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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                        75.258  0.220  75.646
FlowSOMmary                       74.340  0.354  74.786
PlotOutliers                      42.957  0.096  43.179
PlotMarker                        23.876  0.119  24.069
UpdateMetaclusters                22.667  0.044  22.769
PlotStars                         19.328  0.044  19.420
GroupStats                        17.191  0.602  17.841
PlotGroups                        15.577  0.024  15.647
FlowSOM                           15.491  0.032  15.556
Plot2DScatters                    13.203  0.143  13.386
QueryMultiple                     13.022  0.048  13.097
query_multiple                    13.023  0.000  13.055
AddAnnotation                     11.620  0.132  11.779
PlotManualBars                    11.572  0.004  11.613
QueryStarPlot                      9.701  0.024   9.745
PlotNode                           9.597  0.008   9.632
PlotNumbers                        9.375  0.044   9.444
GetFlowJoLabels                    9.263  0.147   9.433
PlotPies                           8.871  0.028   8.925
UpdateNodeSize                     8.572  0.024   8.616
PlotVariable                       8.472  0.051   8.540
CountGroups                        8.221  0.052   8.290
PlotFlowSOM                        7.924  0.052   7.999
GetFeatures                        6.996  0.084   7.094
SaveClustersToFCS                  7.052  0.012   7.080
PlotLabels                         6.978  0.071   7.070
GetPercentages                     6.483  0.403   6.906
PlotOverview2D                     6.497  0.028   6.543
NClusters                          6.445  0.079   6.545
NMetaclusters                      6.432  0.068   6.519
MetaclusterMFIs                    6.396  0.036   6.450
TestOutliers                       6.223  0.007   6.244
GetMFIs                            5.766  0.100   5.881
GetMetaclusterCVs                  5.787  0.076   5.874
GetMetaclusters                    5.785  0.063   5.864
MetaclusterCVs                     5.740  0.100   5.855
GetClusterMFIs                     5.542  0.220   5.774
GetMetaclusterPercentagesPositive  5.653  0.056   5.723
GetMetaclusterMFIs                 5.617  0.076   5.702
print.FlowSOM                      5.626  0.016   5.655
GetClusterPercentagesPositive      5.470  0.131   5.614
GetCounts                          5.488  0.060   5.560
GetClusters                        5.407  0.088   5.511
FlowSOMSubset                      5.248  0.024   5.284
* 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)