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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                        75.380  0.135  75.653
FlowSOMmary                       74.195  0.363  74.569
PlotOutliers                      24.859  0.019  24.982
PlotMarker                        21.682  0.107  21.854
UpdateMetaclusters                21.383  0.011  21.452
PlotStars                         18.360  0.060  18.465
GroupStats                        16.771  0.028  16.842
FlowSOM                           16.003  0.084  16.119
PlotGroups                        15.387  0.016  15.442
AddAnnotation                     11.988  0.531  12.546
QueryMultiple                     11.523  0.056  11.610
query_multiple                    11.463  0.012  11.501
Plot2DScatters                    10.883  0.020  10.935
PlotManualBars                    10.715  0.032  10.783
GetFlowJoLabels                    9.212  0.071   9.307
PlotNode                           9.084  0.052   9.160
PlotVariable                       9.091  0.008   9.123
QueryStarPlot                      8.902  0.016   8.939
CountGroups                        8.889  0.028   8.936
PlotNumbers                        8.737  0.012   8.772
PlotPies                           8.408  0.004   8.434
UpdateNodeSize                     7.970  0.064   8.052
PlotFlowSOM                        7.538  0.048   7.603
SaveClustersToFCS                  7.527  0.020   7.569
GetFeatures                        7.110  0.004   7.133
PlotLabels                         7.048  0.020   7.086
MetaclusterMFIs                    6.886  0.012   6.913
NClusters                          6.862  0.024   6.908
NMetaclusters                      6.821  0.020   6.858
TestOutliers                       6.693  0.000   6.713
PlotOverview2D                     6.329  0.012   6.360
MetaclusterCVs                     6.142  0.008   6.165
print.FlowSOM                      6.112  0.032   6.166
GetPercentages                     6.079  0.008   6.103
GetMetaclusterCVs                  6.061  0.020   6.094
GetMetaclusters                    6.062  0.004   6.080
GetMetaclusterPercentagesPositive  6.002  0.012   6.028
GetMetaclusterMFIs                 5.985  0.016   6.014
GetMFIs                            5.978  0.020   6.010
GetClusterPercentagesPositive      5.834  0.064   5.912
GetClusterMFIs                     5.597  0.072   5.683
GetCounts                          5.592  0.016   5.621
FlowSOMSubset                      5.521  0.032   5.562
GetClusters                        5.511  0.032   5.554
NewData                            4.980  0.016   5.010
* 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)