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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                       72.167  0.339  72.592
PlotDimRed                        68.798  0.148  69.044
PlotOutliers                      42.341  0.064  42.522
PlotMarker                        22.946  0.128  23.135
UpdateMetaclusters                21.858  0.076  21.997
PlotStars                         18.724  0.020  18.797
GroupStats                        16.377  0.104  16.523
FlowSOM                           15.469  0.023  15.532
PlotGroups                        14.728  0.012  14.776
query_multiple                    12.988  0.068  13.093
Plot2DScatters                    12.837  0.071  12.943
QueryMultiple                     12.635  0.012  12.681
AddAnnotation                     11.675  0.104  11.813
PlotManualBars                    11.162  0.024  11.216
GetFlowJoLabels                    9.336  0.083   9.448
QueryStarPlot                      9.348  0.024   9.399
PlotNumbers                        8.878  0.039   8.944
PlotNode                           8.792  0.016   8.831
PlotVariable                       8.355  0.056   8.433
UpdateNodeSize                     8.336  0.008   8.369
PlotPies                           8.072  0.036   8.131
CountGroups                        7.917  0.032   7.969
PlotFlowSOM                        7.324  0.060   7.403
GetFeatures                        7.082  0.020   7.121
SaveClustersToFCS                  7.017  0.064   7.102
PlotLabels                         6.475  0.016   6.511
NClusters                          6.256  0.024   6.297
NMetaclusters                      6.243  0.024   6.284
TestOutliers                       6.000  0.012   6.029
PlotOverview2D                     5.863  0.100   5.979
MetaclusterMFIs                    5.942  0.000   5.957
GetPercentages                     5.829  0.020   5.863
GetClusterPercentagesPositive      5.679  0.020   5.713
GetMFIs                            5.622  0.016   5.653
GetMetaclusterCVs                  5.622  0.012   5.648
GetMetaclusters                    5.574  0.052   5.642
GetMetaclusterPercentagesPositive  5.600  0.012   5.629
print.FlowSOM                      5.550  0.044   5.609
GetMetaclusterMFIs                 5.580  0.008   5.601
MetaclusterCVs                     5.563  0.020   5.598
GetClusterMFIs                     5.459  0.068   5.541
GetClusters                        5.434  0.040   5.490
GetCounts                          5.448  0.016   5.476
FlowSOMSubset                      5.316  0.052   5.385
* 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)