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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                        75.945  0.176  76.261
FlowSOMmary                       75.062  0.327  75.491
PlotOutliers                      42.052  0.088  42.273
PlotMarker                        23.043  0.056  23.168
UpdateMetaclusters                22.344  0.023  22.434
PlotStars                         19.376  0.064  19.501
GroupStats                        16.978  0.064  17.088
PlotGroups                        15.289  0.039  15.372
FlowSOM                           15.221  0.104  15.364
QueryMultiple                     12.980  0.036  13.056
Plot2DScatters                    12.987  0.024  13.044
query_multiple                    13.003  0.008  13.052
AddAnnotation                     11.627  0.204  11.866
PlotManualBars                    11.315  0.028  11.375
QueryStarPlot                      9.458  0.008   9.492
GetFlowJoLabels                    9.345  0.067   9.440
PlotNode                           9.251  0.008   9.289
PlotNumbers                        8.791  0.020   8.840
PlotVariable                       8.465  0.084   8.573
UpdateNodeSize                     8.406  0.052   8.483
PlotPies                           8.311  0.024   8.356
CountGroups                        7.689  0.028   7.738
PlotFlowSOM                        7.377  0.060   7.458
SaveClustersToFCS                  7.286  0.016   7.323
GetFeatures                        7.216  0.008   7.243
PlotLabels                         6.993  0.052   7.062
NClusters                          6.944  0.008   6.969
MetaclusterMFIs                    6.287  0.016   6.320
NMetaclusters                      6.234  0.027   6.278
PlotOverview2D                     6.097  0.099   6.215
TestOutliers                       6.160  0.012   6.190
GetMetaclusterMFIs                 6.005  0.016   6.036
GetMetaclusterPercentagesPositive  5.688  0.056   5.758
GetPercentages                     5.720  0.012   5.749
MetaclusterCVs                     5.719  0.012   5.746
print.FlowSOM                      5.694  0.031   5.742
GetMetaclusters                    5.655  0.028   5.698
GetCounts                          5.670  0.008   5.694
GetMetaclusterCVs                  5.650  0.004   5.667
GetMFIs                            5.561  0.040   5.615
FlowSOMSubset                      5.454  0.020   5.486
GetClusterMFIs                     5.383  0.031   5.429
GetClusterPercentagesPositive      5.359  0.020   5.392
GetClusters                        5.341  0.020   5.379
* 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)