############################################################################## ############################################################################## ### ### 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 95.534 2.769 128.573 PlotDimRed 78.117 2.988 96.500 PlotOutliers 40.859 0.905 49.542 PlotMarker 36.335 1.120 44.061 UpdateMetaclusters 35.238 1.163 45.504 PlotStars 30.380 0.969 35.972 GroupStats 28.265 0.883 33.714 PlotGroups 24.132 0.984 29.562 FlowSOM 24.046 0.974 30.550 QueryMultiple 19.980 0.486 25.222 query_multiple 19.189 0.520 22.845 AddAnnotation 18.175 0.685 23.963 Plot2DScatters 16.613 0.673 20.134 PlotManualBars 15.518 0.691 18.929 GetFlowJoLabels 14.909 0.704 19.167 QueryStarPlot 14.413 0.418 17.960 PlotNode 13.707 0.636 16.357 UpdateNodeSize 13.706 0.329 17.202 PlotVariable 13.137 0.622 18.341 PlotNumbers 12.973 0.627 16.064 GetFeatures 12.803 0.488 16.448 PlotPies 12.305 0.637 14.816 CountGroups 12.031 0.543 14.667 PlotFlowSOM 11.470 0.677 14.268 SaveClustersToFCS 10.285 0.681 13.371 MetaclusterMFIs 10.039 0.700 13.087 PlotLabels 9.941 0.520 12.333 NMetaclusters 9.549 0.680 12.340 TestOutliers 9.130 0.581 11.646 NClusters 8.923 0.615 11.323 FlowSOMSubset 8.735 0.407 11.056 PlotOverview2D 8.589 0.485 10.657 GetMFIs 8.328 0.573 10.855 GetPercentages 8.332 0.566 10.140 GetMetaclusterPercentagesPositive 8.260 0.584 10.480 MetaclusterCVs 8.275 0.509 10.566 GetMetaclusterCVs 8.244 0.537 10.548 GetMetaclusterMFIs 8.184 0.554 10.400 print.FlowSOM 8.164 0.559 10.613 GetMetaclusters 8.168 0.540 10.085 GetClusterPercentagesPositive 8.097 0.437 10.281 GetCounts 7.904 0.450 10.288 GetClusters 7.791 0.450 10.298 GetClusterMFIs 7.784 0.433 10.035 NewData 7.754 0.421 9.714 ReadInput 6.929 0.509 9.028 MetaClustering 6.255 0.471 8.458 metaClustering_consensus 5.442 0.348 7.012 PlotSD 4.418 0.128 5.402 * 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.