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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings FlowSOM_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FlowSOM.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* 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 ‘2.10.0’
* 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 R 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 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 ... OK
* 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                        82.201  1.603  86.084
FlowSOMmary                       79.721  0.295  80.029
PlotOutliers                      22.492  0.048  22.591
UpdateMetaclusters                22.286  0.068  22.405
PlotMarker                        22.055  0.053  22.152
PlotStars                         18.755  0.024  18.819
GroupStats                        16.962  0.060  17.062
FlowSOM                           16.697  0.024  16.756
PlotGroups                        15.883  0.056  15.972
QueryMultiple                     11.680  1.095  13.509
AddAnnotation                     12.395  0.272  12.698
query_multiple                    11.686  0.060  11.772
PlotManualBars                    11.204  0.041  11.272
Plot2DScatters                    10.862  0.056  11.041
GetFlowJoLabels                    9.954  0.120  10.102
PlotNode                           9.672  0.032   9.723
CountGroups                        9.313  0.079   9.412
PlotPies                           9.341  0.024   9.384
PlotNumbers                        9.260  0.068   9.349
PlotVariable                       9.046  0.019   9.113
QueryStarPlot                      8.954  0.035   9.033
UpdateNodeSize                     8.289  0.064   8.373
SaveClustersToFCS                  8.157  0.035   8.212
PlotFlowSOM                        8.023  0.048   8.097
GetMetaclusterMFIs                 7.213  0.785   8.675
GetFeatures                        7.591  0.004   7.611
NClusters                          7.516  0.020   7.553
MetaclusterMFIs                    7.186  0.088   7.294
PlotLabels                         7.217  0.016   7.253
NMetaclusters                      7.182  0.019   7.216
GetMetaclusterPercentagesPositive  6.816  0.171   7.026
GetMetaclusterCVs                  6.878  0.008   6.910
TestOutliers                       6.794  0.024   6.833
GetMFIs                            6.413  0.040   6.468
PlotOverview2D                     6.410  0.040   6.462
MetaclusterCVs                     6.395  0.052   6.460
GetPercentages                     6.397  0.008   6.425
GetMetaclusters                    6.307  0.016   6.339
print.FlowSOM                      6.230  0.024   6.269
GetCounts                          6.155  0.016   6.181
GetClusterMFIs                     5.913  0.080   6.020
GetClusterPercentagesPositive      5.862  0.024   5.899
FlowSOMSubset                      5.800  0.032   5.845
GetClusters                        5.824  0.008   5.844
NewData                            5.265  0.112   5.387
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 10.3.1’
gcc -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -c som.c -o som.o
gcc -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/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)