############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings FlowSOM_2.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘FlowSOM/DESCRIPTION’ ... OK * this is package ‘FlowSOM’ version ‘2.17.0’ * 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 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 loading without being on the library search path ... 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 ... NOTE Non-topic package-anchored link(s) in Rd file 'pipe.Rd': ‘[magrittr:pipe]{%>%}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed FlowSOMmary 47.518 0.367 47.687 PlotDimRed 45.637 0.227 45.824 PlotOutliers 17.128 0.010 17.137 PlotMarker 15.399 0.070 15.471 UpdateMetaclusters 14.854 0.032 14.888 PlotStars 13.316 0.021 13.339 GroupStats 11.956 0.061 12.018 FlowSOM 11.002 0.112 11.115 PlotGroups 10.606 0.021 10.628 AddAnnotation 8.413 0.497 8.915 QueryMultiple 8.816 0.018 8.834 query_multiple 8.089 0.010 8.100 Plot2DScatters 7.680 0.064 7.733 PlotManualBars 6.804 0.014 6.820 GetFlowJoLabels 6.519 0.254 6.650 PlotNode 6.547 0.028 6.576 QueryStarPlot 6.510 0.005 6.515 PlotVariable 6.415 0.021 6.438 PlotNumbers 6.117 0.015 6.133 PlotFlowSOM 5.948 0.059 6.008 PlotPies 5.861 0.010 5.872 UpdateNodeSize 5.398 0.012 5.409 CountGroups 5.021 0.045 5.067 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’ for details.