.Rd: make.lp
  editrules.plotting.Rd: as.igraph
  editrules_package.Rd: as.igraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  USData.Rd: xts
  USRecessions.Rd: zoo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                ^
checkRd: (-1) edm2psd.Rd:10: Lost braces; missing escapes or markup?
    10 | \item{D}{A matrix in the set D_{n}^{-}.}
       |                                    ^
checkRd: (-1) items_ordered_eclsk_atl.Rd:23: Lost braces; missing escapes or markup?
    23 | \item \code{P4SRS10}: Keep working at something until {he/she} is finished?
       |                                                       ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eegfilter.Rd: butter, fir1, filtfilt, freqz_plot
  eegpsd.Rd: imagebar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eem_biological_index.Rd: interp2
  eem_coble_peaks.Rd: interp2
  eem_fluorescence_index.Rd: interp2
  eem_humification_index.Rd: interp2
  eem_peaks.Rd: interp2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  crosstabplot.Rd: mosaic
  gelmansim.Rd: sim
  moves_calc.Rd: data.table
  profpoly.Rd: geom_polygon
  profpoly.data.Rd: geom_polygon
  theme_dpi.Rd: theme_bw
  theme_dpi_map.Rd: theme_bw
  theme_dpi_map2.Rd: theme_bw
  theme_dpi_mapPNG.Rd: theme_bw
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) eesim.Rd:148-151: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:152-155: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) eesim.Rd:156-158: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EESPCACV.Rd: PMA
  RifleInit.Rd: rifle
  RiflePCACV.Rd: rifle, PMA
  TpowerPCACV.Rd: PMA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  OMEGA.Rd: schmid
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  regex.search.Rd: read.fasta
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  effCoef.Rd: get_parameters
  effect.Rd: gls, multinom, polr, lmer, glmer, svyglm, xyplot,
    densityplot, barchart
  effectsTheme.Rd: trellis.device, trellis.par.set
  plot.effect.Rd: sequential_hcl, lattice, xyplot, densityplot,
    print.trellis
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  efs_eval.Rd: roc.test
  ensemble_fs.Rd: randomForest, cforest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following significant warnings:
  polychoric_matrix.c:337:35: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
See 'd:/Rcompile/CRANpkg/local/4.5/EGAnet.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  acor.Rd: zoo
  egcm-package.Rd: adf.test, pp.test
  egcm.Rd: zoo, rlm, adf.test, pp.test
  egcm.set.default.i1test.Rd: adf.test, pp.test
  pgff.test.Rd: adf.test
  ur_power.Rd: adf.test, pp.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'eggCountsExtra'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotCounts.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as_tibble.egor.Rd: tbl_svy, as_tibble, as_survey
  egor.Rd: as_tibble, tibble, tbl_svy
  rowlist.Rd: tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotFluxHistBoot.Rd: printFluxUnitCheatSheet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Constants.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) Constants.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) boxConcMonth.Rd:24: Lost braces; missing escapes or markup?
    24 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxQTwice.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{las}{numeric in {0,1,2,3}; the style of axis labels, see ?par}
       |                       ^
checkRd: (-1) boxResidMonth.Rd:17: Lost braces; missing escapes or markup?
    17 | \item{las}{numeric in {0,1,2,3}; the style of axis labels}
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  join_vars_to_ontol.Rd: tidygraph
  metavariable_agg.Rd: tidygraph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       5.1Mb
    extdata   5.1Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EHyClus.Rd: smooth.terms
  generate_indices.Rd: smooth.terms
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  lr_ancova.Rd: jags
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fit_mean.Rd:54: Lost braces
    54 | \code{t_optims}{optimal parametrizations}
       |                ^
checkRd: (-1) fit_mean.Rd:55: Lost braces
    55 | \code{G_optims}{optimal rotations}
       |                ^
checkRd: (-1) fit_mean.Rd:56: Lost braces
    56 | \code{b_optims}{optimal scalings}
       |                ^
checkRd: (-1) fit_mean.Rd:57: Lost braces
    57 | \code{n_optims}{optimal re-normalization}
       |                ^
checkRd: (-1) fit_mean.Rd:58: Lost braces
    58 | \code{n_iter}{number of iterations until convergence}
       |              ^
checkRd: (-1) docs_delete_by_query.Rd:47: Lost braces; missing escapes or markup?
    47 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
checkRd: (-1) docs_update_by_query.Rd:48: Lost braces; missing escapes or markup?
    48 | as a document at .tasks/task/${taskId}. This is yours to keep or remove
       |                               ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) AuditErrors.Rd:40: Escaped LaTeX specials: \_
checkRd: (-1) compute.audit.errors.Rd:24: Escaped LaTeX specials: \_
checkRd: (-1) compute.stark.t.Rd:35: Escaped LaTeX specials: \_ \_
checkRd: (-1) find.q.Rd:44: Escaped LaTeX specials: \_
checkRd: (-1) find.q.Rd:56: Escaped LaTeX specials: \_
checkRd: (-1) stark.test.Rd:50: Escaped LaTeX specials: \$
checkRd: (-1) stark.test.Rd:101: Escaped LaTeX specials: \$ \$
checkRd: (-1) tri.audit.sim.Rd:47: Escaped LaTeX specials: \_
checkRd: (-1) tri.calc.sample.Rd:34: Escaped LaTeX specials: \_
checkRd: (-1) tri.sample.Rd:34: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:36: Escaped LaTeX specials: \$
checkRd: (-1) tri.sample.Rd:49: Escaped LaTeX specials: \$
checkRd: (-1) weight.function.Rd:16: Escaped LaTeX specials: \_
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dirichlet_tree.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) electData.Rd:16: Lost braces; missing escapes or markup?
