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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_2.19.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-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 ‘2.19.4’
* 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 ... OK
* 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                        83.758  0.164  84.077
FlowSOMmary                       82.914  0.502  83.483
PlotOutliers                      40.253  0.092  40.454
PlotMarker                        25.204  0.052  25.326
UpdateMetaclusters                23.323  0.148  23.535
PlotStars                         20.460  0.028  20.539
GroupStats                        19.350  0.112  19.513
PlotGroups                        17.766  0.100  17.908
FlowSOM                           17.631  0.092  17.764
Plot2DScatters                    15.091  0.084  15.210
query_multiple                    13.818  0.092  13.951
QueryMultiple                     13.835  0.064  13.930
Plot1DScatters                    13.372  0.032  13.432
PlotManualBars                    13.054  0.056  13.139
AddAnnotation                     12.490  0.196  12.713
PlotNumbers                       10.942  0.056  11.034
GetFlowJoLabels                   10.657  0.127  10.815
PlotNode                          10.601  0.016  10.647
QueryStarPlot                     10.440  0.008  10.466
PlotPies                           9.992  0.040  10.058
PlotVariable                      10.021  0.008  10.053
CountGroups                        9.207  0.073   9.301
PlotFlowSOM                        8.977  0.052   9.049
UpdateNodeSize                     8.602  0.008   8.629
PlotLabels                         8.382  0.024   8.426
SaveClustersToFCS                  8.317  0.024   8.357
GetFeatures                        8.192  0.120   8.331
NClusters                          7.974  0.055   8.048
MetaclusterCVs                     7.898  0.092   8.008
MetaclusterMFIs                    7.912  0.060   7.992
NMetaclusters                      7.868  0.036   7.923
GetMFIs                            7.774  0.124   7.915
PlotOverview2D                     7.708  0.056   7.781
PlotMFIHeatmap                     7.673  0.047   7.738
TestOutliers                       7.629  0.004   7.651
GetMetaclusterMFIs                 7.284  0.072   7.373
GetMetaclusterCVs                  7.282  0.064   7.363
GetMajorityLabels                  7.269  0.056   7.346
GetPercentages                     7.237  0.048   7.302
GetClusterMFIs                     7.145  0.087   7.251
GetMetaclusters                    7.182  0.023   7.225
GetMetaclusterPercentagesPositive  7.147  0.036   7.201
GetClusterPercentagesPositive      6.830  0.207   7.054
print.FlowSOM                      6.954  0.052   7.025
GetCounts                          6.840  0.140   6.996
GetClusters                        6.680  0.151   6.846
FlowSOMSubset                      6.045  0.040   6.098
NewData                            6.046  0.015   6.075
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-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 ‘2.19.4’
** 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)