############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.14.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘FlowSOM’ can be installed ... OK * used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’ * 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 loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... 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) PlotDimRed.Rd:55: Lost braces 55 | of the dimred default = function(dimred){dimred$Y}.} | ^ * 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PlotDimRed 82.658 0.296 82.811 FlowSOMmary 78.538 0.534 79.014 PlotOutliers 25.418 0.124 25.564 PlotMarker 23.058 0.363 23.482 UpdateMetaclusters 22.825 0.072 22.933 PlotStars 20.017 0.156 20.126 GroupStats 17.679 0.080 17.714 FlowSOM 17.111 0.124 17.112 PlotGroups 15.863 0.107 15.751 query_multiple 12.854 0.024 12.819 QueryMultiple 12.388 0.040 12.368 AddAnnotation 12.276 0.144 12.364 Plot2DScatters 11.140 0.331 11.405 PlotManualBars 10.960 0.303 11.118 GetFlowJoLabels 9.886 0.163 9.987 CountGroups 9.835 0.091 9.697 QueryStarPlot 9.623 0.044 9.600 PlotNode 9.511 0.100 9.544 PlotVariable 9.315 0.060 9.310 PlotNumbers 9.113 0.108 9.155 PlotPies 9.099 0.064 9.102 SaveClustersToFCS 8.567 0.055 8.469 PlotFlowSOM 8.497 0.052 8.482 UpdateNodeSize 8.265 0.096 8.298 PlotLabels 7.593 0.308 7.830 MetaclusterMFIs 7.835 0.035 7.852 GetFeatures 7.544 0.056 7.534 NMetaclusters 7.447 0.008 7.386 NClusters 7.381 0.056 7.368 MetaclusterCVs 7.137 0.076 7.142 TestOutliers 7.148 0.024 7.101 PlotOverview2D 6.917 0.115 6.965 GetMetaclusters 6.995 0.008 6.977 GetPercentages 6.723 0.076 6.771 GetMetaclusterCVs 6.644 0.056 6.626 print.FlowSOM 6.643 0.048 6.618 NewData 6.457 0.188 6.574 GetMFIs 6.534 0.024 6.486 GetMetaclusterMFIs 6.457 0.064 6.449 GetMetaclusterPercentagesPositive 6.459 0.036 6.425 FlowSOMSubset 6.306 0.020 6.341 GetClusterMFIs 6.165 0.148 6.242 GetClusterPercentagesPositive 6.136 0.127 6.195 GetCounts 6.112 0.092 6.135 GetClusters 6.026 0.072 6.029 ReadInput 4.988 0.044 4.872 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.