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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                        82.658  0.296  82.811
FlowSOMmary                       78.538  0.534  79.014
PlotOutliers                      25.418  0.124  25.564
PlotMarker                        23.058  0.363  23.482
UpdateMetaclusters                22.825  0.072  22.933
PlotStars                         20.017  0.156  20.126
GroupStats                        17.679  0.080  17.714
FlowSOM                           17.111  0.124  17.112
PlotGroups                        15.863  0.107  15.751
query_multiple                    12.854  0.024  12.819
QueryMultiple                     12.388  0.040  12.368
AddAnnotation                     12.276  0.144  12.364
Plot2DScatters                    11.140  0.331  11.405
PlotManualBars                    10.960  0.303  11.118
GetFlowJoLabels                    9.886  0.163   9.987
CountGroups                        9.835  0.091   9.697
QueryStarPlot                      9.623  0.044   9.600
PlotNode                           9.511  0.100   9.544
PlotVariable                       9.315  0.060   9.310
PlotNumbers                        9.113  0.108   9.155
PlotPies                           9.099  0.064   9.102
SaveClustersToFCS                  8.567  0.055   8.469
PlotFlowSOM                        8.497  0.052   8.482
UpdateNodeSize                     8.265  0.096   8.298
PlotLabels                         7.593  0.308   7.830
MetaclusterMFIs                    7.835  0.035   7.852
GetFeatures                        7.544  0.056   7.534
NMetaclusters                      7.447  0.008   7.386
NClusters                          7.381  0.056   7.368
MetaclusterCVs                     7.137  0.076   7.142
TestOutliers                       7.148  0.024   7.101
PlotOverview2D                     6.917  0.115   6.965
GetMetaclusters                    6.995  0.008   6.977
GetPercentages                     6.723  0.076   6.771
GetMetaclusterCVs                  6.644  0.056   6.626
print.FlowSOM                      6.643  0.048   6.618
NewData                            6.457  0.188   6.574
GetMFIs                            6.534  0.024   6.486
GetMetaclusterMFIs                 6.457  0.064   6.449
GetMetaclusterPercentagesPositive  6.459  0.036   6.425
FlowSOMSubset                      6.306  0.020   6.341
GetClusterMFIs                     6.165  0.148   6.242
GetClusterPercentagesPositive      6.136  0.127   6.195
GetCounts                          6.112  0.092   6.135
GetClusters                        6.026  0.072   6.029
ReadInput                          4.988  0.044   4.872
* 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)