############################################################################## ############################################################################## ### ### 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: x86_64-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 Monterey 12.7.4 * 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 14.0.0 (clang-1400.0.29.202)’ * 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 98.169 2.350 113.970 PlotDimRed 78.133 2.309 88.875 PlotOutliers 40.122 0.801 45.136 PlotMarker 36.243 1.026 40.735 UpdateMetaclusters 34.650 1.171 39.508 PlotStars 29.864 0.882 33.335 GroupStats 28.260 0.868 32.129 FlowSOM 23.657 0.921 28.304 PlotGroups 23.540 0.855 26.683 QueryMultiple 19.186 0.407 22.077 query_multiple 19.154 0.437 23.205 AddAnnotation 18.279 0.676 21.416 Plot2DScatters 16.699 0.564 19.027 PlotManualBars 15.275 0.596 17.392 GetFlowJoLabels 14.292 0.540 16.223 PlotNode 13.737 0.601 15.812 QueryStarPlot 13.979 0.342 16.220 PlotPies 12.872 0.878 15.573 UpdateNodeSize 13.335 0.285 15.377 PlotNumbers 12.894 0.638 14.728 PlotVariable 12.596 0.648 14.828 GetFeatures 12.539 0.317 13.776 CountGroups 11.810 0.575 14.278 PlotFlowSOM 11.329 0.647 13.157 PlotLabels 10.217 0.488 11.337 SaveClustersToFCS 9.949 0.639 12.072 MetaclusterMFIs 9.581 0.585 11.522 NClusters 9.495 0.646 11.117 NMetaclusters 9.471 0.563 11.006 TestOutliers 9.065 0.594 10.697 FlowSOMSubset 8.930 0.369 10.700 PlotOverview2D 8.597 0.575 11.038 GetMFIs 8.477 0.536 9.820 MetaclusterCVs 8.365 0.516 9.715 GetPercentages 8.295 0.534 9.643 GetMetaclusters 8.285 0.536 9.824 GetMetaclusterPercentagesPositive 8.298 0.498 9.924 GetMetaclusterMFIs 8.150 0.548 9.746 print.FlowSOM 8.167 0.489 9.890 GetMetaclusterCVs 8.065 0.485 9.093 GetCounts 7.863 0.343 8.957 GetClusters 7.771 0.413 9.196 GetClusterMFIs 7.776 0.404 9.351 NewData 7.774 0.402 8.888 GetClusterPercentagesPositive 7.762 0.364 8.871 ReadInput 6.913 0.411 8.681 MetaClustering 6.742 0.442 7.892 metaClustering_consensus 5.529 0.314 6.602 PlotSD 4.417 0.155 5.220 * 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.