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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_2.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* 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: ‘gcc (conda-forge gcc 14.2.0-1) 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                        84.434  0.239  84.610
FlowSOMmary                       79.600  0.303  79.777
PlotOutliers                      25.420  0.091  25.511
PlotMarker                        22.723  0.205  22.929
UpdateMetaclusters                22.681  0.088  22.725
PlotStars                         19.062  0.088  19.112
GroupStats                        17.673  0.100  17.730
FlowSOM                           17.493  0.088  17.494
PlotGroups                        15.894  0.136  15.820
AddAnnotation                     12.468  0.151  12.569
query_multiple                    12.230  0.059  12.231
QueryMultiple                     11.983  0.047  12.037
PlotManualBars                    11.441  0.052  11.358
Plot2DScatters                    11.157  0.176  11.264
GetFlowJoLabels                    9.999  0.076  10.012
QueryStarPlot                      9.839  0.056   9.828
PlotNode                           9.683  0.094   9.745
PlotNumbers                        9.493  0.036   9.488
PlotVariable                       9.191  0.052   9.213
CountGroups                        9.146  0.072   8.979
PlotPies                           8.929  0.056   8.915
PlotFlowSOM                        8.093  0.140   8.171
SaveClustersToFCS                  7.971  0.012   7.830
GetFeatures                        7.936  0.036   7.904
PlotLabels                         7.890  0.075   7.902
UpdateNodeSize                     7.860  0.012   7.800
NClusters                          7.240  0.200   7.370
NMetaclusters                      7.268  0.107   7.311
MetaclusterMFIs                    6.880  0.259   7.073
TestOutliers                       7.074  0.012   7.015
PlotOverview2D                     6.975  0.040   6.991
GetPercentages                     6.932  0.020   6.881
MetaclusterCVs                     6.757  0.195   6.886
GetMetaclusterCVs                  6.690  0.008   6.627
GetMFIs                            6.598  0.019   6.547
print.FlowSOM                      6.574  0.012   6.581
GetMetaclusterMFIs                 6.553  0.008   6.493
GetMetaclusterPercentagesPositive  6.499  0.052   6.480
GetMetaclusters                    6.359  0.016   6.303
GetCounts                          6.195  0.020   6.142
GetClusters                        6.177  0.016   6.120
GetClusterMFIs                     6.076  0.072   6.076
GetClusterPercentagesPositive      6.089  0.040   6.055
FlowSOMSubset                      5.816  0.020   5.848
NewData                            5.437  0.056   5.419
ReadInput                          4.977  0.052   4.869
* 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-3.20-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-4.4.1/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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)