* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lolR.Rcheck’
* using R Under development (unstable) (2025-02-25 r87824)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘lolR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lolR’ version ‘2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘lolR’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/lolR-00install.html' for details.
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [1s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [10s/13s] OK
* checking Rd files ... [0s/1s] NOTE
checkRd: (-1) lol.project.lrlda.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.lrlda.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.lrlda.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.lrlda.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.lrlda.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.pca.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.pca.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.pca.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.pca.Rd:19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.project.pca.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.sims.fat_tails.Rd:25: Lost braces; missing escapes or markup?
    25 | \item{f}{the fatness scaling of the tail. S2 = f*S1, where S1_{ij} = rho if i != j, and 1 if i == j. Defaults to \code{15}.}
       |                                                               ^
checkRd: (-1) lol.sims.mean_diff.Rd:36: Lost braces; missing escapes or markup?
    36 | \item{s}{the scaling parameter of the covariance matrix. S_{ij} = scaling*1 if i == j, or scaling*offdiag if i != j. Defaults to \code{1}.}
       |                                                            ^
checkRd: (-1) lol.utils.decomp.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.utils.decomp.Rd:22: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.utils.decomp.Rd:23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.utils.decomp.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.utils.decomp.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) lol.xval.eval.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X}, \code{Y}, and has a parameter for \code{alg.dimname} if \code{alg} is supervised, or just \code{X} and \code{alg.dimname} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r <= d} dimensions.}
       |                                                                                                                                                                                                                                                                                                                                    ^
checkRd: (-1) lol.xval.eval.Rd:31: Lost braces; missing escapes or markup?
    31 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X}, \code{Y}, and has a parameter for \code{alg.dimname} if \code{alg} is supervised, or just \code{X} and \code{alg.dimname} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r <= d} dimensions.}
       |                                                                                                                                                                                                                                                                                                                                           ^
checkRd: (-1) lol.xval.eval.Rd:68: Lost braces
    68 | \item{if ]code{rank.low == TRUE}, users cross-validation method with \code{ntrain = min((k-1)/k*n, d)} sample training sets, where \code{d}  is the number of dimensions in \code{X}. This ensures that the training data is always low-rank, \code{ntrain < d + 1}. Note that the resulting training sets may have \code{ntrain < (k-1)/k*n}, but the resulting testing sets will always be properly rotated \code{ntest = n/k} to ensure no dependencies in fold-wise testing.}
       |               ^
checkRd: (-1) lol.xval.optimal_dimselect.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X} and \code{Y} and embedding dimension \code{r} if \code{alg} is supervised, or just \code{X} and embedding dimension \code{r} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r < d} dimensions.}
       |                                                                                                                                                                                                                                                                                                                                      ^
checkRd: (-1) lol.xval.optimal_dimselect.Rd:32: Lost braces; missing escapes or markup?
    32 | \item{alg}{the algorithm to use for embedding. Should be a function that accepts inputs \code{X} and \code{Y} and embedding dimension \code{r} if \code{alg} is supervised, or just \code{X} and embedding dimension \code{r} if \code{alg} is unsupervised.This algorithm should return a list containing a matrix that embeds from {d} to {r < d} dimensions.}
       |                                                                                                                                                                                                                                                                                                                                             ^
checkRd: (-1) lol.xval.optimal_dimselect.Rd:75: Lost braces
    75 | \item{if ]code{rank.low == TRUE}, users cross-validation method with \code{ntrain = min((k-1)/k*n, d)} sample training sets, where \code{d}  is the number of dimensions in \code{X}. This ensures that the training data is always low-rank, \code{ntrain < d + 1}. Note that the resulting training sets may have \code{ntrain < (k-1)/k*n}, but the resulting testing sets will always be properly rotated \code{ntest = n/k} to ensure no dependencies in fold-wise testing.}
       |               ^
checkRd: (-1) predict.nearestCentroid.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.nearestCentroid.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.nearestCentroid.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.randomChance.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.randomChance.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.randomGuess.Rd:12: Lost braces in \itemize; meant \describe ?
checkRd: (-1) predict.randomGuess.Rd:13: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking LazyData ... INFO
  'LazyData' is specified without a 'data' directory
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [5s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [9s/11s] OK
  Running ‘testthat.R’ [9s/11s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [87s/120s] OK
* checking PDF version of manual ... [6s/8s] OK
* checking HTML version of manual ... [1s/2s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE