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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                        79.445  0.272  79.844
FlowSOMmary                       76.093  0.328  76.479
PlotOutliers                      25.162  0.028  25.319
PlotMarker                        22.204  0.100  22.353
UpdateMetaclusters                21.940  0.020  22.007
PlotStars                         18.759  0.115  18.919
GroupStats                        17.479  0.044  17.565
FlowSOM                           16.485  0.100  16.621
PlotGroups                        15.189  0.056  15.276
AddAnnotation                     11.717  0.140  11.886
query_multiple                    11.727  0.028  11.779
QueryMultiple                     11.703  0.007  11.736
Plot2DScatters                    11.055  0.244  11.325
PlotManualBars                    10.501  0.048  10.574
GetFlowJoLabels                    9.530  0.100   9.650
PlotNode                           9.361  0.016   9.397
PlotNumbers                        9.091  0.064   9.176
QueryStarPlot                      9.147  0.008   9.173
PlotVariable                       9.117  0.004   9.141
CountGroups                        8.471  0.051   8.543
PlotPies                           8.419  0.060   8.495
UpdateNodeSize                     7.806  0.044   7.871
PlotFlowSOM                        7.720  0.036   7.773
SaveClustersToFCS                  7.660  0.024   7.699
GetFeatures                        7.280  0.012   7.308
NMetaclusters                      6.956  0.331   7.304
PlotLabels                         7.129  0.031   7.173
NClusters                          6.990  0.072   7.080
GetPercentages                     6.946  0.004   6.964
MetaclusterMFIs                    6.834  0.039   6.892
PlotOverview2D                     6.812  0.016   6.840
TestOutliers                       6.799  0.008   6.821
GetMetaclusterPercentagesPositive  6.575  0.044   6.633
GetMetaclusters                    6.526  0.008   6.549
MetaclusterCVs                     6.298  0.024   6.336
print.FlowSOM                      6.162  0.016   6.190
GetMetaclusterCVs                  6.162  0.008   6.184
GetMFIs                            6.091  0.016   6.119
GetMetaclusterMFIs                 6.085  0.004   6.101
GetClusterMFIs                     5.980  0.084   6.077
GetClusterPercentagesPositive      5.732  0.023   5.769
GetClusters                        5.713  0.028   5.754
GetCounts                          5.684  0.019   5.717
FlowSOMSubset                      5.608  0.048   5.667
NewData                            4.994  0.184   5.189
ReadInput                          5.108  0.032   5.150
* 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)