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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_2.16.0.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 ‘2.16.0’
* 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                        80.821  0.155  81.105
FlowSOMmary                       72.544  0.299  72.850
PlotOutliers                      25.071  0.056  25.190
UpdateMetaclusters                22.330  0.068  22.452
PlotMarker                        22.003  0.072  22.135
PlotStars                         18.889  0.000  18.937
GroupStats                        16.613  0.068  16.718
FlowSOM                           15.892  0.032  15.947
PlotGroups                        15.589  0.052  15.685
QueryMultiple                     12.041  0.052  12.124
AddAnnotation                     11.599  0.168  11.784
query_multiple                    11.654  0.019  11.706
PlotManualBars                    10.673  0.036  10.738
Plot2DScatters                    10.649  0.020  10.697
GetFlowJoLabels                    9.900  0.083  10.009
PlotNode                           9.541  0.028   9.593
QueryStarPlot                      9.015  0.036   9.072
PlotVariable                       8.872  0.012   8.906
PlotNumbers                        8.865  0.004   8.888
CountGroups                        8.819  0.028   8.859
PlotPies                           8.543  0.055   8.619
UpdateNodeSize                     8.173  0.064   8.255
PlotFlowSOM                        7.896  0.048   7.963
SaveClustersToFCS                  7.647  0.008   7.673
GetFeatures                        7.223  0.008   7.251
PlotLabels                         7.191  0.028   7.238
NClusters                          7.194  0.020   7.230
NMetaclusters                      6.911  0.008   6.934
MetaclusterMFIs                    6.803  0.016   7.174
print.FlowSOM                      6.761  0.028   6.803
TestOutliers                       6.681  0.012   6.708
PlotOverview2D                     6.358  0.028   6.400
MetaclusterCVs                     6.215  0.000   6.228
GetMetaclusterCVs                  6.159  0.028   6.222
GetMetaclusterPercentagesPositive  6.090  0.048   6.153
GetPercentages                     6.126  0.008   6.148
GetMetaclusterMFIs                 6.084  0.028   6.126
GetMetaclusters                    6.088  0.004   6.106
GetMFIs                            6.067  0.024   6.104
GetClusterPercentagesPositive      5.755  0.012   5.780
GetClusters                        5.751  0.012   5.774
GetCounts                          5.702  0.012   5.728
GetClusterMFIs                     5.661  0.052   5.728
FlowSOMSubset                      5.592  0.036   5.636
NewData                            5.072  0.008   5.091
* 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 ‘2.16.0’
** 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)