############################################################################## ############################################################################## ### ### 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 4.4.2 (2024-10-31) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403) * 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 PlotDimRed 75.049 0.329 75.596 FlowSOMmary 67.821 0.406 68.309 PlotOutliers 24.660 0.044 24.765 PlotMarker 21.913 0.088 22.058 UpdateMetaclusters 20.939 0.104 21.101 PlotStars 17.724 0.611 18.376 GroupStats 15.589 0.028 15.665 FlowSOM 14.751 0.115 14.908 PlotGroups 14.543 0.028 14.612 QueryMultiple 11.310 0.159 11.501 AddAnnotation 11.050 0.363 11.450 query_multiple 11.023 0.051 11.104 PlotManualBars 10.624 0.012 10.665 Plot2DScatters 9.739 0.056 9.845 PlotNode 9.452 0.064 9.541 GetFlowJoLabels 8.685 0.131 8.849 QueryStarPlot 8.541 0.136 8.700 PlotNumbers 8.468 0.012 8.501 PlotVariable 8.286 0.192 8.499 PlotPies 8.261 0.023 8.306 CountGroups 7.725 0.056 7.803 UpdateNodeSize 7.643 0.072 7.736 SaveClustersToFCS 7.258 0.039 7.317 PlotFlowSOM 7.127 0.028 7.175 PlotLabels 6.986 0.004 7.011 GetFeatures 6.652 0.016 6.690 NMetaclusters 6.506 0.027 6.558 NClusters 6.247 0.024 6.289 MetaclusterMFIs 6.249 0.008 6.273 PlotOverview2D 6.193 0.024 6.235 print.FlowSOM 6.109 0.020 6.147 TestOutliers 6.014 0.052 6.083 GetMetaclusterMFIs 6.007 0.028 6.053 MetaclusterCVs 5.786 0.036 5.840 GetMetaclusterPercentagesPositive 5.793 0.016 5.828 GetPercentages 5.642 0.000 5.658 GetMFIs 5.593 0.016 5.627 GetMetaclusters 5.585 0.020 5.621 GetMetaclusterCVs 5.570 0.008 5.594 GetClusterPercentagesPositive 5.306 0.047 5.371 FlowSOMSubset 5.326 0.012 5.354 GetCounts 5.296 0.016 5.329 GetClusters 5.207 0.032 5.257 GetClusterMFIs 5.146 0.072 5.234 * 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.