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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_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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 ‘2.18.0’
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
  ‘[magrittr:pipe]{%>%}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
FlowSOMmary                       73.897  0.278  74.320
PlotDimRed                        73.772  0.132  74.592
PlotOutliers                      41.950  0.032  42.107
PlotMarker                        23.606  0.072  24.224
UpdateMetaclusters                22.091  0.119  22.269
PlotStars                         19.131  0.092  19.272
GroupStats                        16.810  0.123  16.976
FlowSOM                           15.918  0.092  16.057
PlotGroups                        15.475  0.032  15.550
QueryMultiple                     13.489  0.012  13.539
query_multiple                    13.229  0.040  13.300
Plot2DScatters                    13.199  0.012  13.254
PlotManualBars                    12.096  0.020  12.296
AddAnnotation                     11.667  0.192  11.892
PlotNode                           9.999  0.055  10.080
QueryStarPlot                      9.858  0.004   9.889
GetFlowJoLabels                    9.310  0.179   9.521
UpdateNodeSize                     9.020  0.056   9.100
PlotNumbers                        8.896  0.032   8.950
PlotPies                           8.781  0.084   8.889
PlotVariable                       8.543  0.020   8.582
CountGroups                        7.975  0.055   8.056
GetFeatures                        7.660  0.088   7.770
PlotFlowSOM                        7.412  0.063   7.499
PlotLabels                         6.958  0.012   6.990
SaveClustersToFCS                  6.943  0.024   6.983
NMetaclusters                      6.524  0.004   6.552
PlotOverview2D                     6.319  0.052   6.388
TestOutliers                       6.287  0.012   6.314
MetaclusterMFIs                    6.245  0.020   6.284
print.FlowSOM                      6.201  0.008   6.223
GetMetaclusterPercentagesPositive  5.985  0.072   6.074
MetaclusterCVs                     5.999  0.008   6.026
GetMetaclusterCVs                  5.801  0.199   6.021
NClusters                          5.979  0.012   6.038
GetMetaclusterMFIs                 5.653  0.203   5.873
GetCounts                          5.838  0.016   5.873
GetPercentages                     5.776  0.044   5.841
GetMFIs                            5.627  0.072   5.715
GetMetaclusters                    5.568  0.116   5.699
GetClusters                        5.649  0.016   5.682
GetClusterPercentagesPositive      5.626  0.028   5.670
FlowSOMSubset                      5.577  0.044   5.635
GetClusterMFIs                     5.477  0.072   5.566
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-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-4.5.0/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.18.0’
** 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 -std=gnu23 -I"/home/biocbuild/R/R-4.5.0/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 -std=gnu23 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)