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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 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* 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                        71.990  0.160  72.271
FlowSOMmary                       69.495  0.351  69.904
PlotOutliers                      23.148  0.080  23.283
UpdateMetaclusters                20.118  0.032  20.200
PlotMarker                        20.000  0.091  20.138
PlotStars                         17.420  0.016  17.480
GroupStats                        15.561  0.048  15.646
FlowSOM                           15.018  0.136  15.190
PlotGroups                        14.631  0.012  14.677
AddAnnotation                     11.017  0.583  11.628
QueryMultiple                     10.790  0.024  10.841
query_multiple                    10.700  0.008  10.732
Plot2DScatters                    10.142  0.024  10.195
PlotManualBars                     9.518  0.024   9.563
PlotNode                           8.796  0.036   8.851
GetFlowJoLabels                    8.754  0.044   8.820
PlotNumbers                        8.548  0.016   8.583
CountGroups                        7.987  0.087   8.090
QueryStarPlot                      7.959  0.032   8.012
PlotVariable                       7.902  0.012   7.932
PlotPies                           7.676  0.016   7.712
UpdateNodeSize                     7.014  0.044   7.074
PlotFlowSOM                        6.860  0.048   6.925
GetFeatures                        6.703  0.008   6.726
SaveClustersToFCS                  6.629  0.028   6.672
PlotLabels                         6.568  0.004   6.588
NClusters                          6.237  0.024   6.277
GetMetaclusterCVs                  6.025  0.028   6.065
GetMetaclusterPercentagesPositive  6.046  0.004   6.064
MetaclusterMFIs                    5.984  0.012   6.009
GetPercentages                     5.922  0.016   5.951
GetMetaclusterMFIs                 5.787  0.024   5.825
TestOutliers                       5.791  0.016   5.820
NMetaclusters                      5.778  0.008   5.800
PlotOverview2D                     5.749  0.024   5.786
MetaclusterCVs                     5.566  0.016   5.591
GetMetaclusters                    5.454  0.096   5.563
GetMFIs                            5.497  0.032   5.544
GetClusterPercentagesPositive      5.325  0.048   5.385
print.FlowSOM                      5.338  0.028   5.378
GetClusterMFIs                     5.228  0.087   5.334
GetClusters                        5.235  0.008   5.255
FlowSOMSubset                      5.174  0.040   5.228
GetCounts                          5.148  0.012   5.171
* 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-4.4.3/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-4.4.3/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -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-4.4.3/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.4.3/lib -lR
installing to /home/biocbuild/R/R-4.4.3/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)