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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
FlowSOMmary                       75.042  0.318  75.448
PlotDimRed                        68.603  0.115  69.099
PlotOutliers                      43.232  0.202  43.870
PlotMarker                        22.718  0.461  23.299
UpdateMetaclusters                22.053  0.032  22.139
PlotStars                         19.655  0.275  20.065
GroupStats                        17.294  0.096  17.439
FlowSOM                           15.082  0.028  15.135
PlotGroups                        15.070  0.020  15.200
QueryMultiple                     13.469  0.042  13.647
Plot2DScatters                    13.219  0.072  13.363
query_multiple                    13.157  0.004  13.190
AddAnnotation                     11.531  0.168  11.725
PlotManualBars                    11.285  0.198  11.583
PlotNode                           9.299  0.200   9.530
QueryStarPlot                      9.436  0.000   9.463
GetFlowJoLabels                    9.092  0.127   9.244
PlotNumbers                        9.068  0.052   9.154
UpdateNodeSize                     8.803  0.008   8.831
PlotVariable                       8.527  0.123   8.710
PlotPies                           8.513  0.136   8.670
CountGroups                        8.073  0.064   8.151
PlotFlowSOM                        7.252  0.032   7.322
GetFeatures                        7.032  0.072   7.123
PlotLabels                         6.801  0.068   6.923
SaveClustersToFCS                  6.804  0.004   6.823
PlotOverview2D                     6.643  0.076   6.741
NMetaclusters                      6.640  0.012   6.690
TestOutliers                       6.389  0.012   6.414
MetaclusterMFIs                    6.361  0.012   6.392
GetMetaclusters                    6.240  0.060   6.318
GetMetaclusterMFIs                 6.004  0.056   6.079
NClusters                          5.985  0.020   6.043
GetPercentages                     5.872  0.055   5.945
GetMetaclusterCVs                  5.878  0.040   5.934
GetMFIs                            5.772  0.092   5.879
MetaclusterCVs                     5.783  0.044   5.843
GetMetaclusterPercentagesPositive  5.771  0.028   5.815
print.FlowSOM                      5.699  0.020   5.732
GetCounts                          5.532  0.092   5.637
GetClusterMFIs                     5.364  0.184   5.560
GetClusterPercentagesPositive      5.365  0.123   5.500
GetClusters                        5.317  0.116   5.445
FlowSOMSubset                      5.312  0.016   5.337
* 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)