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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                       73.374  0.363  73.821
PlotDimRed                        72.717  0.159  73.029
PlotOutliers                      43.787  0.112  44.025
PlotMarker                        23.914  0.191  24.172
UpdateMetaclusters                22.835  0.072  22.968
PlotStars                         19.682  0.019  19.759
GroupStats                        17.163  0.115  17.333
FlowSOM                           15.875  0.072  15.992
PlotGroups                        15.691  0.020  15.756
QueryMultiple                     13.478  0.020  13.538
query_multiple                    13.232  0.076  13.346
Plot2DScatters                    13.202  0.064  13.310
AddAnnotation                     12.007  0.107  12.154
PlotManualBars                    11.659  0.016  11.711
QueryStarPlot                     10.300  0.096  10.427
GetFlowJoLabels                    9.440  0.196   9.670
PlotNode                           9.294  0.024   9.347
PlotNumbers                        9.225  0.012   9.263
PlotPies                           8.818  0.024   8.868
PlotVariable                       8.746  0.019   8.793
UpdateNodeSize                     8.559  0.055   8.639
CountGroups                        7.918  0.068   8.006
PlotFlowSOM                        7.386  0.076   7.481
GetFeatures                        7.267  0.079   7.371
SaveClustersToFCS                  7.174  0.032   7.227
PlotOverview2D                     7.043  0.060   7.121
PlotLabels                         7.008  0.008   7.037
NClusters                          6.448  0.016   6.484
MetaclusterMFIs                    6.402  0.028   6.449
TestOutliers                       6.403  0.024   6.444
NMetaclusters                      6.393  0.020   6.437
GetClusterPercentagesPositive      5.836  0.227   6.082
print.FlowSOM                      5.926  0.012   5.955
GetMetaclusterCVs                  5.843  0.075   5.938
MetaclusterCVs                     5.838  0.016   5.873
GetPercentages                     5.778  0.044   5.840
GetMFIs                            5.757  0.056   5.833
GetMetaclusterMFIs                 5.759  0.048   5.824
GetMetaclusterPercentagesPositive  5.708  0.080   5.807
GetMetaclusters                    5.705  0.056   5.779
GetCounts                          5.506  0.132   5.655
GetClusterMFIs                     5.442  0.195   5.655
GetClusters                        5.510  0.100   5.625
FlowSOMSubset                      5.528  0.012   5.558
* 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)