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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_2.19.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* 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 ‘2.19.1’
* 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 ... ERROR
Found the following files with duplicate lower-cased file names:
  man/plotStarLegend.Rd
File names must not differ just by case to be usable on all R
platforms.
Please rename the files and try again.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
 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  /home/biocbuild/bbs-3.23-bioc/R/include/R_ext/PrtUtil.h:35:2: warning: #warning non-API header file R_ext/PrtUtil.h is obsolete and will be removed [-Wcpp]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 ... WARNING
Rd files with duplicated name 'PlotStarLegend':
  ‘PlotStarLegend.Rd’ ‘plotStarLegend.Rd’
Rd files with duplicated alias 'PlotStarLegend':
  ‘PlotStarLegend.Rd’ ‘plotStarLegend.Rd’
* 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        52.513  0.532  52.769
PlotDimRed         44.684  0.130  44.751
PlotOutliers       28.470  0.063  28.534
PlotMarker         19.090  0.030  19.122
UpdateMetaclusters 16.250  0.017  16.267
PlotStars          14.698  0.040  14.739
GroupStats         13.099  0.097  13.178
PlotGroups         11.308  0.041  11.350
FlowSOM            11.233  0.106  11.339
QueryMultiple      10.191  0.058  10.248
Plot2DScatters      9.995  0.013  10.012
query_multiple      9.875  0.008   9.883
Plot1DScatters      9.166  0.012   9.168
AddAnnotation       8.455  0.212   8.671
PlotManualBars      8.108  0.009   8.116
PlotNode            8.021  0.010   8.031
QueryStarPlot       7.657  0.043   7.701
GetFlowJoLabels     7.387  0.061   7.452
PlotNumbers         7.220  0.012   7.234
PlotPies            7.136  0.061   7.197
PlotVariable        6.969  0.050   7.020
PlotOverview2D      6.754  0.060   6.815
PlotFlowSOM         6.517  0.051   6.568
UpdateNodeSize      5.952  0.003   5.955
GetFeatures         5.802  0.067   5.870
PlotLabels          5.747  0.013   5.761
NClusters           5.698  0.015   5.712
SaveClustersToFCS   5.602  0.034   5.637
TestOutliers        5.559  0.010   5.570
MetaclusterMFIs     5.449  0.072   5.521
CountGroups         5.470  0.049   5.520
NMetaclusters       5.317  0.048   5.365
PlotMFIHeatmap      5.068  0.005   5.074
MetaclusterCVs      5.025  0.008   5.035
* 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 ERROR, 2 WARNINGs, 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 ‘2.19.1’
** 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)