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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  /home/biocbuild/bbs-3.23-bioc/R/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]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                   53.813  0.697  54.169
PlotDimRed                    47.451  0.200  47.592
PlotOutliers                  29.540  0.468  30.012
PlotMarker                    19.412  0.609  20.027
UpdateMetaclusters            16.615  0.129  16.745
PlotStars                     14.174  0.190  14.366
GroupStats                    12.908  0.122  13.009
Plot2DScatters                12.092  0.105  12.197
FlowSOM                       11.363  0.033  11.397
PlotGroups                    11.076  0.082  11.158
PlotManualBars                 9.836  1.090  10.927
Plot1DScatters                10.775  0.101  10.975
query_multiple                 9.878  0.068   9.947
QueryMultiple                  9.766  0.058   9.828
AddAnnotation                  8.221  0.167   8.394
PlotNode                       8.024  0.187   8.213
PlotNumbers                    7.623  0.227   7.852
GetFlowJoLabels                7.561  0.147   7.709
PlotPies                       7.594  0.070   7.665
QueryStarPlot                  7.392  0.007   7.399
PlotVariable                   6.711  0.065   6.776
GetFeatures                    6.245  0.162   6.408
CountGroups                    5.919  0.178   6.097
PlotFlowSOM                    6.053  0.022   6.076
SaveClustersToFCS              5.888  0.018   5.907
UpdateNodeSize                 5.805  0.072   5.877
PlotLabels                     5.756  0.036   5.792
PlotOverview2D                 5.478  0.191   5.669
MetaclusterMFIs                5.507  0.073   5.584
GetClusterPercentagesPositive  5.269  0.236   5.506
NClusters                      5.249  0.013   5.263
NMetaclusters                  5.224  0.009   5.233
TestOutliers                   5.136  0.010   5.147
PlotMFIHeatmap                 5.038  0.008   5.047
GetPercentages                 4.942  0.059   5.001
* 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)