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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_2.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.24-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 ‘2.21.0’
* 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 ... OK
* 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                        78.751  0.132  79.014
FlowSOMmary                       77.397  0.386  77.866
PlotOutliers                      41.929  0.140  42.160
PlotMarker                        25.065  0.060  25.174
UpdateMetaclusters                23.657  0.060  23.766
PlotStars                         19.444  0.071  19.551
GroupStats                        18.672  0.040  18.757
FlowSOM                           16.394  0.036  16.464
PlotGroups                        16.073  0.044  16.152
Plot2DScatters                    14.858  0.051  14.944
query_multiple                    14.117  0.303  14.457
QueryMultiple                     13.812  0.024  13.864
Plot1DScatters                    12.526  0.072  12.627
PlotManualBars                    12.452  0.079  12.559
AddAnnotation                     12.204  0.144  12.376
GetFlowJoLabels                   10.445  0.068  10.539
PlotNumbers                       10.182  0.068  10.272
QueryStarPlot                     10.222  0.028  10.269
PlotNode                          10.206  0.032  10.259
PlotPies                          10.142  0.068  10.231
UpdateNodeSize                     8.966  0.387   9.377
PlotVariable                       9.056  0.060   9.132
CountGroups                        8.620  0.040   8.678
PlotFlowSOM                        8.234  0.060   8.313
PlotLabels                         7.709  0.028   7.754
GetFeatures                        7.564  0.008   7.591
SaveClustersToFCS                  7.526  0.032   7.570
MetaclusterMFIs                    7.163  0.004   7.184
NMetaclusters                      7.128  0.016   7.161
NClusters                          6.989  0.064   7.068
PlotOverview2D                     6.960  0.032   7.005
TestOutliers                       6.760  0.079   6.850
print.FlowSOM                      6.465  0.227   6.710
GetMetaclusterCVs                  6.631  0.020   6.666
PlotMFIHeatmap                     6.624  0.012   6.648
MetaclusterCVs                     6.522  0.020   6.557
GetMajorityLabels                  6.478  0.024   6.518
GetMetaclusterMFIs                 6.474  0.027   6.517
GetMFIs                            6.425  0.012   6.451
GetClusters                        6.376  0.024   6.414
GetPercentages                     6.321  0.060   6.395
GetMetaclusterPercentagesPositive  6.360  0.008   6.381
GetMetaclusters                    6.175  0.016   6.204
GetClusterPercentagesPositive      6.093  0.052   6.158
GetClusterMFIs                     6.028  0.036   6.077
GetCounts                          6.030  0.016   6.060
FlowSOMSubset                      5.476  0.024   5.513
NewData                            5.375  0.008   5.396
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.24-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 ‘2.21.0’
** 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)