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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_2.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.15.0’
* 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                        79.884  0.279  80.274
FlowSOMmary                       76.578  0.188  76.839
PlotOutliers                      26.017  0.112  26.184
PlotMarker                        22.496  0.024  22.563
UpdateMetaclusters                22.244  0.076  22.361
PlotStars                         19.170  0.040  19.249
GroupStats                        16.982  0.076  17.098
FlowSOM                           16.619  0.031  16.684
PlotGroups                        15.607  0.016  15.657
AddAnnotation                     12.075  0.148  12.253
QueryMultiple                     11.918  0.034  11.977
query_multiple                    11.913  0.028  11.970
PlotManualBars                    10.778  0.020  10.824
Plot2DScatters                    10.531  0.040  10.587
GetFlowJoLabels                   10.099  0.155  10.281
PlotNode                           9.848  0.016   9.886
QueryStarPlot                      9.540  0.032   9.589
PlotPies                           9.167  0.008   9.195
PlotVariable                       9.059  0.060   9.138
PlotNumbers                        9.048  0.008   9.073
CountGroups                        8.780  0.020   8.815
PlotFlowSOM                        7.838  0.095   7.951
UpdateNodeSize                     7.892  0.008   7.916
SaveClustersToFCS                  7.698  0.008   7.721
PlotLabels                         7.674  0.012   7.702
GetFeatures                        7.485  0.064   7.563
MetaclusterMFIs                    7.256  0.008   7.274
NClusters                          6.856  0.056   6.921
NMetaclusters                      6.866  0.012   6.887
TestOutliers                       6.848  0.016   6.877
PlotOverview2D                     6.582  0.036   6.631
GetMetaclusterCVs                  6.313  0.064   6.389
GetMetaclusterPercentagesPositive  6.317  0.044   6.371
GetPercentages                     6.258  0.028   6.298
MetaclusterCVs                     6.224  0.052   6.286
GetMetaclusterMFIs                 6.241  0.028   6.281
print.FlowSOM                      6.246  0.012   6.270
GetMFIs                            6.206  0.048   6.267
GetMetaclusters                    6.178  0.072   6.261
GetClusterPercentagesPositive      5.959  0.171   6.142
FlowSOMSubset                      5.977  0.040   6.027
GetCounts                          5.903  0.108   6.023
GetClusterMFIs                     5.909  0.100   6.020
GetClusters                        5.846  0.132   5.989
ReadInput                          5.181  0.020   5.211
NewData                            5.018  0.064   5.088
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.15.0’
** 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/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/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)