    16 | Variables: \code{id}  = {identification number},
       |                         ^
checkRd: (-1) electData.Rd:17: Lost braces; missing escapes or markup?
    17 | \code{state} = {state}, \code{age} = age in years on a shifted scale (current age minus 70),
       |                ^
checkRd: (-1) summary.elect.Rd:25: Lost braces; missing escapes or markup?
    25 |  TRUE for output on start-state totals e_{r.} (for \code{S}>0)
       |                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_aws_terrain.Rd: st_crs
  get_elev_point.Rd: st_crs
  get_elev_raster.Rd: st_crs
  get_opentopo.Rd: st_crs
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Error(s) in re-building vignettes:
--- re-building 'ElevDistr.Rmd' using rmarkdown

Quitting from lines 38-45 [unnamed-chunk-5] (ElevDistr.Rmd)
Error: processing vignette 'ElevDistr.Rmd' failed with diagnostics:
[rast] file does not exist: /vsicurl/https://os.zhdk.cloud.switch.ch/envicloud/chelsa/chelsa_V2/GLOBAL/climatologies/1981-2010/bio/CHELSA_gst_1981-2010_V.2.1.tif
--- failed re-building 'ElevDistr.Rmd'

SUMMARY: processing the following file failed:
  'ElevDistr.Rmd'

Error: Vignette re-building failed.
Execution halted
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) prepareInitsLM.Rd:21-23: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  elisa_batch-class.Rd: nls.lm
  elisa_batch.Rd: nls.lm
  elisa_plate-class.Rd: nls.lm
  elisa_plate.Rd: nls.lm
  elisa_run-class.Rd: nls.lm
  elisa_run.Rd: nls.lm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'ellipsis/libs/x64/ellipsis.dll':
  Found non-API calls to R: 'PRVALUE', 'Rf_findVarInFrame3'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) elliptic-package.Rd:92: Lost braces
    92 |     J. Kotus and M. Urb\'{a}nski 2003.  \emph{Hausdorff dimension and Hausdorff
       |                          ^
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) elo.run.Rd:80: Lost braces
    80 | \code{\link{score}}, \link{elo.run.helpers}{elo.run helpers}, \code{\link{elo.calc}},
       |                                            ^
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
GNU make is a SystemRequirements.
checkRd: (-1) Emas.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:61: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Emas.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EMAS.manhattan.Rd: manhattan
  Emas.parallel.Rd: sem, lavaan
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  step_collapse_cart.Rd: selections, bake, prep, tidy.recipe
  step_collapse_stringdist.Rd: selections, prep, tidy.recipe
  step_discretize_cart.Rd: selections, tidy.recipe
  step_discretize_xgb.Rd: selections, tidy.recipe
  step_embed.Rd: tidy.recipe
  step_feature_hash.Rd: tidy.recipe
  step_lencode_bayes.Rd: tidy.recipe
  step_lencode_glm.Rd: tidy.recipe
  step_lencode_mixed.Rd: tidy.recipe
  step_pca_sparse.Rd: selections, prep, tidy.recipe
  step_pca_sparse_bayes.Rd: selections, prep, tidy.recipe
  step_pca_truncated.Rd: prep, step_center, step_scale, tidy.recipe,
    case_weights
  step_umap.Rd: prep, bake, tidy.recipe
  step_woe.Rd: selections, step_discretize, tidy.recipe
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) NEWS.Rd:194: Lost braces; missing escapes or markup?
   194 |             \item added {d,r}betabinom
       |                         ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  apply2d.Rd: create_progress_bar
  curve3d.Rd: create_progress_bar
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write.excel.Rd: openxlsx
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  em.prec.Rd: glassoFast
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  hfit.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) minimize.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) minimize.Rd:33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) EmiStatR-methods.Rd:86: Lost braces; missing escapes or markup?
    86 | execute {EmiStatR} function
       |         ^
checkRd: (-1) input-class.Rd:136: Lost braces; missing escapes or markup?
   136 |     \item{EmiStatR}{\code{signature(x = "input")}: execute {EmiStatR} function }
       |                                                            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  write_eml.Rd: write_xml
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EMMA.Rd: rotations, nnls
  GUI.Rd: runApp
  test.robustness.Rd: rotations
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) macacaModels.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) macacaModels.Rd:10-11: Lost braces in \itemize; meant \describe ?
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
checkRd: (-1) medal.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) medal.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) WRegTest.Rd:43: Lost braces
    43 | For ordinary least squares estimator, \code{psifun} should be the identity function psifun <- function(t){t}.
       |                                                                                                          ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  empChurn.Rd: prediction
  empCreditScoring.Rd: prediction
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
checkRd: (-1) em.Rd:25: Lost braces
    25 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.clogit.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.default.Rd:65: Lost braces
    65 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.fitdist.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.glmerMod.Rd:50: Lost braces
    50 |  \code{terms} the code{terms} object used.
       |                       ^
checkRd: (-1) em.panelmodel.Rd:49: Lost braces
    49 |  \code{terms} the code{terms} object used.
       |                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  get_trackdata.Rd: wrasspOutputInfos, tibble
  query.Rd: tibble
  requery_hier.Rd: tibble
  requery_seq.Rd: tibble
  serve.Rd: stopAllServers, httpuv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                              ^
checkRd: (-1) droso.Rd:8: Lost braces; missing escapes or markup?
