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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_2.13.0.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 ‘2.13.0’
* 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 (GCC) 10.3.1’
* 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                        83.335  0.171  83.643
FlowSOMmary                       78.502  0.667  79.204
PlotOutliers                      24.919  0.212  25.183
PlotMarker                        23.900  0.427  24.381
UpdateMetaclusters                22.414  0.136  22.601
PlotStars                         19.188  0.104  19.335
GroupStats                        17.569  0.076  17.685
FlowSOM                           16.640  0.215  16.892
PlotGroups                        15.961  0.056  16.049
QueryMultiple                     12.974  0.040  13.044
AddAnnotation                     12.387  0.391  12.806
query_multiple                    12.309  0.060  12.397
Plot2DScatters                    10.776  0.036  10.830
PlotManualBars                    10.608  0.012  10.644
GetFlowJoLabels                    9.781  0.112   9.920
PlotNode                           9.397  0.243   9.663
QueryStarPlot                      9.392  0.044   9.459
PlotNumbers                        9.168  0.136   9.323
CountGroups                        9.069  0.108   9.196
PlotVariable                       8.994  0.092   9.107
PlotPies                           8.973  0.035   9.028
PlotFlowSOM                        7.934  0.028   7.980
SaveClustersToFCS                  7.782  0.079   7.881
UpdateNodeSize                     7.837  0.016   7.870
GetFeatures                        7.269  0.116   7.402
PlotLabels                         7.328  0.020   7.364
NMetaclusters                      7.143  0.044   7.202
NClusters                          7.111  0.040   7.168
MetaclusterMFIs                    6.986  0.040   7.041
TestOutliers                       6.675  0.032   6.721
PlotOverview2D                     6.575  0.067   6.657
GetMetaclusterCVs                  6.402  0.056   6.473
GetMFIs                            6.301  0.091   6.407
GetPercentages                     6.314  0.032   6.357
GetMetaclusterPercentagesPositive  6.282  0.040   6.342
GetMetaclusterMFIs                 6.286  0.036   6.336
GetCounts                          6.250  0.068   6.332
print.FlowSOM                      6.278  0.024   6.317
MetaclusterCVs                     6.278  0.015   6.305
GetMetaclusters                    6.221  0.064   6.299
GetClusterMFIs                     5.804  0.256   6.070
GetClusters                        5.914  0.092   6.025
GetClusterPercentagesPositive      5.782  0.135   5.931
FlowSOMSubset                      5.627  0.024   5.662
NewData                            5.145  0.036   5.192
* 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 (GCC) 10.3.1’
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)