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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 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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: ‘aarch64-unknown-linux-gnu-gcc (GCC) 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                        74.259  0.200  74.574
FlowSOMmary                       64.903  0.347  65.300
PlotOutliers                      22.408  0.096  22.564
UpdateMetaclusters                19.488  0.483  20.016
PlotMarker                        19.663  0.140  19.848
PlotStars                         16.462  0.068  16.566
GroupStats                        15.137  0.052  15.231
FlowSOM                           14.385  0.112  14.528
PlotGroups                        13.861  0.167  14.059
QueryMultiple                     10.729  0.024  10.775
AddAnnotation                     10.320  0.088  10.434
query_multiple                    10.042  0.152  10.216
Plot2DScatters                     9.912  0.039   9.977
PlotManualBars                     9.253  0.040   9.320
GetFlowJoLabels                    8.407  0.092   8.525
PlotNode                           8.092  0.036   8.148
QueryStarPlot                      8.105  0.012   8.132
PlotVariable                       7.933  0.100   8.050
PlotNumbers                        7.688  0.047   7.754
PlotPies                           7.553  0.012   7.586
CountGroups                        7.445  0.059   7.519
UpdateNodeSize                     7.212  0.171   7.405
PlotFlowSOM                        7.063  0.156   7.236
SaveClustersToFCS                  6.375  0.032   6.419
NMetaclusters                      6.369  0.016   6.400
PlotLabels                         6.271  0.076   6.359
GetFeatures                        6.321  0.020   6.354
MetaclusterMFIs                    6.242  0.068   6.325
NClusters                          6.129  0.008   6.151
GetMetaclusterPercentagesPositive  5.722  0.044   5.780
TestOutliers                       5.578  0.012   5.601
MetaclusterCVs                     5.483  0.000   5.496
PlotOverview2D                     5.395  0.044   5.449
GetMetaclusterCVs                  5.424  0.004   5.441
print.FlowSOM                      5.332  0.080   5.425
GetPercentages                     5.362  0.004   5.380
GetMFIs                            5.303  0.028   5.346
GetMetaclusterMFIs                 5.295  0.004   5.311
GetMetaclusters                    5.243  0.008   5.264
FlowSOMSubset                      5.043  0.020   5.074
GetClusterMFIs                     4.945  0.064   5.020
GetClusterPercentagesPositive      4.942  0.055   5.009
* 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-4.4.2/site-library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -c som.c -o som.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/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)