############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CellTrails.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CellTrails_1.23.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CellTrails.Rcheck' * using R version 4.4.0 RC (2024-04-16 r86468 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'CellTrails/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CellTrails' version '1.23.0' * 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 hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'CellTrails' can be installed ... OK * 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 ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... 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 ... OK * checking Rd files ... NOTE checkRd: (-1) connectStates.Rd:55: Lost braces; missing escapes or markup? 55 | where D is a matrix containing all collected {l}-nearest neighbor sample | ^ checkRd: (-1) dot-bhtsne.Rd:10-14: Lost braces 10 | .reduceDimensions_def <- function(x, s) { | ^ checkRd: (-1) dot-trajLandmark-set.Rd:14: Lost braces; missing escapes or markup? 14 | \item{type}{A character in {"type", "id", "shape"}} | ^ checkRd: (-1) dot-trajLandmark.Rd:14: Lost braces; missing escapes or markup? 14 | \item{type}{A character in {"type", "id", "shape"}} | ^ checkRd: (-1) dot-validatePlotParams.Rd:24: Lost braces; missing escapes or markup? 24 | {'featureName', 'phenoName'}. Parameter \code{name} needs | ^ checkRd: (-1) dot-validatePlotParams.Rd:26: Lost braces; missing escapes or markup? 26 | {colnames(colData(object)), state, landmark}. | ^ checkRd: (-1) plotMap.Rd:24: Lost braces; missing escapes or markup? 24 | \item{type}{Type of map; one of {"raw","surface.fit","surface.se"}} | ^ checkRd: (-1) write.ygraphml.Rd:52: Lost braces; missing escapes or markup? 52 | \code{color_by='phenoName'} and {name='landmark'}. States can be indicated | ^ checkRd: (-1) write.ygraphml.Rd:53: Lost braces; missing escapes or markup? 53 | by \code{color_by='phenoName'} and {name='state'}. | ^ * 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 ... NOTE Documented arguments not in \usage in Rd file 'dot-adjustLayoutByPtime.Rd': 'layout' Documented arguments not in \usage in Rd file 'dot-findStates_def.Rd': 'ming.g' Documented arguments not in \usage in Rd file 'dot-plotStateTrajectory_def.Rd': 'label' Documented arguments not in \usage in Rd file 'dot-rbf.Rd': 'x' 'sigma' Documented arguments not in \usage in Rd file 'dot-spatmed.Rd': 'x' Documented arguments not in \usage in Rd file 'dot-write_ygraphml_def.Rd': 'tlayout' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMap 5.84 0.42 6.36 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/CellTrails.Rcheck/00check.log' for details.