     8 | The dataset contains 400 true donor sites, 400 false donor sites and 50 false sites as test set. Each sequence is of 40 nucleotides long. The conserved di-nucleotides GT are present at $21^{st}$ and $22^{nd}$ positions respectively.
       |                                                                                                                                                                                                            ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  APR.Feature.Rd: DNAStringSet
  Bayes.Feature.Rd: DNAStringSet
  Density.Feature.Rd: DNAStringSet
  MM1.Feature.Rd: DNAStringSet
  MM2.Feature.Rd: DNAStringSet
  MN.Fdtf.Feature.Rd: DNAStringSet
  Maldoss.Feature.Rd: DNAStringSet
  PN.Fdtf.Feature.Rd: DNAStringSet
  POS.Feature.Rd: DNAStringSet
  Predoss.Feature.Rd: DNAStringSet
  SAE.Feature.Rd: DNAStringSet
  Sparse.Feature.Rd: DNAStringSet
  Trint.Dist.Feature.Rd: DNAStringSet
  WAM.Feature.Rd: DNAStringSet
  WMM.Feature.Rd: DNAStringSet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) encode.character.Rd:22: Escaped LaTeX specials: \~
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  genkeys.Rd: openssl
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  endoSwitch.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) enetLTS-package.Rd:41: Lost braces; missing escapes or markup?
    41 |   \code{family="binomial"} should be a factor with two levels which is coded as \code{0} and {1}.
       |                                                                                              ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plotEnrich.Rd: ggplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) CTN.Rd:22: Lost braces; missing escapes or markup?
    22 | less memory. Genetic data consists of nucleotide data {A,T,C,G} and are usually saved
       |                                                       ^
checkRd: (-1) ALL.Regression.Config-class.Rd:39: Lost braces
    39 |     \item{code{shrinkage}:}{Object of class \code{"numeric"}, defining the shrinkage parameter applied to each tree in expansion.}
       |               ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Regression.Select.MinAvgErr.Config-class.Rd: Instance.List-class,
    Regression.Select.Config-class
  Regression.Select.MinAvgErr.FitObj-class.Rd:
    Regression.Select.Config-class, RegressionSelectPred-class,
    Regression.Select.FitObj-class
  ecv.regression.Rd: Instance.List-class,
    Regression.CV.Batch.FitObj-class, Regression.Batch.FitObj-class
  ecv.regression.baselearner.control.Rd: rmse.error
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Regression.Integrator.PCR.SelMin.Config-class.Rd:
    Regression.Integrator.Config-class
  Regression.Integrator.PCR.SelMin.FitObj-class.Rd:
    Regression.Integrator.FitObj-class
  epcreg.Rd: Instance.List-class, Regression.CV.Batch.FitObj-class,
    Regression.Batch.FitObj-class
  epcreg.baselearner.control.Rd: rmse.error
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Regression.Integrator.PenReg.SelMin.Config-class.Rd:
    Regression.Integrator.Config-class
  Regression.Integrator.PenReg.SelMin.FitObj-class.Rd:
    Regression.Integrator.FitObj-class
  epenreg.Rd: Instance.List-class, Regression.CV.Batch.FitObj-class,
    Regression.Batch.FitObj-class
  epenreg.baselearner.control.Rd: rmse.error
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
checkRd: (-1) entropy.Dirichlet.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Dirichlet.Rd:69: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) entropy.Rd:42: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  envcpt.Rd: cpt-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'enviPat/libs/x64/enviPat.dll':
  Found non-API call to R: 'SETLENGTH'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  envi-package.Rd: sparr, spatstat.geom, sf, terra, future, doFuture,
    doRNG, foreach
  lrren.Rd: future, doFuture, doRNG, foreach
  perlrren.Rd: future, doFuture, doRNG, foreach
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) metrics.Rd:124: Lost braces
   124 | Avg = 0.5 (sum | P_i - Q_i| + max{ | P_i - Q_i |})
       |                                  ^
'LazyData' is specified without a 'data' directory
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   3.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  eoa3.Rd: ppersist
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                           ^
checkRd: (-1) misClustRate.Rd:18: Lost braces; missing escapes or markup?
