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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_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.16.0’
* 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                       83.389  0.318  83.781
PlotDimRed                        80.798  0.143  81.103
PlotOutliers                      43.899  0.091  44.094
PlotMarker                        25.111  0.088  25.274
UpdateMetaclusters                23.889  0.143  24.094
PlotStars                         20.539  0.032  20.613
GroupStats                        18.046  0.039  18.140
PlotGroups                        17.013  0.016  17.074
FlowSOM                           16.819  0.111  16.999
query_multiple                    14.025  0.032  14.091
Plot2DScatters                    13.873  0.052  13.983
QueryMultiple                     13.678  0.028  13.738
PlotManualBars                    12.594  0.020  12.651
AddAnnotation                     12.304  0.170  12.515
PlotNode                          10.271  0.036  10.329
QueryStarPlot                     10.046  0.020  10.084
PlotPies                          10.012  0.028  10.060
GetFlowJoLabels                    9.841  0.072   9.942
PlotNumbers                        9.627  0.016   9.665
PlotVariable                       9.438  0.028   9.491
CountGroups                        8.827  0.125   8.999
UpdateNodeSize                     8.799  0.016   8.837
PlotFlowSOM                        8.580  0.060   8.663
SaveClustersToFCS                  8.296  0.020   8.333
PlotLabels                         7.607  0.004   7.632
GetFeatures                        7.495  0.024   7.541
NMetaclusters                      7.144  0.028   7.193
PlotOverview2D                     7.041  0.076   7.131
MetaclusterMFIs                    7.014  0.044   7.079
TestOutliers                       6.887  0.004   6.905
NClusters                          6.725  0.020   6.764
print.FlowSOM                      6.497  0.028   6.540
GetMetaclusterCVs                  6.463  0.012   6.493
GetMetaclusterMFIs                 6.367  0.052   6.437
MetaclusterCVs                     6.403  0.008   6.438
GetPercentages                     6.366  0.036   6.420
GetClusterMFIs                     6.315  0.044   6.375
GetMetaclusters                    6.331  0.011   6.361
GetMFIs                            6.333  0.004   6.355
GetMetaclusterPercentagesPositive  6.220  0.032   6.269
FlowSOMSubset                      6.157  0.035   6.225
GetCounts                          6.013  0.015   6.044
GetClusterPercentagesPositive      6.015  0.008   6.044
GetClusters                        6.017  0.000   6.034
NewData                            5.257  0.008   5.280
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** 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/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/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)