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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: 2026-04-01 03:13:40 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                       52.981  0.486  53.164
PlotDimRed                        48.075  0.187  48.980
PlotOutliers                      28.687  0.153  28.840
PlotMarker                        17.702  0.067  17.770
UpdateMetaclusters                16.406  0.017  16.423
PlotStars                         14.395  0.015  14.410
GroupStats                        13.259  0.066  13.306
FlowSOM                           12.020  0.033  12.055
query_multiple                    10.982  0.013  10.996
PlotGroups                        10.438  0.026  10.464
QueryMultiple                     10.296  0.016  10.312
Plot2DScatters                     9.990  0.018  10.009
AddAnnotation                      8.932  0.206   9.140
Plot1DScatters                     8.746  0.068   8.800
PlotNode                           8.095  0.099   8.194
QueryStarPlot                      8.150  0.012   8.161
GetFlowJoLabels                    7.802  0.168   7.971
PlotManualBars                     7.927  0.013   7.941
PlotPies                           7.373  0.011   7.384
PlotNumbers                        7.239  0.015   7.255
PlotVariable                       7.133  0.010   7.143
MetaclusterMFIs                    6.197  0.015   6.212
UpdateNodeSize                     5.917  0.006   5.922
PlotOverview2D                     5.863  0.059   5.922
SaveClustersToFCS                  5.871  0.037   5.907
PlotFlowSOM                        5.876  0.018   5.895
TestOutliers                       5.867  0.009   5.877
CountGroups                        5.644  0.045   5.690
GetMFIs                            5.648  0.009   5.657
GetFeatures                        5.587  0.011   5.598
GetMetaclusters                    5.552  0.018   5.571
print.FlowSOM                      5.507  0.010   5.518
GetMajorityLabels                  5.303  0.010   5.314
PlotLabels                         5.292  0.015   5.307
GetMetaclusterCVs                  5.270  0.019   5.290
NMetaclusters                      5.196  0.065   5.260
GetMetaclusterPercentagesPositive  5.250  0.007   5.259
GetMetaclusterMFIs                 5.228  0.007   5.235
GetPercentages                     5.099  0.048   5.150
NClusters                          5.095  0.011   5.105
GetClusters                        5.093  0.006   5.100
* 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)