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### Running command:
###
###   /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_2.19.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘2.19.3’
* 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 ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-3.23-bioc/R/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
See ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck/00install.out’ for details.
* 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 ... 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                       52.768  0.535  52.970
PlotDimRed                        45.993  0.140  46.047
PlotOutliers                      30.438  0.084  30.523
UpdateMetaclusters                21.902  0.020  22.001
PlotMarker                        19.129  0.086  19.215
PlotStars                         14.664  0.019  14.684
GroupStats                        12.948  0.038  12.970
PlotGroups                        11.704  0.046  11.750
FlowSOM                           11.502  0.036  11.539
query_multiple                    10.879  0.021  10.901
Plot2DScatters                    10.269  0.026  10.296
QueryMultiple                      9.987  0.017  10.007
Plot1DScatters                     9.521  0.060   9.563
PlotManualBars                     9.351  0.009   9.362
PlotNumbers                        8.602  0.022   8.625
PlotNode                           8.471  0.097   8.569
AddAnnotation                      8.236  0.136   8.374
PlotVariable                       8.102  0.025   8.127
GetMetaclusterPercentagesPositive  7.943  0.055   8.163
PlotPies                           7.915  0.053   7.969
QueryStarPlot                      7.815  0.043   7.860
GetFlowJoLabels                    7.555  0.092   7.653
PlotOverview2D                     6.534  0.047   6.581
GetFeatures                        6.006  0.011   6.018
PlotLabels                         5.998  0.014   6.012
PlotFlowSOM                        5.937  0.013   5.950
NClusters                          5.917  0.012   5.931
UpdateNodeSize                     5.861  0.008   5.868
SaveClustersToFCS                  5.816  0.032   5.849
CountGroups                        5.715  0.054   5.769
print.FlowSOM                      5.613  0.012   5.625
MetaclusterMFIs                    5.586  0.010   5.597
NMetaclusters                      5.447  0.079   5.527
GetMetaclusterCVs                  5.424  0.016   5.441
TestOutliers                       5.376  0.011   5.387
GetMetaclusterMFIs                 5.278  0.073   5.352
PlotMFIHeatmap                     5.254  0.010   5.264
GetClusters                        5.060  0.015   5.074
GetMetaclusters                    5.049  0.011   5.073
* 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 WARNING, 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 ‘2.19.3’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 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
In file included from som.c:11:
/home/biocbuild/bbs-3.23-bioc/R/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]
   35 | #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed
      |  ^~~~~~~
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)