    18 | Compute the empirical MCR, assuming that #{cluster} = #{block},
       |                                                        ^
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   2.5Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clean_admin_names.Rd: countrycode
  clean_names_strings.Rd: janitor
  consistency_check.Rd: ggplot2
  export.Rd: rio
  import.Rd: rio
  missing_plot.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) risk.display.rd:98: Escaped LaTeX specials: \$
checkRd: (-1) estimate_R.Rd:59-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:64-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:67-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:70-72: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:79-80: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:82: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) estimate_R.Rd:84-86: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:51-52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:53-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:54-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:55-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:56-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) wallinga_teunis.Rd:58-59: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  estimate_R.Rd: incidence
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  sub-.epiflows.Rd: [.epicontacts
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  DiscreteCovariatesToOneHot.Rd: dplyr_tidy_select
  charlson_score.Rd: dplyr_data_masking
  flatten_date_intervals.Rd: dplyr_tidy_select, dplyr_data_masking
  lms.Rd: dplyr_data_masking
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  plot.epictmcmc.Rd: mcmc, plot.mcmc
  summary.epictmcmc.Rd: mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  epimcmc.Rd: MCMC, adaptMCMC
  plot.epimcmc.Rd: mcmc, plot.mcmc
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Running 'EpiILM.network.R' [5s]
  Comparing 'EpiILM.network.Rout' to 'EpiILM.network.Rout.save' ...9817c9817
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
19695c19695
<  [ reached 'max' / getOption("max.print") -- omitted 301 rows ]
---
>  [ reached getOption("max.print") -- omitted 301 rows ]
  Running 'EpiILM.spatial.R' [5s]
  Comparing 'EpiILM.spatial.Rout' to 'EpiILM.spatial.Rout.save' ... OK
Package suggested but not available for checking: 'epidict'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.network.transmat.Rd: network
  as.phylo.transmat.Rd: phylo
  brewer_ramp.Rd: brewer.pal, RColorBrewer
  control.dcm.Rd: ode
  netdx.Rd: control.simulate.formula.tergm
  netest.Rd: control.tergm
  plot.dcm.Rd: RColorBrewer, brewer.pal.info
  plot.netsim.Rd: plot.network
  plot.transmat.Rd: plot.network
  print.netdx.Rd: effectiveSize
  tedgelist_to_toggles.Rd: as.data.frame.networkDynamic
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) runSim.Rd:111: Lost braces
   111 | \ifelse{html}{\out{<i>r</i><sub>1</sub> = 1}}{{\eqn{r_1 = 1}}{r_1 = 1}} while the individual with the lowest phenotypic value
       |                                                              ^
checkRd: (-1) runSim.Rd:112: Lost braces
   112 | is given the rank \ifelse{html}{\out{<i>r<sub>n</sub></i> = <i>n</i>}}{{\eqn{r_n = n}}{r_n = n}}), the probability of an individual
       |                                                                                       ^
checkRd: (-1) runSim.Rd:120-122: Lost braces
   120 | }{
       |  ^
Package suggested but not available for checking: 'cmdstanr'
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   2.3Mb
    libs      6.6Mb
GNU make is a SystemRequirements.
checkRd: (-1) getAgeGender.Rd:52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getAgeGender.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:44-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:46-48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getMap.Rd:49-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSeason.Rd:58: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTableByMS.Rd:61-62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:55: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getTrend.Rd:56: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotAgeGender.Rd:47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotSeasonality.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotTS12MAvg.Rd:28: Lost braces in \itemize; meant \describe ?
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getAgeGender.Rd: ggplot2, officer
  getMap.Rd: officer
  getSeason.Rd: ggplot2, officer
  getTableByMS.Rd: flextable, officer
  getTrend.Rd: ggplot2, officer
  plotAge.Rd: ggplot2
  plotAgeGender.Rd: ggplot2
  plotBar.Rd: ggplot2
  plotBarGrouped.Rd: ggplot2
  plotBarGroupedH.Rd: ggplot2
  plotBarH.Rd: ggplot2
  plotPie.Rd: ggplot2
  plotSeasonality.Rd: ggplot2
  plotTS.Rd: ggplot2
  plotTS12MAvg.Rd: ggplot2
  plotTSGrouped.Rd: ggplot2
  shapeECDCFlexTable.Rd: set_header_df, flextable
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  boot.bias.Rd: boot
  plot.episensr.booted.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fit_disc_gamma.Rd: distcrete
  gamma_tools.Rd: distcrete
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  epoc.Rd: lassoshooting
  epoc.survival.Rd: survdiff
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Cmip6Dict.Rd: data.table
  summary_database.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  renderEq.Rd: shiny
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  equiv.boot.Rd: boot
  equivalence.xyplot.Rd: xyplot
  rtost.Rd: yuen.t.test
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
checkRd: (-1) Tm.Rd:46-48: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:49-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:52-54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:55-57: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) Tm.Rd:58-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:36-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:40-42: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:43-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) fitpot.Rd:47-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:54-56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:57-59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:60-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:63-65: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:66-68: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:69-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:72-74: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) thrselect.Rd:75-77: Lost braces in \itemize; \value handles \item{}{} directly
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Binomial-ergmReference-cdff43a4.Rd: ergmTerm, ergmReference
  CMB-ergmTerm-5a51afe9.Rd: ergmTerm
