############################################################################## ############################################################################## ### ### 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_2.18.0.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 ‘2.18.0’ * 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 73.374 0.363 73.821 PlotDimRed 72.717 0.159 73.029 PlotOutliers 43.787 0.112 44.025 PlotMarker 23.914 0.191 24.172 UpdateMetaclusters 22.835 0.072 22.968 PlotStars 19.682 0.019 19.759 GroupStats 17.163 0.115 17.333 FlowSOM 15.875 0.072 15.992 PlotGroups 15.691 0.020 15.756 QueryMultiple 13.478 0.020 13.538 query_multiple 13.232 0.076 13.346 Plot2DScatters 13.202 0.064 13.310 AddAnnotation 12.007 0.107 12.154 PlotManualBars 11.659 0.016 11.711 QueryStarPlot 10.300 0.096 10.427 GetFlowJoLabels 9.440 0.196 9.670 PlotNode 9.294 0.024 9.347 PlotNumbers 9.225 0.012 9.263 PlotPies 8.818 0.024 8.868 PlotVariable 8.746 0.019 8.793 UpdateNodeSize 8.559 0.055 8.639 CountGroups 7.918 0.068 8.006 PlotFlowSOM 7.386 0.076 7.481 GetFeatures 7.267 0.079 7.371 SaveClustersToFCS 7.174 0.032 7.227 PlotOverview2D 7.043 0.060 7.121 PlotLabels 7.008 0.008 7.037 NClusters 6.448 0.016 6.484 MetaclusterMFIs 6.402 0.028 6.449 TestOutliers 6.403 0.024 6.444 NMetaclusters 6.393 0.020 6.437 GetClusterPercentagesPositive 5.836 0.227 6.082 print.FlowSOM 5.926 0.012 5.955 GetMetaclusterCVs 5.843 0.075 5.938 MetaclusterCVs 5.838 0.016 5.873 GetPercentages 5.778 0.044 5.840 GetMFIs 5.757 0.056 5.833 GetMetaclusterMFIs 5.759 0.048 5.824 GetMetaclusterPercentagesPositive 5.708 0.080 5.807 GetMetaclusters 5.705 0.056 5.779 GetCounts 5.506 0.132 5.655 GetClusterMFIs 5.442 0.195 5.655 GetClusters 5.510 0.100 5.625 FlowSOMSubset 5.528 0.012 5.558 * 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.