############################################################################## ############################################################################## ### ### 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_2.13.0.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 ‘2.13.0’ * 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 (GCC) 10.3.1’ * 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 83.335 0.171 83.643 FlowSOMmary 78.502 0.667 79.204 PlotOutliers 24.919 0.212 25.183 PlotMarker 23.900 0.427 24.381 UpdateMetaclusters 22.414 0.136 22.601 PlotStars 19.188 0.104 19.335 GroupStats 17.569 0.076 17.685 FlowSOM 16.640 0.215 16.892 PlotGroups 15.961 0.056 16.049 QueryMultiple 12.974 0.040 13.044 AddAnnotation 12.387 0.391 12.806 query_multiple 12.309 0.060 12.397 Plot2DScatters 10.776 0.036 10.830 PlotManualBars 10.608 0.012 10.644 GetFlowJoLabels 9.781 0.112 9.920 PlotNode 9.397 0.243 9.663 QueryStarPlot 9.392 0.044 9.459 PlotNumbers 9.168 0.136 9.323 CountGroups 9.069 0.108 9.196 PlotVariable 8.994 0.092 9.107 PlotPies 8.973 0.035 9.028 PlotFlowSOM 7.934 0.028 7.980 SaveClustersToFCS 7.782 0.079 7.881 UpdateNodeSize 7.837 0.016 7.870 GetFeatures 7.269 0.116 7.402 PlotLabels 7.328 0.020 7.364 NMetaclusters 7.143 0.044 7.202 NClusters 7.111 0.040 7.168 MetaclusterMFIs 6.986 0.040 7.041 TestOutliers 6.675 0.032 6.721 PlotOverview2D 6.575 0.067 6.657 GetMetaclusterCVs 6.402 0.056 6.473 GetMFIs 6.301 0.091 6.407 GetPercentages 6.314 0.032 6.357 GetMetaclusterPercentagesPositive 6.282 0.040 6.342 GetMetaclusterMFIs 6.286 0.036 6.336 GetCounts 6.250 0.068 6.332 print.FlowSOM 6.278 0.024 6.317 MetaclusterCVs 6.278 0.015 6.305 GetMetaclusters 6.221 0.064 6.299 GetClusterMFIs 5.804 0.256 6.070 GetClusters 5.914 0.092 6.025 GetClusterPercentagesPositive 5.782 0.135 5.931 FlowSOMSubset 5.627 0.024 5.662 NewData 5.145 0.036 5.192 * 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.