############################################################################## ############################################################################## ### ### 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_2.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.3 (2025-02-28) * 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 13.7.1 * 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: ‘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 56.897 2.667 59.890 PlotDimRed 51.171 3.412 55.136 PlotMarker 16.824 1.328 18.255 UpdateMetaclusters 16.582 1.164 17.776 PlotOutliers 16.149 0.853 17.037 PlotStars 13.411 1.193 14.639 GroupStats 13.408 0.974 14.452 FlowSOM 13.066 1.088 14.294 PlotGroups 10.664 1.475 12.266 AddAnnotation 9.301 0.625 9.970 QueryMultiple 9.086 0.566 9.790 query_multiple 8.986 0.553 9.562 Plot2DScatters 8.530 0.681 9.252 GetFlowJoLabels 7.856 0.652 8.538 PlotManualBars 7.675 0.761 8.464 PlotVariable 7.629 0.802 8.480 CountGroups 7.248 0.610 8.006 PlotNode 6.828 0.633 7.474 QueryStarPlot 6.753 0.436 7.190 PlotPies 6.297 0.806 7.127 PlotNumbers 6.288 0.743 7.053 PlotFlowSOM 5.910 0.661 6.592 SaveClustersToFCS 5.766 0.631 6.409 GetMFIs 5.389 0.735 6.193 NClusters 4.961 1.067 6.199 PlotLabels 5.379 0.603 6.004 MetaclusterMFIs 5.247 0.614 5.982 TestOutliers 5.335 0.518 5.858 GetFeatures 5.461 0.372 5.850 UpdateNodeSize 5.412 0.230 5.650 PlotOverview2D 5.026 0.571 5.605 print.FlowSOM 4.903 0.680 5.643 MetaclusterCVs 4.944 0.613 5.638 GetMetaclusters 4.835 0.709 5.581 GetClusterPercentagesPositive 4.869 0.643 5.550 GetMetaclusterPercentagesPositive 4.807 0.645 5.514 GetMetaclusterMFIs 4.825 0.624 5.467 GetPercentages 4.827 0.607 5.443 GetClusters 4.547 0.632 5.206 GetCounts 4.492 0.593 5.097 GetClusterMFIs 4.441 0.562 5.012 NMetaclusters 4.344 0.655 5.390 GetMetaclusterCVs 4.393 0.585 5.057 * 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.