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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_2.17.0.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 ‘2.17.0’
* 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                       69.686  0.275  70.051
PlotDimRed                        66.019  0.215  66.393
PlotOutliers                      24.833  0.079  24.984
PlotMarker                        21.137  0.196  21.392
UpdateMetaclusters                20.030  0.274  20.431
PlotStars                         18.343  0.032  18.433
GroupStats                        16.227  0.036  16.319
FlowSOM                           15.090  0.064  15.199
PlotGroups                        14.467  0.227  14.736
AddAnnotation                     11.189  0.291  11.516
QueryMultiple                     11.241  0.016  11.296
query_multiple                    10.846  0.035  10.936
PlotManualBars                    10.254  0.075  10.362
Plot2DScatters                    10.090  0.024  10.148
PlotNode                           8.937  0.024   8.986
QueryStarPlot                      8.763  0.167   8.965
PlotNumbers                        8.826  0.084   8.935
GetFlowJoLabels                    8.677  0.099   8.811
PlotVariable                       8.261  0.028   8.312
CountGroups                        8.064  0.064   8.152
PlotPies                           7.908  0.056   7.987
PlotFlowSOM                        7.322  0.208   7.553
UpdateNodeSize                     7.177  0.068   7.271
SaveClustersToFCS                  6.750  0.199   6.984
GetFeatures                        6.932  0.004   6.957
PlotLabels                         6.669  0.124   6.811
NMetaclusters                      6.449  0.020   6.488
PlotOverview2D                     6.257  0.048   6.323
MetaclusterMFIs                    6.236  0.036   6.292
NClusters                          6.214  0.027   6.262
TestOutliers                       5.903  0.127   6.054
GetMetaclusterMFIs                 5.931  0.008   5.959
GetMetaclusterPercentagesPositive  5.883  0.032   5.937
GetMetaclusterCVs                  5.667  0.023   5.710
MetaclusterCVs                     5.566  0.048   5.632
GetMetaclusters                    5.578  0.012   5.608
GetMFIs                            5.530  0.036   5.584
GetPercentages                     5.543  0.008   5.568
GetClusterMFIs                     5.406  0.060   5.484
print.FlowSOM                      5.418  0.020   5.482
GetClusterPercentagesPositive      5.427  0.004   5.448
GetClusters                        5.383  0.008   5.407
GetCounts                          5.256  0.012   5.284
FlowSOMSubset                      5.143  0.060   5.218
* 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 ‘2.17.0’
** 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)