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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                        73.090  0.143  74.000
FlowSOMmary                       70.803  0.374  72.574
PlotOutliers                      42.197  0.220  42.966
PlotMarker                        23.360  0.327  23.738
UpdateMetaclusters                22.256  0.079  22.404
PlotStars                         19.035  0.048  19.162
GroupStats                        17.865  0.131  18.048
PlotGroups                        15.421  0.327  15.846
FlowSOM                           14.833  0.096  14.972
Plot2DScatters                    13.253  0.052  13.339
QueryMultiple                     13.078  0.016  13.142
query_multiple                    12.972  0.020  13.020
PlotManualBars                    11.365  0.208  11.614
AddAnnotation                     11.370  0.163  11.580
QueryStarPlot                      9.507  0.036   9.575
GetFlowJoLabels                    9.315  0.156   9.506
PlotNode                           9.157  0.071   9.426
PlotNumbers                        8.646  0.028   9.396
UpdateNodeSize                     8.599  0.064   8.689
PlotVariable                       8.582  0.020   8.634
PlotPies                           8.400  0.012   8.693
PlotFlowSOM                        7.573  0.056   7.652
CountGroups                        7.551  0.036   7.610
GetFeatures                        7.165  0.039   7.228
SaveClustersToFCS                  7.155  0.020   7.195
PlotLabels                         6.934  0.211   7.194
MetaclusterMFIs                    6.723  0.016   6.759
NClusters                          6.612  0.024   6.655
NMetaclusters                      6.518  0.048   6.581
PlotOverview2D                     6.128  0.107   6.308
GetMetaclusterPercentagesPositive  6.170  0.052   6.243
TestOutliers                       6.036  0.016   6.110
MetaclusterCVs                     5.966  0.036   6.037
GetPercentages                     5.872  0.028   5.919
GetMetaclusterCVs                  5.793  0.055   5.869
GetMetaclusterMFIs                 5.704  0.064   5.787
GetMFIs                            5.680  0.080   5.784
GetClusterPercentagesPositive      5.657  0.040   5.741
print.FlowSOM                      5.617  0.080   5.709
GetMetaclusters                    5.614  0.048   5.680
GetClusterMFIs                     5.484  0.108   5.611
GetClusters                        5.548  0.020   5.586
GetCounts                          5.445  0.080   5.543
FlowSOMSubset                      5.265  0.032   5.313
* 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)