############################################################################## ############################################################################## ### ### 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_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’ * using R Under development (unstable) (2025-01-22 r87618) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.15.0’ * 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 50.495 2.273 52.824 PlotDimRed 42.176 2.710 45.252 PlotOutliers 20.256 0.835 21.338 PlotMarker 18.189 1.336 19.807 UpdateMetaclusters 17.294 1.478 19.034 PlotStars 15.474 1.326 17.021 GroupStats 13.795 0.951 14.858 PlotGroups 12.977 1.361 14.543 FlowSOM 11.953 1.005 13.053 Plot2DScatters 9.312 0.833 10.250 AddAnnotation 9.480 0.638 10.207 QueryMultiple 9.451 0.479 10.051 query_multiple 9.084 0.568 9.753 PlotManualBars 7.729 0.880 8.672 PlotNode 7.532 0.754 8.389 GetFlowJoLabels 7.591 0.648 8.322 PlotNumbers 6.963 0.803 7.863 PlotVariable 6.957 0.794 7.846 PlotPies 6.790 0.870 7.762 QueryStarPlot 7.117 0.344 7.542 PlotLabels 6.224 0.719 7.001 SaveClustersToFCS 5.988 0.833 6.923 CountGroups 6.110 0.625 6.790 PlotFlowSOM 5.872 0.814 6.741 MetaclusterMFIs 5.801 0.797 6.682 NMetaclusters 5.689 0.904 6.673 NClusters 5.578 0.835 6.481 UpdateNodeSize 6.125 0.251 6.449 MetaclusterCVs 5.582 0.792 6.456 GetFeatures 5.457 0.478 6.000 TestOutliers 5.203 0.685 5.969 PlotOverview2D 4.800 0.612 5.488 GetMFIs 4.581 0.801 5.459 GetMetaclusterCVs 4.728 0.626 5.391 GetMetaclusterMFIs 4.676 0.620 5.384 GetMetaclusters 4.468 0.785 5.298 GetMetaclusterPercentagesPositive 4.575 0.659 5.275 print.FlowSOM 4.355 0.688 5.095 GetPercentages 4.371 0.602 5.013 GetClusterPercentagesPositive 4.457 0.500 5.003 * 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-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.