############################################################################## ############################################################################## ### ### 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 84.434 0.239 84.610 FlowSOMmary 79.600 0.303 79.777 PlotOutliers 25.420 0.091 25.511 PlotMarker 22.723 0.205 22.929 UpdateMetaclusters 22.681 0.088 22.725 PlotStars 19.062 0.088 19.112 GroupStats 17.673 0.100 17.730 FlowSOM 17.493 0.088 17.494 PlotGroups 15.894 0.136 15.820 AddAnnotation 12.468 0.151 12.569 query_multiple 12.230 0.059 12.231 QueryMultiple 11.983 0.047 12.037 PlotManualBars 11.441 0.052 11.358 Plot2DScatters 11.157 0.176 11.264 GetFlowJoLabels 9.999 0.076 10.012 QueryStarPlot 9.839 0.056 9.828 PlotNode 9.683 0.094 9.745 PlotNumbers 9.493 0.036 9.488 PlotVariable 9.191 0.052 9.213 CountGroups 9.146 0.072 8.979 PlotPies 8.929 0.056 8.915 PlotFlowSOM 8.093 0.140 8.171 SaveClustersToFCS 7.971 0.012 7.830 GetFeatures 7.936 0.036 7.904 PlotLabels 7.890 0.075 7.902 UpdateNodeSize 7.860 0.012 7.800 NClusters 7.240 0.200 7.370 NMetaclusters 7.268 0.107 7.311 MetaclusterMFIs 6.880 0.259 7.073 TestOutliers 7.074 0.012 7.015 PlotOverview2D 6.975 0.040 6.991 GetPercentages 6.932 0.020 6.881 MetaclusterCVs 6.757 0.195 6.886 GetMetaclusterCVs 6.690 0.008 6.627 GetMFIs 6.598 0.019 6.547 print.FlowSOM 6.574 0.012 6.581 GetMetaclusterMFIs 6.553 0.008 6.493 GetMetaclusterPercentagesPositive 6.499 0.052 6.480 GetMetaclusters 6.359 0.016 6.303 GetCounts 6.195 0.020 6.142 GetClusters 6.177 0.016 6.120 GetClusterMFIs 6.076 0.072 6.076 GetClusterPercentagesPositive 6.089 0.040 6.055 FlowSOMSubset 5.816 0.020 5.848 NewData 5.437 0.056 5.419 ReadInput 4.977 0.052 4.869 * 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.