############################################################################## ############################################################################## ### ### 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: aarch64-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 Ventura 13.6.5 * 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 15.0.0 (clang-1500.1.0.2.5)’ * 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 53.076 1.730 71.373 PlotDimRed 39.223 1.669 57.191 PlotOutliers 20.101 0.601 27.959 PlotMarker 19.160 1.022 25.855 UpdateMetaclusters 18.414 0.892 26.084 PlotStars 15.693 0.762 20.988 GroupStats 14.520 0.766 20.552 FlowSOM 14.101 0.760 19.301 PlotGroups 12.539 0.810 17.715 AddAnnotation 10.757 0.488 14.699 QueryMultiple 10.720 0.427 15.190 query_multiple 10.567 0.404 14.598 Plot2DScatters 9.304 0.582 15.963 PlotManualBars 8.697 0.595 12.436 GetFlowJoLabels 8.520 0.487 12.105 PlotNumbers 8.291 0.684 10.783 QueryStarPlot 8.440 0.332 12.787 PlotNode 7.967 0.654 10.686 PlotVariable 7.762 0.544 10.640 PlotPies 7.570 0.526 11.361 CountGroups 7.319 0.437 10.427 PlotFlowSOM 6.741 0.615 9.322 PlotOverview2D 6.813 0.459 10.267 PlotLabels 6.613 0.524 10.248 SaveClustersToFCS 6.539 0.512 9.754 UpdateNodeSize 6.573 0.162 9.534 GetFeatures 6.416 0.300 9.406 NMetaclusters 6.101 0.589 7.623 print.FlowSOM 6.078 0.588 8.889 NClusters 6.081 0.578 8.630 MetaclusterMFIs 5.955 0.615 8.345 TestOutliers 6.074 0.472 8.448 GetCounts 6.036 0.357 8.932 GetMetaclusterPercentagesPositive 5.663 0.566 8.867 FlowSOMSubset 5.936 0.272 8.190 GetMetaclusters 5.563 0.559 8.658 MetaclusterCVs 5.620 0.466 7.871 GetPercentages 5.598 0.486 8.676 GetMetaclusterMFIs 5.548 0.498 7.859 GetMFIs 5.510 0.490 7.870 GetMetaclusterCVs 5.344 0.491 7.165 GetClusterMFIs 5.173 0.360 8.313 GetClusterPercentagesPositive 5.159 0.345 8.109 GetClusters 5.130 0.363 8.256 NewData 5.019 0.375 7.021 ReadInput 4.029 0.407 6.050 * 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.