############################################################################## ############################################################################## ### ### 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_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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 ‘2.15.0’ * 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 PlotDimRed 78.779 0.144 78.979 FlowSOMmary 74.883 0.339 75.225 PlotOutliers 25.362 0.044 25.458 PlotMarker 22.079 0.072 22.186 UpdateMetaclusters 21.561 0.044 21.648 PlotStars 18.336 0.020 18.395 GroupStats 16.478 0.044 16.547 FlowSOM 15.926 0.040 15.992 PlotGroups 15.106 0.020 15.155 AddAnnotation 11.726 0.140 11.889 QueryMultiple 11.553 0.072 11.650 query_multiple 11.454 0.012 11.486 Plot2DScatters 10.636 0.056 10.711 PlotManualBars 10.431 0.012 10.462 GetFlowJoLabels 9.336 0.124 9.476 PlotNumbers 9.269 0.012 9.297 PlotNode 9.121 0.024 9.161 PlotVariable 9.073 0.016 9.107 QueryStarPlot 8.847 0.016 8.880 CountGroups 8.624 0.068 8.706 PlotPies 8.374 0.067 8.460 UpdateNodeSize 8.013 0.056 8.083 PlotFlowSOM 7.677 0.040 7.731 SaveClustersToFCS 7.497 0.012 7.524 NMetaclusters 7.262 0.067 7.341 GetFeatures 7.191 0.087 7.291 PlotLabels 7.077 0.016 7.104 MetaclusterMFIs 6.962 0.016 6.995 NClusters 6.889 0.012 6.910 GetMetaclusterCVs 6.580 0.040 6.629 TestOutliers 6.593 0.004 6.608 GetMetaclusters 6.468 0.012 6.489 PlotOverview2D 6.350 0.024 6.386 MetaclusterCVs 6.262 0.020 6.292 GetMFIs 6.123 0.080 6.212 print.FlowSOM 6.140 0.032 6.184 GetMetaclusterMFIs 6.082 0.064 6.155 GetMetaclusterPercentagesPositive 6.041 0.032 6.081 GetPercentages 6.062 0.004 6.082 GetClusterMFIs 5.617 0.184 5.810 GetClusters 5.677 0.084 5.770 GetClusterPercentagesPositive 5.639 0.056 5.705 GetCounts 5.660 0.004 5.674 FlowSOMSubset 5.522 0.016 5.547 NewData 5.049 0.008 5.065 * 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-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.