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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                        81.801  0.184  82.092
FlowSOMmary                       77.853  0.208  78.090
PlotOutliers                      25.835  0.219  26.114
PlotMarker                        23.572  0.359  23.994
UpdateMetaclusters                21.994  0.112  22.154
PlotStars                         18.844  0.068  18.951
GroupStats                        17.423  0.132  17.590
FlowSOM                           16.274  0.020  16.327
PlotGroups                        15.523  0.016  15.574
AddAnnotation                     11.996  0.115  12.144
query_multiple                    11.894  0.016  11.935
QueryMultiple                     11.802  0.043  11.871
Plot2DScatters                    11.262  0.064  11.347
PlotManualBars                    11.181  0.028  11.239
GetFlowJoLabels                    9.543  0.144   9.707
PlotNode                           9.479  0.132   9.632
CountGroups                        9.315  0.024   9.381
PlotNumbers                        9.084  0.107   9.212
PlotVariable                       9.090  0.076   9.185
QueryStarPlot                      8.932  0.056   9.007
PlotPies                           8.869  0.036   8.923
PlotFlowSOM                        8.003  0.044   8.062
UpdateNodeSize                     7.892  0.028   7.937
SaveClustersToFCS                  7.839  0.020   7.875
PlotLabels                         7.704  0.048   7.771
GetFeatures                        7.395  0.044   7.449
MetaclusterMFIs                    7.136  0.012   7.160
NClusters                          7.087  0.020   7.119
NMetaclusters                      7.004  0.016   7.031
TestOutliers                       6.837  0.008   6.857
GetPercentages                     6.825  0.000   6.838
PlotOverview2D                     6.756  0.064   6.835
GetMetaclusters                    6.720  0.008   6.739
MetaclusterCVs                     6.463  0.052   6.526
GetMetaclusterCVs                  6.410  0.056   6.477
GetMFIs                            6.258  0.068   6.336
print.FlowSOM                      6.265  0.004   6.281
GetMetaclusterPercentagesPositive  6.188  0.019   6.218
GetMetaclusterMFIs                 6.156  0.048   6.216
GetClusterMFIs                     5.965  0.103   6.082
GetClusters                        5.859  0.080   5.950
GetCounts                          5.823  0.035   5.868
GetClusterPercentagesPositive      5.827  0.020   5.858
FlowSOMSubset                      5.649  0.028   5.688
ReadInput                          5.220  0.032   5.263
NewData                            5.195  0.008   5.212
* 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)