############################################################################## ############################################################################## ### ### 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 4.4.1 (2024-06-14) * 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 ‘2.12.0’ * 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 98.070 2.630 121.135 PlotDimRed 77.717 2.748 92.409 PlotOutliers 41.085 0.903 51.695 PlotMarker 35.714 1.149 41.278 UpdateMetaclusters 34.777 1.077 41.759 PlotStars 30.808 1.048 36.640 GroupStats 27.994 0.853 33.879 PlotGroups 24.021 0.946 28.038 FlowSOM 23.440 0.884 28.389 QueryMultiple 19.519 0.504 23.136 query_multiple 19.273 0.500 22.665 AddAnnotation 18.299 0.702 23.362 Plot2DScatters 16.690 0.605 19.479 PlotManualBars 15.577 0.679 18.770 GetFlowJoLabels 14.687 0.551 17.969 PlotNode 14.059 0.615 16.464 QueryStarPlot 14.156 0.359 17.095 PlotNumbers 13.464 0.705 17.066 UpdateNodeSize 13.644 0.306 15.866 PlotVariable 12.933 0.670 15.969 GetFeatures 13.096 0.329 15.426 PlotPies 12.283 0.670 14.809 CountGroups 11.752 0.533 14.592 PlotFlowSOM 11.116 0.621 13.408 SaveClustersToFCS 10.096 0.645 12.557 PlotLabels 10.080 0.549 12.519 NClusters 9.567 0.677 12.222 MetaclusterMFIs 9.466 0.593 12.053 TestOutliers 9.404 0.564 11.462 NMetaclusters 8.977 0.591 11.226 FlowSOMSubset 8.951 0.374 10.751 GetMFIs 8.507 0.608 11.017 PlotOverview2D 8.494 0.531 10.170 MetaclusterCVs 8.283 0.573 10.625 GetMetaclusterMFIs 8.261 0.573 10.691 GetMetaclusterCVs 8.303 0.504 10.499 GetMetaclusters 8.240 0.539 10.210 GetPercentages 8.284 0.480 10.178 GetMetaclusterPercentagesPositive 8.246 0.502 10.430 print.FlowSOM 8.143 0.593 9.875 GetCounts 7.976 0.410 9.627 GetClusterPercentagesPositive 7.908 0.375 9.673 GetClusters 7.824 0.386 9.540 NewData 7.708 0.438 9.312 GetClusterMFIs 7.697 0.380 9.460 MetaClustering 7.069 0.562 9.272 ReadInput 6.878 0.416 8.522 metaClustering_consensus 5.287 0.367 6.338 PlotSD 4.350 0.160 5.024 * 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.