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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
PlotDimRed                        79.925  0.147  80.177
FlowSOMmary                       75.188  0.267  75.486
PlotOutliers                      26.032  0.056  26.142
PlotMarker                        22.891  0.092  23.026
UpdateMetaclusters                21.952  0.052  22.052
PlotStars                         18.382  0.056  18.471
GroupStats                        16.779  0.080  16.900
FlowSOM                           16.717  0.047  16.799
PlotGroups                        15.793  0.032  15.859
QueryMultiple                     12.061  0.064  12.150
AddAnnotation                     11.920  0.116  12.062
query_multiple                    11.912  0.012  11.950
PlotManualBars                    10.963  0.084  11.073
Plot2DScatters                    10.754  0.044  10.825
GetFlowJoLabels                    9.479  0.140   9.637
PlotNumbers                        9.474  0.016   9.509
PlotNode                           9.272  0.016   9.302
PlotPies                           9.204  0.028   9.249
CountGroups                        9.155  0.020   9.211
QueryStarPlot                      9.025  0.044   9.089
PlotVariable                       8.946  0.039   9.004
SaveClustersToFCS                  8.120  0.020   8.156
PlotFlowSOM                        7.967  0.016   7.998
UpdateNodeSize                     7.851  0.024   7.891
GetFeatures                        7.374  0.108   7.494
PlotLabels                         7.342  0.016   7.371
NClusters                          7.179  0.063   7.260
MetaclusterCVs                     7.189  0.020   7.227
MetaclusterMFIs                    7.130  0.024   7.170
NMetaclusters                      7.082  0.051   7.148
TestOutliers                       6.790  0.016   6.819
GetMetaclusterCVs                  6.721  0.068   6.800
print.FlowSOM                      6.767  0.016   6.796
PlotOverview2D                     6.656  0.052   6.720
GetClusterPercentagesPositive      6.161  0.199   6.370
GetMetaclusters                    6.259  0.080   6.352
GetPercentages                     6.298  0.020   6.331
GetMetaclusterPercentagesPositive  6.246  0.060   6.318
GetMetaclusterMFIs                 6.263  0.008   6.284
GetMFIs                            6.170  0.055   6.236
GetClusterMFIs                     5.783  0.236   6.028
GetClusters                        5.842  0.128   5.979
GetCounts                          5.828  0.088   5.926
FlowSOMSubset                      5.845  0.012   5.873
NewData                            5.126  0.024   5.162
* 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)