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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_2.16.0.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 ‘2.16.0’
* 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: ‘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                        84.011  0.107  84.239
FlowSOMmary                       76.425  0.335  76.775
PlotOutliers                      25.469  0.095  25.623
UpdateMetaclusters                22.606  0.068  22.729
PlotMarker                        22.397  0.088  22.535
PlotStars                         19.118  0.032  19.188
GroupStats                        16.509  0.068  16.616
FlowSOM                           16.289  0.108  16.430
PlotGroups                        15.592  0.028  15.656
AddAnnotation                     12.225  0.463  12.716
QueryMultiple                     12.166  0.008  12.202
query_multiple                    11.839  0.020  11.884
PlotManualBars                    10.946  0.004  10.975
Plot2DScatters                    10.743  0.028  10.801
GetFlowJoLabels                    9.799  0.096   9.918
PlotNumbers                        9.473  0.020   9.516
PlotNode                           9.397  0.036   9.455
CountGroups                        9.276  0.096   9.391
QueryStarPlot                      9.182  0.056   9.258
PlotPies                           9.025  0.028   9.072
PlotVariable                       8.961  0.064   9.046
UpdateNodeSize                     8.103  0.004   8.126
PlotFlowSOM                        8.023  0.068   8.109
PlotLabels                         7.907  0.024   7.948
GetFeatures                        7.710  0.071   7.799
SaveClustersToFCS                  7.714  0.012   7.744
MetaclusterMFIs                    7.007  0.024   7.047
NClusters                          6.982  0.012   7.010
NMetaclusters                      6.914  0.016   6.946
print.FlowSOM                      6.770  0.032   6.818
MetaclusterCVs                     6.744  0.032   6.791
TestOutliers                       6.746  0.012   6.774
PlotOverview2D                     6.451  0.055   6.521
GetMetaclusterCVs                  6.417  0.011   6.443
GetMFIs                            6.304  0.016   6.332
GetMetaclusterMFIs                 6.175  0.012   6.203
GetPercentages                     6.144  0.012   6.170
GetMetaclusterPercentagesPositive  6.128  0.016   6.159
GetMetaclusters                    6.076  0.012   6.103
GetCounts                          5.819  0.012   5.842
GetClusterPercentagesPositive      5.807  0.020   5.840
GetClusterMFIs                     5.751  0.052   5.815
GetClusters                        5.779  0.004   5.797
FlowSOMSubset                      5.723  0.040   5.776
NewData                            5.048  0.008   5.067
* 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 ‘2.16.0’
** 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)