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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
FlowSOMmary                       73.200  0.409  73.745
PlotDimRed                        69.977  0.164  70.214
PlotOutliers                      41.636  0.188  41.906
PlotMarker                        23.074  0.147  23.264
UpdateMetaclusters                21.901  0.068  22.009
PlotStars                         18.924  0.124  19.083
GroupStats                        17.654  0.144  17.835
FlowSOM                           15.618  0.104  15.771
PlotGroups                        15.011  0.044  15.082
QueryMultiple                     13.137  0.048  13.211
Plot2DScatters                    12.878  0.056  12.959
query_multiple                    12.871  0.020  12.914
AddAnnotation                     11.695  0.143  11.887
PlotManualBars                    11.553  0.012  11.588
QueryStarPlot                      9.686  0.020   9.725
GetFlowJoLabels                    9.146  0.156   9.320
PlotNode                           9.046  0.012   9.081
PlotNumbers                        8.737  0.015   8.769
PlotVariable                       8.521  0.016   8.551
PlotPies                           8.225  0.048   8.288
UpdateNodeSize                     8.127  0.012   8.153
CountGroups                        7.843  0.071   7.940
SaveClustersToFCS                  7.264  0.020   7.297
PlotFlowSOM                        7.226  0.028   7.268
GetFeatures                        6.995  0.036   7.045
PlotLabels                         6.758  0.008   6.778
NMetaclusters                      6.254  0.040   6.304
NClusters                          6.128  0.028   6.166
TestOutliers                       6.153  0.000   6.164
PlotOverview2D                     6.064  0.040   6.114
MetaclusterMFIs                    5.996  0.020   6.028
GetPercentages                     5.893  0.016   5.920
MetaclusterCVs                     5.839  0.028   5.878
GetClusters                        5.757  0.104   5.872
GetMetaclusters                    5.782  0.048   5.846
GetMFIs                            5.693  0.087   5.791
GetMetaclusterCVs                  5.688  0.063   5.762
GetMetaclusterPercentagesPositive  5.675  0.056   5.743
GetMetaclusterMFIs                 5.560  0.060   5.630
print.FlowSOM                      5.586  0.016   5.611
GetClusterMFIs                     5.425  0.148   5.585
GetCounts                          5.445  0.088   5.544
GetClusterPercentagesPositive      5.369  0.119   5.500
FlowSOMSubset                      5.221  0.068   5.308
MetaClustering                     4.965  0.063   5.038
* 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)