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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
PlotDimRed                        70.056  0.315  70.473
FlowSOMmary                       68.402  0.303  68.765
PlotOutliers                      24.418  0.075  24.558
PlotMarker                        21.124  0.160  21.339
UpdateMetaclusters                20.642  0.064  20.751
PlotStars                         17.943  0.028  18.018
GroupStats                        16.075  0.036  16.137
FlowSOM                           14.874  0.012  14.920
PlotGroups                        14.631  0.176  14.845
AddAnnotation                     11.024  0.116  11.161
QueryMultiple                     11.014  0.060  11.100
query_multiple                    11.016  0.008  11.050
Plot2DScatters                    10.123  0.036  10.182
PlotManualBars                     9.751  0.056   9.837
GetFlowJoLabels                    9.341  0.104   9.463
PlotNode                           8.880  0.044   8.948
PlotNumbers                        8.544  0.076   8.646
CountGroups                        8.260  0.044   8.317
QueryStarPlot                      8.257  0.012   8.289
PlotVariable                       8.241  0.016   8.278
PlotPies                           7.759  0.012   7.790
UpdateNodeSize                     7.628  0.056   7.701
PlotFlowSOM                        7.209  0.116   7.342
GetFeatures                        6.956  0.016   6.984
SaveClustersToFCS                  6.874  0.008   6.897
PlotLabels                         6.566  0.039   6.623
TestOutliers                       6.190  0.000   6.201
NMetaclusters                      6.170  0.012   6.192
MetaclusterMFIs                    5.894  0.032   5.936
NClusters                          5.866  0.024   5.900
PlotOverview2D                     5.766  0.076   5.861
MetaclusterCVs                     5.589  0.024   5.622
GetMetaclusterCVs                  5.568  0.024   5.601
GetMetaclusterPercentagesPositive  5.564  0.004   5.577
GetPercentages                     5.522  0.016   5.547
GetMFIs                            5.468  0.060   5.538
print.FlowSOM                      5.498  0.016   5.525
GetMetaclusterMFIs                 5.496  0.016   5.521
GetMetaclusters                    5.446  0.024   5.480
FlowSOMSubset                      5.324  0.036   5.374
GetClusterPercentagesPositive      5.179  0.047   5.236
GetCounts                          5.187  0.024   5.220
GetClusters                        5.153  0.008   5.171
GetClusterMFIs                     5.100  0.060   5.169
* 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)