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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings FlowSOM_2.19.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-15 03:47:02 UTC
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.19.4’
* 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 13.3.0-6ubuntu2~24.04.1) 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 ... OK
* 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 ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
FlowSOMmary                       54.067  0.620  54.315
PlotDimRed                        47.470  0.133  47.554
PlotOutliers                      28.931  0.076  29.007
PlotMarker                        18.887  0.032  18.919
UpdateMetaclusters                16.894  0.023  16.917
PlotStars                         15.152  0.018  15.171
GroupStats                        13.008  0.097  13.084
query_multiple                    12.488  0.017  13.617
PlotGroups                        11.754  0.016  11.770
FlowSOM                           11.429  0.042  11.471
QueryMultiple                     10.522  0.040  10.562
Plot2DScatters                     9.653  0.041   9.706
Plot1DScatters                     8.885  0.047   8.915
PlotManualBars                     8.699  0.015   8.714
GetFlowJoLabels                    8.578  0.035   8.616
AddAnnotation                      8.157  0.156   8.316
QueryStarPlot                      8.166  0.009   8.175
PlotPies                           7.748  0.045   7.793
PlotNumbers                        7.712  0.013   7.725
PlotVariable                       7.685  0.018   7.703
PlotNode                           7.449  0.028   7.477
CountGroups                        6.603  0.045   6.649
MetaClustering                     6.365  0.051   7.014
GetMajorityLabels                  6.035  0.025   6.061
PlotFlowSOM                        5.988  0.030   6.018
UpdateNodeSize                     5.952  0.004   5.956
SaveClustersToFCS                  5.933  0.018   5.951
GetFeatures                        5.865  0.004   5.869
GetMetaclusterPercentagesPositive  5.784  0.012   5.797
PlotOverview2D                     5.688  0.047   5.735
PlotLabels                         5.683  0.013   5.697
GetMFIs                            5.528  0.018   5.575
MetaclusterCVs                     5.438  0.065   5.510
MetaclusterMFIs                    5.327  0.014   5.352
GetMetaclusterCVs                  5.289  0.017   5.307
NMetaclusters                      5.239  0.053   5.292
NClusters                          5.244  0.012   5.256
TestOutliers                       5.177  0.006   5.183
GetMetaclusterMFIs                 5.151  0.019   5.170
PlotMFIHeatmap                     5.137  0.005   5.143
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.19.4’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c som.c -o som.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-FlowSOM/00new/FlowSOM/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FlowSOM)