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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 (2026-03-30 r89742)
* 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: 2026-04-04 03:35:30 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                       56.882  0.535  57.085
PlotDimRed                        47.691  0.325  47.979
PlotOutliers                      33.576  0.542  35.299
PlotMarker                        18.897  0.029  18.927
UpdateMetaclusters                17.210  0.245  17.456
PlotStars                         15.996  0.719  16.718
GroupStats                        13.966  0.339  14.284
PlotGroups                        11.637  0.041  11.678
FlowSOM                           11.308  0.048  11.356
Plot2DScatters                    10.977  0.099  11.077
QueryMultiple                     10.615  0.416  11.031
query_multiple                    10.230  0.126  10.502
AddAnnotation                      9.001  0.168   9.171
PlotPies                           7.895  1.004   8.900
PlotOverview2D                     7.400  1.388   8.788
Plot1DScatters                     8.663  0.088   8.739
PlotVariable                       8.016  0.383   8.398
PlotManualBars                     8.268  0.034   8.303
QueryStarPlot                      7.999  0.258   8.258
GetFlowJoLabels                    7.612  0.033   7.646
PlotNode                           7.213  0.010   7.223
PlotNumbers                        6.990  0.020   7.012
SaveClustersToFCS                  6.144  0.155   6.300
GetMajorityLabels                  6.187  0.010   6.199
PlotFlowSOM                        6.003  0.041   6.044
UpdateNodeSize                     5.942  0.045   5.987
CountGroups                        5.708  0.032   5.742
TestOutliers                       5.543  0.105   5.648
GetMetaclusterMFIs                 5.313  0.317   5.630
GetMetaclusterPercentagesPositive  5.269  0.259   5.528
PlotLabels                         5.462  0.014   5.476
NClusters                          5.336  0.099   5.435
GetFeatures                        5.367  0.008   5.375
GetMetaclusterCVs                  5.357  0.014   5.371
MetaclusterMFIs                    5.243  0.045   5.288
NMetaclusters                      5.194  0.060   5.253
print.FlowSOM                      5.165  0.078   5.242
MetaclusterCVs                     5.118  0.118   5.237
GetMetaclusters                    4.928  0.179   5.108
GetPercentages                     4.949  0.138   5.087
* 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/usr/local/lib -o FlowSOM.so som.o
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)