############################################################################## ############################################################################## ### ### 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 4.4.3 (2025-02-28) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 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 FlowSOMmary 69.004 0.279 69.343 PlotDimRed 66.645 0.148 66.904 PlotOutliers 22.915 0.028 23.001 PlotMarker 20.598 0.052 20.702 UpdateMetaclusters 19.764 0.024 19.839 PlotStars 17.364 0.064 17.477 GroupStats 15.880 0.064 15.981 FlowSOM 15.423 0.044 15.505 PlotGroups 14.369 0.008 14.407 AddAnnotation 11.120 0.152 11.297 query_multiple 10.828 0.004 10.865 QueryMultiple 10.604 0.020 10.652 Plot2DScatters 9.884 0.064 9.972 PlotManualBars 9.699 0.016 9.742 GetFlowJoLabels 9.170 0.227 9.421 PlotNode 8.523 0.012 8.558 PlotNumbers 8.221 0.024 8.267 QueryStarPlot 8.040 0.004 8.067 CountGroups 7.783 0.032 7.833 PlotVariable 7.760 0.016 7.794 PlotPies 7.693 0.016 7.730 UpdateNodeSize 7.380 0.000 7.399 PlotFlowSOM 7.273 0.088 7.379 GetFeatures 6.950 0.048 7.015 SaveClustersToFCS 6.623 0.016 6.658 PlotLabels 6.366 0.016 6.395 NMetaclusters 6.183 0.036 6.232 NClusters 6.126 0.019 6.158 MetaclusterMFIs 5.995 0.020 6.031 TestOutliers 5.804 0.016 5.836 GetMetaclusterMFIs 5.701 0.080 5.794 GetPercentages 5.693 0.064 5.771 MetaclusterCVs 5.691 0.040 5.744 PlotOverview2D 5.658 0.067 5.741 GetMetaclusters 5.647 0.052 5.710 GetClusterMFIs 5.520 0.139 5.673 GetMetaclusterPercentagesPositive 5.635 0.020 5.670 GetMetaclusterCVs 5.565 0.050 5.627 GetMFIs 5.495 0.052 5.557 GetCounts 5.373 0.119 5.505 GetClusterPercentagesPositive 5.242 0.196 5.451 print.FlowSOM 5.397 0.020 5.431 GetClusters 5.262 0.128 5.401 FlowSOMSubset 5.115 0.016 5.148 * 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.