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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) (2024-11-24 r87369)
* 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 ‘2.15.0’
* 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 ... OK
* 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                        81.732  0.144  82.010
FlowSOMmary                       74.760  0.335  75.148
PlotOutliers                      24.118  0.052  24.225
PlotMarker                        22.155  0.079  22.283
UpdateMetaclusters                21.631  0.056  21.733
PlotStars                         18.956  0.096  19.091
GroupStats                        16.642  0.084  16.766
FlowSOM                           16.184  0.032  16.253
PlotGroups                        15.240  0.044  15.316
AddAnnotation                     11.734  0.168  11.927
query_multiple                    11.720  0.020  11.766
QueryMultiple                     11.566  0.004  11.595
Plot2DScatters                    10.672  0.011  10.706
PlotManualBars                    10.528  0.032  10.586
GetFlowJoLabels                   10.280  0.132  10.438
PlotNode                           9.137  0.064   9.220
PlotNumbers                        8.952  0.012   8.984
QueryStarPlot                      8.911  0.004   8.933
PlotVariable                       8.749  0.036   8.803
PlotPies                           8.509  0.016   8.542
CountGroups                        8.492  0.032   8.544
PlotFlowSOM                        8.210  0.056   8.286
SaveClustersToFCS                  8.058  0.008   8.084
UpdateNodeSize                     7.872  0.011   7.901
PlotLabels                         7.578  0.008   7.603
GetFeatures                        7.397  0.032   7.447
MetaclusterMFIs                    7.241  0.020   7.279
NMetaclusters                      6.788  0.064   6.867
TestOutliers                       6.829  0.008   6.848
NClusters                          6.760  0.020   6.796
GetPercentages                     6.538  0.040   6.594
PlotOverview2D                     6.402  0.020   6.434
GetMetaclusterCVs                  6.253  0.047   6.315
print.FlowSOM                      6.171  0.044   6.229
FlowSOMSubset                      6.180  0.024   6.218
MetaclusterCVs                     6.182  0.012   6.211
GetMetaclusterMFIs                 6.156  0.028   6.197
GetMetaclusterPercentagesPositive  6.087  0.024   6.126
GetMetaclusters                    6.095  0.008   6.118
GetMFIs                            6.082  0.020   6.118
GetCounts                          5.861  0.016   5.890
GetClusters                        5.763  0.052   5.829
GetClusterPercentagesPositive      5.790  0.016   5.818
GetClusterMFIs                     5.701  0.036   5.750
NewData                            5.002  0.016   5.028
* 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-3.21-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-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘FlowSOM’ ...
** 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 -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 -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-4.5.0-devel_2024-11-24/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)