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### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings FlowSOM_2.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    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 ‘2.12.0’
* 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                        81.638  0.259  82.035
FlowSOMmary                       79.201  0.375  79.598
PlotOutliers                      24.745  0.151  24.952
PlotMarker                        22.844  0.199  23.088
UpdateMetaclusters                21.455  0.096  21.597
PlotStars                         18.958  0.124  19.119
GroupStats                        17.189  0.044  17.271
FlowSOM                           16.867  0.111  17.016
PlotGroups                        15.822  0.311  16.163
QueryMultiple                     12.678  0.056  12.758
AddAnnotation                     12.158  0.164  12.347
query_multiple                    11.785  0.020  11.831
Plot2DScatters                    10.757  0.184  10.956
PlotManualBars                    10.440  0.160  10.625
GetFlowJoLabels                   10.293  0.092  10.409
PlotNode                           9.372  0.060   9.452
CountGroups                        9.164  0.088   9.271
PlotNumbers                        9.073  0.072   9.164
QueryStarPlot                      9.098  0.036   9.154
PlotVariable                       8.857  0.019   8.893
PlotPies                           8.768  0.016   8.803
PlotFlowSOM                        7.984  0.367   8.364
UpdateNodeSize                     8.246  0.012   8.277
PlotLabels                         7.624  0.160   7.800
SaveClustersToFCS                  7.397  0.075   7.488
GetFeatures                        7.379  0.012   7.404
NClusters                          7.034  0.244   7.292
MetaclusterMFIs                    7.112  0.119   7.246
NMetaclusters                      6.936  0.167   7.118
MetaclusterCVs                     6.649  0.016   6.679
TestOutliers                       6.534  0.020   6.567
PlotOverview2D                     6.477  0.068   6.559
GetMetaclusterCVs                  6.368  0.020   6.400
GetMFIs                            6.176  0.012   6.199
GetMetaclusterMFIs                 6.160  0.024   6.196
GetMetaclusters                    6.136  0.048   6.196
GetMetaclusterPercentagesPositive  6.174  0.004   6.190
GetPercentages                     6.134  0.028   6.176
print.FlowSOM                      6.072  0.040   6.125
GetCounts                          5.965  0.024   6.001
GetClusters                        5.899  0.044   5.956
FlowSOMSubset                      5.894  0.044   5.951
GetClusterMFIs                     5.872  0.040   5.925
GetClusterPercentagesPositive      5.838  0.012   5.862
NewData                            5.071  0.084   5.166
* 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-3.19-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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)