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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_2.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.15.0’
* 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                        85.041  0.168  85.363
FlowSOMmary                       76.661  0.331  77.049
PlotOutliers                      25.777  0.135  25.970
PlotMarker                        23.432  0.419  23.906
UpdateMetaclusters                22.313  0.067  22.428
PlotStars                         18.868  0.099  18.999
GroupStats                        16.922  0.056  17.020
FlowSOM                           16.485  0.075  16.597
PlotGroups                        15.739  0.044  15.818
AddAnnotation                     12.067  0.244  12.341
query_multiple                    12.087  0.044  12.156
QueryMultiple                     11.855  0.020  11.903
Plot2DScatters                    11.132  0.039  11.199
PlotManualBars                    10.810  0.116  10.954
GetFlowJoLabels                   10.079  0.131  10.239
PlotNode                           9.424  0.072   9.518
QueryStarPlot                      9.390  0.000   9.408
PlotNumbers                        9.101  0.052   9.173
PlotVariable                       9.019  0.064   9.102
PlotPies                           8.858  0.052   8.931
CountGroups                        8.632  0.020   8.673
UpdateNodeSize                     8.206  0.036   8.259
SaveClustersToFCS                  8.064  0.060   8.141
PlotFlowSOM                        7.884  0.067   7.973
PlotLabels                         7.730  0.020   7.768
GetFeatures                        7.535  0.028   7.582
NClusters                          7.494  0.016   7.530
MetaclusterMFIs                    6.979  0.008   7.009
TestOutliers                       6.827  0.052   6.893
NMetaclusters                      6.669  0.032   6.717
PlotOverview2D                     6.522  0.036   6.571
GetMetaclusterCVs                  6.384  0.016   6.415
MetaclusterCVs                     6.278  0.024   6.314
print.FlowSOM                      6.251  0.024   6.287
GetPercentages                     6.234  0.024   6.274
GetMFIs                            6.174  0.036   6.225
GetMetaclusterMFIs                 6.155  0.024   6.192
GetMetaclusterPercentagesPositive  6.154  0.020   6.188
GetMetaclusters                    6.145  0.024   6.184
FlowSOMSubset                      5.929  0.048   5.990
GetClusterPercentagesPositive      5.888  0.012   5.914
GetClusters                        5.886  0.008   5.907
GetClusterMFIs                     5.857  0.036   5.906
GetCounts                          5.835  0.012   5.859
NewData                            5.109  0.020   5.142
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.15.0’
** 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/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/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)