############################################################################## ############################################################################## ### ### 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 12.7.6 * 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 93.485 2.565 115.374 PlotDimRed 75.493 2.595 89.771 PlotOutliers 39.153 0.787 47.373 PlotMarker 33.253 1.096 39.258 UpdateMetaclusters 33.069 1.185 40.804 PlotStars 28.471 0.920 33.096 GroupStats 26.547 0.879 32.121 FlowSOM 23.185 0.969 28.880 PlotGroups 22.550 0.905 26.603 AddAnnotation 17.336 0.700 22.200 QueryMultiple 17.511 0.432 20.343 query_multiple 17.366 0.494 20.279 Plot2DScatters 16.318 0.639 19.658 PlotManualBars 15.078 0.661 18.344 GetFlowJoLabels 13.873 0.664 16.969 PlotNode 12.995 0.612 15.432 PlotNumbers 12.665 0.594 15.070 QueryStarPlot 12.727 0.308 14.652 UpdateNodeSize 12.629 0.269 15.815 PlotVariable 12.247 0.645 14.770 GetFeatures 12.362 0.388 14.841 PlotPies 11.675 0.615 13.641 CountGroups 11.427 0.580 14.960 PlotFlowSOM 10.462 0.688 12.735 MetaclusterMFIs 9.928 0.698 12.717 SaveClustersToFCS 9.809 0.592 11.391 PlotLabels 9.614 0.555 11.601 NMetaclusters 9.227 0.660 11.667 NClusters 9.285 0.570 12.445 TestOutliers 9.052 0.564 10.905 GetMetaclusterPercentagesPositive 8.700 0.596 11.065 FlowSOMSubset 8.758 0.378 10.710 MetaclusterCVs 8.535 0.589 11.105 GetMetaclusterCVs 8.480 0.538 10.928 GetMFIs 8.404 0.582 10.636 PlotOverview2D 8.335 0.520 10.753 GetMetaclusters 8.026 0.539 10.418 print.FlowSOM 7.999 0.552 10.015 GetPercentages 8.010 0.540 9.931 GetMetaclusterMFIs 7.996 0.519 10.086 GetClusterMFIs 7.937 0.516 10.190 GetClusterPercentagesPositive 7.656 0.444 9.464 GetCounts 7.669 0.410 9.407 GetClusters 7.605 0.439 9.402 NewData 7.527 0.406 9.230 ReadInput 6.690 0.454 7.950 MetaClustering 6.562 0.433 8.241 metaClustering_consensus 5.319 0.367 6.705 PlotSD 4.630 0.228 5.409 * 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.