  CMP-ergmTerm-4d501174.Rd: ergmTerm
  Disc-ergmProposal-b6c6e5ca.Rd: DiscUnif-ergmReference, ergmProposal
  DiscTNT-ergmProposal-c3c2e8cb.Rd: DiscUnif-ergmReference,
    ergmProposal, TNT-ergmProposal
  Geometric-ergmReference-1ee5c5ac.Rd: sum-ergmTerm, ergmReference
  Poisson-ergmReference-40df5ec8.Rd: ergmTerm, ergmReference
  ZIPoisson-ergmProposal-bba55a81.Rd: ergmProposal
  ergm.count-package.Rd: ergm-package, ergmReference, ergmTerm, ergm,
    control.ergm
  zach.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  EgoStat-internal.Rd: egor
  as.egor.egodata.Rd: egor
  as.egor.network.Rd: network, egor
  control.ergm.ego.Rd: network
  degreedist.egor.Rd: egor
  ergm.ego-terms.Rd: egor
  ergm.ego.Rd: egor
  gof.ergm.ego.Rd: control.gof.formula, control.gof.ergm
  mixingmatrix.egor.Rd: egor
  nodal_attributes-API.Rd: check.ErgmTerm, egor, network
  simulate.ergm.ego.Rd: network, ergm, simulate.ergm
  summary_formula.egor.Rd: egor
  template_network.Rd: egor, tibble
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simEGP.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  nvertex.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AlterSwap-ergmProposal-7e827ae4.Rd: ergmProposal
  CompleteOrder-ergmReference-f40141c3.Rd: ergmReference
  ergm.rank-package.Rd: ergm-package, ergm
  rankdeference-ergmTerm-73181c43.Rd: ergmTerm
  rankedgecov-ergmTerm-5905bc22.Rd: ergmTerm
  rankinconsistency-ergmTerm-b232ab56.Rd: network, ergmTerm
  ranknodeicov-ergmTerm-856bed59.Rd: ergmTerm
  ranknonconformity-ergmTerm-a4593778.Rd: ergmTerm
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  approx.hotelling.diff.test.Rd: mcmc.list
  call.ErgmTerm.Rd: network
  control.ergm.Rd: mcmc.list
  degreedist.Rd: network
  ergm-errors.Rd: abort, warn, inform
  ergm.Rd: network, %v%, %n%
  ergm.design.Rd: network
  ergm.estfun.Rd: mcmc, mcmc.list
  ergm.geodistdist.Rd: network
  ergm.getnetwork.Rd: network
  ergm.godfather.Rd: network, mcmc
  ergmConstraint.Rd: network
  ergmMPLE.Rd: network
  ergmReference.Rd: network
  ergmTerm.Rd: network, %v%, %n%
  ergm_MCMC_sample.Rd: mcmc.list
  ergm_dyadgen_select.Rd: network
  ergm_model.Rd: term_list
  ergm_plot.mcmc.list.Rd: mcmc.list
  ergm_preprocess_response.Rd: network
  ergm_proposal.Rd: term_list
  ergm_state.Rd: network, tibble, edgelist
  ergm_symmetrize.Rd: network, tibble
  ergmlhs.Rd: network
  get.node.attr.Rd: network
  geweke.diag.mv.Rd: mcmc, mcmc.list
  gof.Rd: network
  is.valued.Rd: edgelist, network
  network.list.Rd: network
  nvattr.copy.network.Rd: network, network.initialize,
    set.vertex.attribute, set.network.attribute
  rlebdm.Rd: tibble, edgelist, network, as.edgelist
  samplk.Rd: network
  sampson.Rd: network
  san.Rd: network
  simulate.ergm.Rd: network, mcmc, mcmc.list, edgelist
  spectrum0.mvar.Rd: spectrum0.ar
  summary.ergm_model.Rd: network
  summary.formula.Rd: network
  summary_formula.Rd: network
  to_ergm_Cdouble.Rd: network
  update.network.Rd: network
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'ergm/libs/x64/ergm.dll':
  Found non-API call to R: 'SET_TYPEOF'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
checkRd: (-1) ifa.Rd:16: Lost braces; missing escapes or markup?
    16 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then Sigma^{-1} 
       |                                                                         ^
checkRd: (-1) ifa.Rd:17: Lost braces; missing escapes or markup?
    17 | has the corresponding q-factor decomposition Sigma^{-1}=diag(phi)(I-theta theta')diag(phi), where theta is a mxq matrix and phi the vector of 
       |                                                    ^
checkRd: (-1) ifa.Rd:21: Lost braces; missing escapes or markup?
    21 | \item{iSB}{m x q matrix (diag(Psi)+BB')^{-1}B.}
       |                                         ^
checkRd: (-1) isqrtfa.Rd:15: Lost braces; missing escapes or markup?
    15 | If Sigma has the q-factor decomposition Sigma=diag(Psi)+BB', then the function returns a matrix Omega such that Sigma^{-1} = Omega Omega'. Equivalently,
       |                                                                                                                       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  elastic.Rd: glmnet
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  errorist_init.Rd: searcher
  shims.Rd: searcher
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MipRules-class.Rd: validator
  errorlocate-package.Rd: validate
  errorlocation.Rd: values
  is_linear.Rd: validator
  replace_errors.Rd: validator
  translate_mip_lp.Rd: lp.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
checkRd: (-1) enp.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) enp.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) evolat.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) psns.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc  13.3Mb
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  gui_models.Rd: runApp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) festRidge.Rd:80: Lost braces; missing escapes or markup?
    80 | \item{XtXlamIinv}{explicit value of (X'X + diag(penalty))^{-1}.  Useful
       |                                                           ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) USA_state_N.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) USA_state_N.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) confirmed.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) death.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) recovered.Rd:11: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
File 'essentials/libs/x64/essentials.dll':
  Found non-API call to R: 'UNSET_S4_OBJECT'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) momento.central.Rd:12: Lost braces; missing escapes or markup?
    12 | \item{orden}{Es un valor numérico que representa el orden del momento central (orden = {1,2,3,4,...})}
       |                                                                                        ^
'LazyData' is specified without a 'data' directory
checkRd: (-1) aic.Rd:25: Escaped LaTeX specials: \&
checkRd: (-1) aic.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:56: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:60: Escaped LaTeX specials: \&
checkRd: (-1) ictab.Rd:64: Escaped LaTeX specials: \&
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  W_sampler.Rd: R6Class
  beta_sampler.Rd: R6Class
  rho_sampler.Rd: R6Class
  sigma_sampler.Rd: R6Class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) integration.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) integration.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:25-26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) loess.options.Rd:27-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) maxlogLreg.Rd:138: Lost braces; missing escapes or markup?
