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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings FlowSOM_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.18.0’
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
* 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
PlotDimRed                        78.019  0.175  78.357
FlowSOMmary                       74.444  0.375  74.935
PlotOutliers                      43.216  0.099  43.425
PlotMarker                        23.865  0.108  24.038
UpdateMetaclusters                23.371  0.056  23.491
PlotStars                         19.247  0.044  19.340
GroupStats                        16.758  0.099  16.888
PlotGroups                        16.581  0.020  16.644
FlowSOM                           15.381  0.079  15.491
QueryMultiple                     13.828  0.092  13.950
Plot2DScatters                    13.237  0.028  13.295
query_multiple                    13.010  0.056  13.093
PlotManualBars                    11.901  0.032  11.970
AddAnnotation                     11.482  0.164  11.676
QueryStarPlot                      9.681  0.016   9.718
PlotNumbers                        9.552  0.020   9.598
PlotNode                           9.502  0.016   9.543
GetFlowJoLabels                    9.240  0.092   9.351
PlotVariable                       8.820  0.056   8.897
UpdateNodeSize                     8.753  0.076   8.850
PlotPies                           8.748  0.076   8.844
PlotFlowSOM                        7.796  0.040   7.859
CountGroups                        7.722  0.060   7.800
PlotLabels                         7.249  0.016   7.285
GetFeatures                        7.051  0.080   7.143
SaveClustersToFCS                  6.977  0.028   7.022
PlotOverview2D                     6.672  0.068   6.755
NMetaclusters                      6.536  0.071   6.622
NClusters                          6.562  0.028   6.604
MetaclusterMFIs                    6.294  0.040   6.347
TestOutliers                       6.176  0.008   6.197
GetMetaclusterCVs                  5.840  0.075   5.929
GetMetaclusters                    5.763  0.061   5.835
GetCounts                          5.737  0.072   5.818
GetPercentages                     5.736  0.059   5.807
GetMetaclusterPercentagesPositive  5.718  0.052   5.781
GetClusterMFIs                     5.612  0.144   5.769
GetClusterPercentagesPositive      5.585  0.171   5.767
GetMetaclusterMFIs                 5.695  0.048   5.756
print.FlowSOM                      5.665  0.020   5.699
GetMFIs                            5.616  0.064   5.691
MetaclusterCVs                     5.673  0.004   5.688
GetClusters                        5.396  0.080   5.486
FlowSOMSubset                      5.368  0.036   5.416
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.18.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c som.c -o som.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)