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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
PlotDimRed                        77.351  0.140  77.660
FlowSOMmary                       72.785  0.267  73.150
PlotOutliers                      42.953  0.064  43.135
PlotMarker                        24.245  0.111  24.423
UpdateMetaclusters                22.874  0.076  23.006
PlotStars                         19.566  0.035  19.657
GroupStats                        17.255  0.024  17.328
PlotGroups                        16.530  0.032  16.609
FlowSOM                           15.809  0.136  15.991
QueryMultiple                     13.622  0.008  13.673
query_multiple                    13.448  0.060  13.544
Plot2DScatters                    13.175  0.071  13.282
AddAnnotation                     11.845  0.143  12.027
PlotManualBars                    11.659  0.016  11.705
QueryStarPlot                      9.832  0.044   9.905
GetFlowJoLabels                    9.704  0.068   9.801
PlotNode                           9.732  0.016   9.774
PlotPies                           9.252  0.020   9.295
PlotNumbers                        8.893  0.004   8.918
PlotVariable                       8.807  0.016   8.850
UpdateNodeSize                     8.739  0.068   8.830
CountGroups                        8.295  0.060   8.380
PlotFlowSOM                        8.038  0.052   8.114
GetFeatures                        7.213  0.007   7.237
SaveClustersToFCS                  7.174  0.032   7.225
PlotOverview2D                     6.970  0.064   7.053
PlotLabels                         6.952  0.048   7.018
NMetaclusters                      6.542  0.000   6.560
NClusters                          6.390  0.012   6.419
TestOutliers                       6.263  0.028   6.308
MetaclusterMFIs                    5.977  0.028   6.021
GetMFIs                            5.947  0.024   5.988
GetMetaclusterCVs                  5.923  0.004   5.947
GetCounts                          5.900  0.020   5.935
print.FlowSOM                      5.888  0.015   5.920
MetaclusterCVs                     5.819  0.012   5.851
GetPercentages                     5.753  0.020   5.787
GetMetaclusterMFIs                 5.756  0.004   5.775
GetMetaclusters                    5.726  0.016   5.757
GetMetaclusterPercentagesPositive  5.596  0.032   5.643
GetClusterMFIs                     5.538  0.084   5.639
GetClusterPercentagesPositive      5.506  0.020   5.542
GetClusters                        5.421  0.020   5.455
FlowSOMSubset                      5.336  0.028   5.384
* 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)