############################################################################## ############################################################################## ### ### 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_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.12.0’ * 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 49.820 2.338 52.121 PlotDimRed 39.156 2.510 41.943 PlotMarker 18.672 1.504 20.291 PlotOutliers 18.136 1.248 19.475 UpdateMetaclusters 15.946 1.848 18.037 PlotStars 14.142 1.438 15.678 GroupStats 12.664 1.147 13.876 FlowSOM 11.695 1.211 12.966 PlotGroups 11.351 1.413 12.820 query_multiple 9.675 0.561 10.291 AddAnnotation 9.492 0.647 10.177 QueryMultiple 8.706 0.682 9.429 Plot2DScatters 7.754 1.107 8.931 PlotManualBars 7.478 1.053 8.585 GetFlowJoLabels 7.719 0.749 8.518 PlotNode 6.851 0.925 7.832 PlotPies 6.544 1.109 7.709 PlotVariable 6.545 1.016 7.601 PlotNumbers 6.430 1.019 7.497 QueryStarPlot 7.036 0.373 7.442 SaveClustersToFCS 5.708 1.063 6.859 NClusters 5.647 1.009 6.724 CountGroups 5.962 0.678 6.668 MetaclusterMFIs 5.428 1.124 6.624 PlotFlowSOM 5.536 0.861 6.437 UpdateNodeSize 5.871 0.281 6.172 PlotLabels 5.121 0.950 6.126 NMetaclusters 5.031 0.961 6.041 TestOutliers 4.911 0.976 5.940 GetMetaclusterMFIs 4.810 0.972 5.820 GetFeatures 5.105 0.523 5.654 print.FlowSOM 4.656 0.848 5.557 PlotOverview2D 4.612 0.850 5.508 GetMetaclusters 4.300 1.134 5.496 GetMFIs 4.616 0.815 5.477 MetaclusterCVs 4.447 0.857 5.349 GetPercentages 4.392 0.871 5.316 GetMetaclusterCVs 4.584 0.662 5.277 GetClusters 4.443 0.690 5.170 FlowSOMSubset 4.582 0.480 5.100 * 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-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.