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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_2.17.0.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 ‘2.17.0’
* 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                        72.158  0.148  72.445
FlowSOMmary                       70.109  0.291  70.496
PlotOutliers                      25.177  0.068  25.317
UpdateMetaclusters                21.660  0.082  21.811
PlotMarker                        20.856  0.032  20.942
PlotStars                         18.103  0.052  18.214
GroupStats                        16.143  0.056  16.249
FlowSOM                           15.108  0.036  15.185
PlotGroups                        14.507  0.012  14.555
AddAnnotation                     11.351  0.195  11.584
QueryMultiple                     11.065  0.015  11.116
query_multiple                    11.003  0.004  11.036
Plot2DScatters                    10.251  0.016  10.298
PlotManualBars                     9.873  0.023   9.927
GetFlowJoLabels                    9.256  0.116   9.401
PlotNode                           8.588  0.036   8.647
QueryStarPlot                      8.428  0.008   8.461
PlotVariable                       8.331  0.040   8.397
PlotNumbers                        8.271  0.012   8.310
PlotPies                           7.943  0.020   7.985
CountGroups                        7.865  0.056   7.947
UpdateNodeSize                     7.677  0.013   7.711
PlotFlowSOM                        7.540  0.060   7.619
GetFeatures                        7.204  0.040   7.265
PlotOverview2D                     6.952  0.064   7.034
SaveClustersToFCS                  6.864  0.008   6.892
PlotLabels                         6.578  0.044   6.639
NMetaclusters                      6.365  0.016   6.395
MetaclusterMFIs                    6.355  0.015   6.389
NClusters                          6.311  0.024   6.353
TestOutliers                       6.098  0.000   6.117
MetaclusterCVs                     5.769  0.008   5.792
GetMetaclusterCVs                  5.611  0.008   5.633
GetMetaclusterMFIs                 5.611  0.008   5.631
print.FlowSOM                      5.612  0.004   5.631
GetMetaclusterPercentagesPositive  5.559  0.004   5.579
GetPercentages                     5.545  0.004   5.564
GetMFIs                            5.505  0.020   5.539
GetMetaclusters                    5.480  0.008   5.503
GetCounts                          5.434  0.028   5.480
GetClusterPercentagesPositive      5.336  0.008   5.360
GetClusters                        5.286  0.024   5.324
FlowSOMSubset                      5.231  0.044   5.290
GetClusterMFIs                     5.195  0.051   5.263
* 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 ‘2.17.0’
** 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)