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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                        85.078  0.120  85.329
FlowSOMmary                       76.074  0.271  76.361
PlotOutliers                      25.516  0.044  25.607
PlotMarker                        22.874  0.096  23.017
UpdateMetaclusters                22.498  0.016  22.559
PlotStars                         19.517  0.052  19.603
GroupStats                        16.928  0.064  17.035
FlowSOM                           16.502  0.071  16.608
PlotGroups                        15.918  0.016  15.969
query_multiple                    12.369  0.008  12.399
AddAnnotation                     11.995  0.136  12.158
QueryMultiple                     12.068  0.024  12.117
Plot2DScatters                    10.814  0.032  10.876
PlotManualBars                    10.806  0.020  10.850
PlotNode                          10.145  0.012  10.177
GetFlowJoLabels                    9.636  0.152   9.813
PlotVariable                       9.197  0.008   9.223
CountGroups                        9.157  0.036   9.213
QueryStarPlot                      9.116  0.008   9.143
PlotNumbers                        9.068  0.052   9.135
PlotPies                           8.688  0.068   8.772
SaveClustersToFCS                  8.276  0.047   8.341
UpdateNodeSize                     8.050  0.052   8.119
PlotFlowSOM                        7.899  0.032   7.947
GetFeatures                        7.473  0.072   7.562
PlotLabels                         7.307  0.012   7.333
MetaclusterMFIs                    7.020  0.020   7.056
NMetaclusters                      7.022  0.016   7.054
NClusters                          6.980  0.004   7.000
TestOutliers                       6.896  0.016   6.925
GetMetaclusterPercentagesPositive  6.629  0.039   6.684
PlotOverview2D                     6.489  0.008   6.507
print.FlowSOM                      6.371  0.012   6.397
GetMetaclusterCVs                  6.326  0.048   6.389
MetaclusterCVs                     6.334  0.016   6.367
GetPercentages                     6.202  0.060   6.275
GetMetaclusterMFIs                 6.203  0.044   6.261
GetMFIs                            6.196  0.012   6.222
GetMetaclusters                    6.146  0.024   6.183
GetClusterMFIs                     5.890  0.160   6.065
GetClusterPercentagesPositive      5.894  0.112   6.021
GetClusters                        5.860  0.111   5.986
GetCounts                          5.882  0.064   5.959
FlowSOMSubset                      5.753  0.020   5.787
NewData                            5.132  0.056   5.200
* 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)