############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed FlowSOMmary 60.585 2.774 64.418 PlotDimRed 53.194 2.958 56.934 PlotMarker 18.941 1.161 20.192 UpdateMetaclusters 17.818 1.297 19.228 PlotOutliers 17.166 0.683 18.011 PlotStars 15.267 1.030 16.405 GroupStats 13.950 0.986 15.396 FlowSOM 13.788 1.004 16.321 PlotGroups 11.527 0.993 12.626 AddAnnotation 10.317 0.656 12.119 query_multiple 10.213 0.517 10.803 QueryMultiple 9.748 0.373 10.246 Plot2DScatters 8.958 0.653 9.905 GetFlowJoLabels 8.725 0.700 9.629 PlotVariable 7.709 0.730 8.484 PlotManualBars 7.656 0.690 8.416 QueryStarPlot 7.548 0.400 7.978 CountGroups 7.225 0.649 9.636 PlotNode 7.115 0.643 7.824 PlotPies 6.847 0.758 7.641 PlotNumbers 6.709 0.687 7.470 PlotFlowSOM 6.327 0.613 6.981 TestOutliers 6.240 0.680 6.953 SaveClustersToFCS 6.197 0.696 6.923 MetaclusterMFIs 5.834 0.729 6.615 NClusters 5.837 0.722 6.599 GetPercentages 5.720 0.741 6.531 NMetaclusters 5.836 0.605 6.485 UpdateNodeSize 6.149 0.244 6.417 PlotLabels 5.875 0.501 6.452 GetFeatures 5.944 0.381 6.452 print.FlowSOM 5.300 0.757 6.096 MetaclusterCVs 5.377 0.642 6.166 PlotOverview2D 5.290 0.673 5.992 GetMetaclusterCVs 5.308 0.603 6.098 GetMetaclusters 5.192 0.651 5.883 GetMFIs 5.238 0.576 6.107 GetMetaclusterMFIs 5.202 0.610 5.846 GetClusters 5.191 0.513 5.733 FlowSOMSubset 5.270 0.369 5.681 GetClusterPercentagesPositive 4.879 0.477 5.402 GetMetaclusterPercentagesPositive 4.791 0.545 5.483 GetClusterMFIs 4.838 0.463 5.329 GetCounts 4.772 0.491 5.304 NewData 4.606 0.458 5.155 * 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.