* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/prevtoinc.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘prevtoinc/DESCRIPTION’ ... OK
* this is package ‘prevtoinc’ version ‘0.12.0’
* 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 whether package ‘prevtoinc’ can be installed ... [3s/5s] OK
See 'https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/prevtoinc-00install.html' for details.
* checking installed package size ... OK
* checking package directory ... 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 ... [1s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the package can be unloaded cleanly ... [0s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
* checking loading without being on the library search path ... [1s/2s] 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 ... [3s/5s] OK
* checking Rd files ... [0s/1s] NOTE
checkRd: (-1) calculate_CI_I_pp.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_CI_I_pp.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_CI_I_pp.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_CI_I_pp.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_CI_I_pp.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_CI_I_pp.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calculate_I_mixed.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_mixed.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_mixed.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_mixed.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_mixed.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_mixed.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_mixed.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_mixed.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_rhame.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:30: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:32: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calculate_I_smooth.Rd:34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) simulate_incidence_stats.Rd:20: Lost braces; missing escapes or markup?
    20 |    \item{x.los - average length of stay x_{los}} 
       |                                           ^
checkRd: (-1) simulate_incidence_stats.Rd:21: Lost braces; missing escapes or markup?
    21 |    \item{x.loi - average length of infection x_{loi}}
       |                                                ^
* checking Rd metadata ... 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 ... NOTE
  'LazyData' is specified without a 'data' directory
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] OK
  Running ‘testthat.R’ [1s/1s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [16s/22s] OK
* checking PDF version of manual ... [6s/8s] OK
* DONE
Status: 2 NOTEs
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 1:19