   138 | $j^{th}$ for all the observations.
       |    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  maxlogL.Rd: DEoptim
  maxlogLreg.Rd: DEoptim, DEoptim.control
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  simulate_background_earthquakes.Rd: etas
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  catalog.Rd: inside.owin
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ETC-package.Rd:28-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:30-31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ETC-package.Rd:32: Lost braces in \itemize; meant \describe ?
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dbWipe.Rd: DBIConnection-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                    ^
checkRd: (-1) data_cls.Rd:24: Lost braces
    24 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability 0.10 for
       |                            ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                    ^
checkRd: (-1) data_reg.Rd:21: Lost braces
    21 | \item Graphs: Erd\"{o}s-R\'{e}nyi graphs with connection probability given by
       |                            ^
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  map_non_standard_calendar.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  set_key.Rd: setkey
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  freq_binom_one_simons_twostage.Rd: ph2simon
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) FuzzyCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "fcm {ppclust}"
       |                                                       ^
checkRd: (-1) pamCluster.Rd:15: Lost braces; missing escapes or markup?
    15 | A list of cluster labels and a R object of class "pam {cluster}"
       |                                                       ^
checkRd: (-1) dist.evaluate.core.Rd:26: Lost braces; missing escapes or markup?
    26 | the \code{names} column in {data} as labels. If \code{NULL} (default),
       |                            ^
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
checkRd: (-1) colplot.Rd:52: Lost braces
    52 | \item{legend}{should a legend be added? Defaults to code{FALSE}}
       |                                                         ^
checkRd: (-1) colplot.Rd:56: Lost braces
    56 | \item{legend.pretty}{logical: should the legend values produced by \[base]{pretty}? Othewrwise they are exact. Defaults to \code{TRUE}}
       |                                                                           ^
checkRd: (-1) calculateGLR.Rd:43: Escaped LaTeX specials: \&
checkRd: (-1) glr.Rd:5: Lost braces
     5 |   Conducts a generalized likelihood ratio test testing whether {\eqn{\beta \in}  (-\code{c},\code{c})}. Covariates can be accommodated.
       |                                                                ^
checkRd: (-1) glr.Rd:34: Lost braces
    34 |   This is a similar function to the main function \code{evian}. Instead of testing H0: \eqn{\beta}=0, it tests for whether H0:{\eqn{\beta \in} (-\code{c},\code{c})}.
       |                                                                                                                               ^
checkRd: (-1) Snoring.Rd:21: Escaped LaTeX specials: \&
checkRd: (-1) fmgammagpd.Rd:183: Lost braces; missing escapes or markup?
   183 |  \item {nlumgammagpd} and {proflumgammagpd} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], sigmau, xi)}
       |                           ^
checkRd: (-1) fmgammagpdcon.Rd:181: Lost braces; missing escapes or markup?
   181 |  \item {nlumgammagpdcon} and {proflumgammagpdcon} - \code{c(mgshape, mgscale, mgweight[1:(M-1)], xi)}
       |                              ^
checkRd: (-1) kernels.Rd:87: Lost braces
    87 | code{\link[evmix:kernels]{kd*}}  and \code{\link[evmix:kernels]{kp*}} give the
       |     ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  MantelCor.Rd: mantel
  MantelModTest.Rd: mantel
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Almer.Rd: lme4, lmer, merMod
  Almer_SE.Rd: lmer, merMod
  Almer_sim.Rd: simulate.merMod
  rate_gls.Rd: phylo
  simulate_rate.Rd: phylo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                         ^
checkRd: (-1) ShapeDist.Rd:18: Lost braces; missing escapes or markup?
    18 | Procrustes distance provides a measure of coincidence of two point sets {xi} and {yi}, i=1..N. For this purpose the variance of point deviations is calculated at the optimal superposition of the sets. It allows to characterize the shape proximity of a given simplex to shape of a reference one.
       |                                                                                  ^
'LazyData' is specified without a 'data' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.6Mb
    extdata   2.4Mb
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  clockrate_dens_plot.Rd: facet_wrap, geom_density
  clockrate_reg_plot.Rd: geom_smooth, geom_point
  plot_treerates_sgn.Rd: scale_color_steps2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) stop_rule.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:21: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) stop_rule.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  power2x2.Rd: uniroot.integer, ss.nonadh
  unirootGrid.Rd: uniroot.integer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  powerBinom.Rd: uniroot.integer
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++14: please drop specification unless essential
Package suggested but not available for checking: 'ExactData'
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    exiftool  14.1Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Package suggested but not available for checking: 'cec2013'
checkRd: (-1) ccF.Rd:5: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:32: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:29: Escaped LaTeX specials: \&
checkRd: (-1) ccF.Rd:42: Lost braces
    42 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
checkRd: (-1) ccF.Rd:41: Lost braces
    41 | CALI\'{N}SKI, T.; CORSTEN, L. C. A. Clustering
       |       ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  expectreg-package.Rd: BayesX-package, mboost-package
  india.bnd.Rd: BayesX-package
  northger.bnd.Rd: BayesX-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ExplainPrediction-package.Rd: CORElearn, CoreModel, predict.CoreModel
  explanation.Rd: CoreModel, discretize, semiArtificial-package,
    CORElearn, predict.CoreModel, attrEval
  wrap4Explanation.Rd: nnet, CORElearn-package
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  graph2office.Rd: emf
  table2office.Rd: tidy
  table2spreadsheet.Rd: tidy
  table2tex.Rd: tidy
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  epGraphs.Rd: prettyGraphs, createColorVectorsByDesign, prettyPlot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  mrset.Rd: text_expand
  vars.Rd: text_expand
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Malformed Description field: should contain one or more complete sentences.
'LazyData' is specified without a 'data' directory
checkRd: (-1) MatIn.Rd:6: Lost braces
     6 | Computation of aggregation matrices for generalized interactions that are used in code{\link{extRC}} to estimate extended RC models.
       |                                                                                       ^
checkRd: (-1) plot.Rd:5: Lost braces
     5 | \description{It plots the output of code{\link{extRC}} function for a vector of lambda values.}
       |                                         ^
checkRd: (-1) print.Rd:5: Lost braces
     5 | \description{Given the output of code{\link{extRC}} function, it is written in a readable form.}
       |                                      ^
checkRd: (-1) summary.Rd:5: Lost braces
     5 | \description{Summary method for the output of code{\link{extRC}} function.}
       |                                                   ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  cox.adapt.Rd: coxph
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ci.fevd.Rd: ci
  datagrabber.Rd: datagrabber
  decluster.Rd: datagrabber
  distill.fevd.Rd: distill
  fevd.Rd: ci, distill, datagrabber
  findpars.Rd: distill
  xbooter.Rd: booter
  xtibber.Rd: tibber, booter
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  distLquantile.Rd: quantileMean
  distLweights.Rd: dist.list
  plotLexBoot.Rd: ciBand
  plotLextreme.Rd: logAxis
  plotLfit.Rd: logAxis
  printL.Rd: rainbow2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Package suggested but not available for checking: 'exuberdata'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  autoplot.ds_radf.Rd: ggplot2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) read_edf.Rd:32: Lost braces
    32 | code{TRUE}}
       |     ^
checkRd: (-1) read_edf.Rd:35: Lost braces
    35 | code{TRUE}}
       |     ^
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    Functions and objects (details)
checkRd: (-1) va.Rd:80: Lost braces
    80 | \doi{10.1016/s0002-9394(02)01825-1}{Beck et al.}, and
       |                                    ^
checkRd: (-1) codePasses.Rd:64: Escaped LaTeX specials: \#
Package suggested but not available for checking: 'doMC'
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  ezCutoffs.Rd: boot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) EEzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EEzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_fit.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) EzGP_predict.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:59: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LEzGP_fit.Rd:60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) LLF_gradients.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
'LazyData' is specified without a 'data' directory
checkRd: (-1) ez-package.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:26: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) ez-package.Rd:33: Lost braces in \itemize; meant \describe ?
'LazyData' is specified without a 'data' directory
Problems with news in 'NEWS.md':
No news entries found.
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  pspline.Rd: gam, mgcv
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) fmCov.Rd:37: Lost braces; missing escapes or markup?
    37 | where, \code{alpha(i)} is the intercept, \code{f(t)} is a {K x 1} vector of 
       |                                                           ^
checkRd: (-1) plot.ffm.Rd:82: Lost braces; missing escapes or markup?
    82 | \item{las}{one of {0, 1, 2, 3} to set the direction of axis labels, same as
       |                   ^
checkRd: (-1) summary.ffm.Rd:39: Lost braces; missing escapes or markup?
    39 | Returned object is of class {summary.ffm}.
       |                             ^
checkRd: (-1) fviz_nbclust.Rd:75: Lost braces; missing escapes or markup?
    75 | (2001) proposed: "the smallest k such that gap(k) >= gap(k+1) - s_{k+1}". 
       |                                                                   ^
checkRd: (-1) fviz_nbclust.Rd:77: Lost braces; missing escapes or markup?
    77 | SE.factor*s_{k+1}" where SE.factor is a numeric value which can be 1
       |             ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  Investigate.Rd: CA
  classif.Rd: HCPC
  description.Rd: CA
  factoGraph.Rd: CA
  graphHab.Rd: CA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  HCPC.Rd: agnes
  plotellipses.Rd: xyplot
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Problems with news in 'NEWS.md':
  Cannot extract version info from the following section titles:
    minor changes
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  factorplot.Rd: glht, summary.glht
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  CAshiny.Rd: CA, plot.CA
  FAMDshiny.Rd: FAMD, plot.FAMD
  HCPCshiny.Rd: HCPC, plot.HCPC
  MCAshiny.Rd: MCA, dimdesc, plot.MCA
  MFAshiny.Rd: PCA, plot.PCA
  PCAshiny.Rd: PCA, plot.PCA
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SMART.Rd: data.table
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
checkRd: (-1) FADPclust.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:36: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) FADPclust.Rd:37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) happy.Rd:14: Lost braces
    14 |                  code{Pretty happy} <  \code{Very happy}}
       |                      ^
checkRd: (-1) fra_sf.Rd:22: Lost braces; missing escapes or markup?
