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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                       74.879  0.418  75.554
PlotDimRed                        71.717  0.163  72.042
PlotOutliers                      43.065  0.068  43.801
PlotMarker                        24.372  0.108  24.631
UpdateMetaclusters                22.706  0.024  22.856
PlotStars                         19.372  0.104  19.794
GroupStats                        17.563  0.039  17.804
PlotGroups                        15.738  0.020  15.807
FlowSOM                           15.673  0.068  15.780
query_multiple                    13.457  0.035  13.665
QueryMultiple                     13.422  0.011  13.517
Plot2DScatters                    12.687  0.020  12.734
AddAnnotation                     11.495  0.207  11.784
PlotManualBars                    11.627  0.016  11.720
QueryStarPlot                      9.914  0.003   9.968
PlotNode                           9.900  0.016  10.005
GetFlowJoLabels                    9.104  0.171   9.667
PlotPies                           9.020  0.024   9.142
PlotNumbers                        8.771  0.020   8.815
PlotVariable                       8.581  0.020   8.636
UpdateNodeSize                     8.593  0.008   8.620
PlotFlowSOM                        7.781  0.036   7.840
CountGroups                        7.747  0.032   7.800
SaveClustersToFCS                  7.192  0.040   7.278
GetFeatures                        7.005  0.044   7.064
PlotLabels                         6.848  0.016   6.951
TestOutliers                       6.403  0.012   6.909
MetaclusterMFIs                    6.365  0.024   6.403
PlotOverview2D                     6.265  0.079   6.572
NMetaclusters                      6.204  0.020   6.237
NClusters                          6.186  0.008   6.207
GetMetaclusterCVs                  5.851  0.064   5.929
MetaclusterCVs                     5.869  0.016   5.899
FlowSOMSubset                      5.795  0.036   5.845
GetMetaclusters                    5.810  0.012   5.837
GetPercentages                     5.755  0.024   5.793
GetMetaclusterMFIs                 5.741  0.024   5.779
GetMetaclusterPercentagesPositive  5.714  0.016   5.743
GetClusterPercentagesPositive      5.551  0.136   5.700
GetMFIs                            5.588  0.088   5.693
GetClusterMFIs                     5.485  0.163   5.661
print.FlowSOM                      5.622  0.024   5.658
GetCounts                          5.502  0.124   5.638
GetClusters                        5.294  0.087   5.399
* 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)