############################################################################## ############################################################################## ### ### 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_2.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.16.0’ * 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'pipe.Rd': ‘[magrittr:pipe]{%>%}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 62.252 3.216 66.252 PlotDimRed 52.095 4.098 56.952 PlotOutliers 29.531 0.774 30.431 PlotMarker 19.321 1.618 21.245 UpdateMetaclusters 17.614 1.416 19.163 PlotStars 15.297 0.976 16.318 GroupStats 12.996 1.359 14.663 FlowSOM 12.832 1.014 14.011 PlotGroups 11.680 1.457 13.290 QueryMultiple 10.980 0.685 11.788 query_multiple 10.701 0.623 11.343 Plot2DScatters 10.620 0.645 11.386 AddAnnotation 9.747 0.727 10.665 PlotManualBars 9.221 0.992 10.368 GetFlowJoLabels 8.686 0.752 9.482 PlotPies 8.529 0.695 9.266 PlotNode 7.800 1.017 8.929 PlotVariable 7.765 0.879 8.662 QueryStarPlot 8.126 0.446 8.590 PlotNumbers 6.900 0.705 7.646 PlotFlowSOM 6.394 1.183 7.711 CountGroups 6.863 0.623 7.539 PlotOverview2D 6.857 0.598 7.469 NClusters 5.749 1.168 7.033 PlotLabels 6.102 0.677 6.833 SaveClustersToFCS 6.044 0.691 6.748 NMetaclusters 5.454 1.244 6.779 GetMetaclusterMFIs 5.660 0.957 6.686 GetFeatures 5.942 0.655 6.674 print.FlowSOM 5.752 0.773 6.550 UpdateNodeSize 6.143 0.300 6.468 TestOutliers 5.587 0.782 6.411 MetaclusterMFIs 5.690 0.670 6.407 GetMetaclusterCVs 5.199 0.989 6.244 GetClusterMFIs 5.400 0.491 6.154 MetaclusterCVs 5.284 0.572 5.901 GetClusters 5.278 0.568 5.868 GetCounts 4.998 0.831 5.904 GetMetaclusters 5.192 0.624 5.855 GetPercentages 5.172 0.625 5.846 GetMFIs 5.155 0.619 5.811 GetMetaclusterPercentagesPositive 5.029 0.580 5.646 NewData 5.037 0.464 5.555 GetClusterPercentagesPositive 4.923 0.550 5.509 FlowSOMSubset 4.746 0.660 5.553 * 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: 3 NOTEs See ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.