############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:FlowSOM.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings FlowSOM_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 whether package 'FlowSOM' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.3.0' * 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 for x64 is not available File 'E:/biocbuild/bbs-3.21-bioc/R/library/FlowSOM/libs/x64/FlowSOM.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 54.25 1.97 56.33 PlotDimRed 44.67 0.64 45.26 PlotOutliers 21.45 0.72 22.20 PlotMarker 19.83 1.12 20.95 UpdateMetaclusters 17.50 1.21 18.70 PlotStars 17.27 1.22 18.48 GroupStats 15.08 1.02 16.10 FlowSOM 14.09 0.79 14.89 PlotGroups 13.14 1.44 14.60 QueryMultiple 11.26 0.64 11.94 AddAnnotation 10.58 0.55 11.25 query_multiple 10.55 0.58 11.13 Plot2DScatters 9.25 1.61 11.27 PlotManualBars 8.75 0.80 9.58 PlotVariable 8.61 0.72 9.33 GetFlowJoLabels 8.27 0.98 9.64 QueryStarPlot 8.31 0.51 8.82 PlotNumbers 8.14 0.66 8.89 PlotPies 7.71 0.64 8.36 PlotNode 7.33 0.58 7.91 PlotFlowSOM 6.87 0.97 7.84 CountGroups 6.94 0.79 7.74 NClusters 6.59 0.86 7.45 PlotLabels 6.58 0.70 7.28 SaveClustersToFCS 6.33 0.83 7.16 UpdateNodeSize 6.89 0.25 7.14 GetFeatures 6.64 0.47 7.11 NMetaclusters 6.19 0.86 7.14 print.FlowSOM 5.86 0.80 6.65 MetaclusterMFIs 5.60 0.88 6.47 GetMFIs 5.41 0.74 6.14 GetMetaclusterPercentagesPositive 5.25 0.82 6.06 GetMetaclusters 5.26 0.79 6.07 TestOutliers 5.52 0.48 6.00 GetMetaclusterCVs 5.14 0.77 5.90 GetMetaclusterMFIs 5.07 0.76 5.83 FlowSOMSubset 5.40 0.42 5.81 PlotOverview2D 5.05 0.64 5.69 GetCounts 4.87 0.80 5.67 GetClusterMFIs 4.97 0.66 5.63 GetClusterPercentagesPositive 4.90 0.72 5.62 MetaclusterCVs 4.78 0.79 5.58 NewData 5.12 0.42 5.55 GetClusters 4.66 0.84 5.50 GetPercentages 4.78 0.72 5.50 * 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 'E:/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log' for details.