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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings FlowSOM_2.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘2.16.0’
* 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) 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 ... NOTE
checkRd: (-1) PlotDimRed.Rd:55: Lost braces
    55 | of the dimred default = function(dimred){dimred$Y}.}
       |                                         ^
* 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
FlowSOMmary        50.502  0.593  50.890
PlotDimRed         44.061  0.197  44.236
PlotOutliers       30.376  0.055  30.436
PlotMarker         17.445  0.021  17.467
UpdateMetaclusters 16.233  0.016  16.256
PlotStars          14.795  0.068  14.864
GroupStats         12.274  0.009  12.283
FlowSOM            11.474  0.038  11.513
PlotGroups         10.710  0.034  10.745
query_multiple      9.707  0.006   9.713
Plot2DScatters      9.349  0.022   9.360
QueryMultiple       9.293  0.014   9.307
AddAnnotation       8.710  0.190   8.900
PlotManualBars      8.265  0.013   8.279
PlotNode            7.633  0.015   7.647
QueryStarPlot       7.296  0.013   7.309
PlotPies            7.172  0.061   7.233
PlotNumbers         6.949  0.013   6.963
GetFlowJoLabels     6.669  0.092   6.762
PlotVariable        6.435  0.025   6.460
UpdateNodeSize      5.842  0.007   5.849
PlotOverview2D      5.735  0.097   5.833
PlotLabels          5.570  0.010   5.581
CountGroups         5.501  0.038   5.540
SaveClustersToFCS   5.375  0.014   5.390
MetaclusterMFIs     5.258  0.020   5.278
PlotFlowSOM         5.085  0.076   5.162
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL FlowSOM
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** 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-3.21-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/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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)