    22 | A map of France as {sf} object. Can be used as dataset or for maps
       |                    ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getFormula.Rd: createLipidDB, assignDB
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    help   1.2Mb
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  famos.Rd: future
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) pi0FAMT.Rd:18: Lost braces
    18 | \code{pi0}{The estimated proportion \code{pi0} of null hypotheses.}}
       |           ^
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  as.FAMTdata.Rd: impute.knn
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  kmPredictWrapper.Rd: predict.km, fast99
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
File 'fansi/libs/x64/fansi.dll':
  Found non-API call to R: 'R_nchar'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Problems with news in 'NEWS.md':
No news entries found.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  robustMD.Rd: cov.rob
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  farm.select.Rd: ncvreg
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.3Mb
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    9.2Mb
    help   1.8Mb
    libs   2.0Mb
Specified C++11: please drop specification unless essential
Running 'spelling.R' [0s]
  Comparing 'spelling.Rout' to 'spelling.Rout.save' ...6c6
< NULL
---
> All Done!
  Running 'testthat.R' [9s]
Specified C++11: please drop specification unless essential
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    images   3.1Mb
    libs     1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.1Mb
    libs   1.1Mb
GNU make is a SystemRequirements.
Specified C++11: please drop specification unless essential
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fastJT-package.Rd: Rcpp
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Specified C++11: please drop specification unless essential
Package suggested but not available for checking: 'coxKM'
checkRd: (-1) KITdesign.Rd:36: Lost braces; missing escapes or markup?
    36 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) KITkernel.Rd:51: Lost braces; missing escapes or markup?
    51 |  \item{trait}{One of {'c','d','s',NULL} indicating the type
       |                      ^
checkRd: (-1) geno.Rd:19: Lost braces; missing escapes or markup?
    19 |                 Must be one of {'ibs', 'linear', 'quadratic'}.
       |                                ^
checkRd: (-1) geno.Rd:31: Lost braces; missing escapes or markup?
    31 |                      {'add', 'dom', 'rec'} indicating additive,
       |                      ^
checkRd: (-1) nongeno.Rd:14: Lost braces; missing escapes or markup?
    14 |                 Must be one of {'interactive', 'linear', 'quadratic'}.
       |                                ^
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.2Mb
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                ^
checkRd: (-1) eigen_compute_single_entry_of_diagonal_matrix.Rd:17: Lost braces; missing escapes or markup?
    17 | The value of m^{-1}_{j,j}
       |                     ^
'LazyData' is specified without a 'data' directory
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API calls to R: 'NAMED', 'SETLENGTH', 'SET_NAMED',
    'STRING_PTR', 'VECTOR_PTR'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual,
and section 'Moving into C API compliance' for issues with the use of
non-API entry points.
Specified C++11: please drop specification unless essential
'LazyData' is specified without a 'data' directory
'LazyData' is specified without a 'data' directory
Specified C++11: please drop specification unless essential
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  SSplot.Rd: rand
  col.fastR.Rd: trellis.par.set, show.settings
  maxLik2.Rd: maxLik
  plot.maxLik2.Rd: maxLik
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  directed_erdos_renyi.Rd: Matrix
  directed_factor_model.Rd: Matrix
  erdos_renyi.Rd: Matrix
  undirected_factor_model.Rd: Matrix
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) update_nhl_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_nhl_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:51-53: Lost braces in \itemize; meant \describe ?
checkRd: (-1) update_phf_db.Rd:54-57: Lost braces in \itemize; meant \describe ?
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    Rcgi      2.6Mb
    cgi-bin   2.5Mb
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Undefined global functions or variables:
  init run
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  WebPlot.Rd: Cairo
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
'LazyData' is specified without a 'data' directory
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
    libs   1.2Mb
GNU make is a SystemRequirements.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  fat2Lpoly.Rd: kinship
  fat2Lpoly.withinR.Rd: kinship
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
checkRd: (-1) Error-Classes.Rd:107-119: Lost braces
   107 |   \item \code{do_verbose(response, template)} {
       |                                               ^
checkRd: (-1) Error.Rd:33-45: Lost braces
    33 |   \item \code{do(response, mssg)} {
       |                                   ^
checkRd: (-1) fh_bounds.Rd:14: Lost braces
    14 | \item{params1}{Arguments to pass to the r{dist} function for distribution 1}
       |                                          ^
checkRd: (-1) fh_bounds.Rd:16: Lost braces
    16 | \item{params2}{Arguments to pass to the r{dist} function for distribution 2}
       |                                          ^
Running 'testthat.R' [93s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(faux)
  
  ************
  Welcome to faux. For support and examples visit:
  https://debruine.github.io/faux/
  - Get and set global package options with: faux_options()
  ************
  > 
  > expect_equal <- function(...) {
  +   testthat::expect_equal(..., check.environment=FALSE)
  + }
  > 
  > test_check("faux")
  [ FAIL 1 | WARN 5 | SKIP 14 | PASS 1368 ]
  
  ══ Skipped tests (14) ══════════════════════════════════════════════════════════
  • On CRAN (12): 'test-distributions.R:59:3', 'test-distributions.R:90:3',
    'test-distributions.R:113:3', 'test-distributions.R:136:3',
    'test-distributions.R:160:3', 'test-distributions.R:234:3',
    'test-distributions.R:292:3', 'test-distributions.R:340:3',
    'test-distributions.R:369:3', 'test-distributions.R:569:3',
    'test-plot_design.R:51:3', 'test-plot_design.R:341:3'
  • Too variable (1): 'test-distributions.R:473:3'
  • long checking function (1): 'test-norta.R:55:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-getcols.R:2:3'): error ───────────────────────────────────────
  `getcols()` did not throw an error.
  
  [ FAIL 1 | WARN 5 | SKIP 14 | PASS 1368 ]
  Error: Test failures
  Execution halted