############################################################################## ############################################################################## ### ### 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_2.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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 ‘2.17.0’ * 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'pipe.Rd': ‘[magrittr:pipe]{%>%}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 75.042 0.318 75.448 PlotDimRed 68.603 0.115 69.099 PlotOutliers 43.232 0.202 43.870 PlotMarker 22.718 0.461 23.299 UpdateMetaclusters 22.053 0.032 22.139 PlotStars 19.655 0.275 20.065 GroupStats 17.294 0.096 17.439 FlowSOM 15.082 0.028 15.135 PlotGroups 15.070 0.020 15.200 QueryMultiple 13.469 0.042 13.647 Plot2DScatters 13.219 0.072 13.363 query_multiple 13.157 0.004 13.190 AddAnnotation 11.531 0.168 11.725 PlotManualBars 11.285 0.198 11.583 PlotNode 9.299 0.200 9.530 QueryStarPlot 9.436 0.000 9.463 GetFlowJoLabels 9.092 0.127 9.244 PlotNumbers 9.068 0.052 9.154 UpdateNodeSize 8.803 0.008 8.831 PlotVariable 8.527 0.123 8.710 PlotPies 8.513 0.136 8.670 CountGroups 8.073 0.064 8.151 PlotFlowSOM 7.252 0.032 7.322 GetFeatures 7.032 0.072 7.123 PlotLabels 6.801 0.068 6.923 SaveClustersToFCS 6.804 0.004 6.823 PlotOverview2D 6.643 0.076 6.741 NMetaclusters 6.640 0.012 6.690 TestOutliers 6.389 0.012 6.414 MetaclusterMFIs 6.361 0.012 6.392 GetMetaclusters 6.240 0.060 6.318 GetMetaclusterMFIs 6.004 0.056 6.079 NClusters 5.985 0.020 6.043 GetPercentages 5.872 0.055 5.945 GetMetaclusterCVs 5.878 0.040 5.934 GetMFIs 5.772 0.092 5.879 MetaclusterCVs 5.783 0.044 5.843 GetMetaclusterPercentagesPositive 5.771 0.028 5.815 print.FlowSOM 5.699 0.020 5.732 GetCounts 5.532 0.092 5.637 GetClusterMFIs 5.364 0.184 5.560 GetClusterPercentagesPositive 5.365 0.123 5.500 GetClusters 5.317 0.116 5.445 FlowSOMSubset 5.312 0.016 5.337 * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.