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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                        81.649  0.082  81.865
FlowSOMmary                       74.990  0.283  75.308
PlotOutliers                      24.977  0.040  25.072
PlotMarker                        22.368  0.103  22.518
UpdateMetaclusters                22.017  0.044  22.099
PlotStars                         19.163  0.060  19.266
GroupStats                        16.945  0.028  17.013
FlowSOM                           16.230  0.104  16.361
PlotGroups                        15.466  0.032  15.533
AddAnnotation                     11.762  0.188  11.974
QueryMultiple                     11.658  0.056  11.738
query_multiple                    11.460  0.004  11.481
Plot2DScatters                    10.817  0.039  10.891
PlotManualBars                    10.571  0.060  10.657
GetFlowJoLabels                   10.312  0.067  10.405
CountGroups                        9.182  0.043   9.243
PlotNode                           9.195  0.004   9.214
QueryStarPlot                      8.845  0.000   8.861
PlotNumbers                        8.815  0.020   8.850
PlotVariable                       8.656  0.015   8.689
PlotPies                           8.502  0.080   8.600
PlotFlowSOM                        8.033  0.008   8.056
UpdateNodeSize                     7.680  0.028   7.722
SaveClustersToFCS                  7.460  0.020   7.492
GetFeatures                        7.363  0.008   7.388
PlotLabels                         7.065  0.016   7.097
NMetaclusters                      6.935  0.035   6.990
MetaclusterMFIs                    6.951  0.016   6.982
NClusters                          6.874  0.016   6.912
TestOutliers                       6.655  0.004   6.670
PlotOverview2D                     6.313  0.024   6.350
MetaclusterCVs                     6.292  0.008   6.315
GetMetaclusterCVs                  6.287  0.008   6.310
GetPercentages                     6.253  0.000   6.267
GetMetaclusterMFIs                 6.229  0.012   6.254
GetMFIs                            6.216  0.020   6.249
GetMetaclusters                    6.184  0.016   6.214
GetMetaclusterPercentagesPositive  6.157  0.020   6.191
print.FlowSOM                      6.157  0.012   6.180
GetCounts                          5.917  0.016   5.948
GetClusters                        5.833  0.024   5.878
GetClusterMFIs                     5.738  0.108   5.859
GetClusterPercentagesPositive      5.795  0.028   5.836
FlowSOMSubset                      5.675  0.016   5.703
MetaClustering                     5.214  0.016   5.243
NewData                            5.110  0.008   5.130
* 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)