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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                       68.542  0.302  68.929
PlotDimRed                        68.498  0.120  68.759
PlotOutliers                      24.385  0.358  24.835
UpdateMetaclusters                21.174  0.064  21.302
PlotMarker                        20.553  0.594  21.212
PlotStars                         17.412  0.067  17.547
GroupStats                        15.798  0.068  15.900
FlowSOM                           14.873  0.032  14.938
PlotGroups                        14.021  0.020  14.063
query_multiple                    11.610  0.008  11.647
AddAnnotation                     11.290  0.307  11.627
QueryMultiple                     11.106  0.028  11.171
PlotManualBars                    10.370  0.028  10.476
Plot2DScatters                    10.303  0.020  10.350
GetFlowJoLabels                    8.986  0.160   9.171
PlotNode                           8.454  0.242   8.718
QueryStarPlot                      8.435  0.056   8.518
PlotPies                           8.243  0.060   8.338
PlotVariable                       8.118  0.072   8.212
PlotNumbers                        8.049  0.124   8.195
UpdateNodeSize                     8.060  0.064   8.145
CountGroups                        7.829  0.052   7.897
SaveClustersToFCS                  6.958  0.056   7.031
GetFeatures                        6.872  0.052   6.938
PlotFlowSOM                        6.838  0.043   6.893
PlotLabels                         6.758  0.020   6.795
MetaclusterMFIs                    6.217  0.024   6.254
PlotOverview2D                     6.106  0.100   6.233
NMetaclusters                      6.154  0.024   6.193
TestOutliers                       6.063  0.039   6.123
GetMetaclusterMFIs                 5.892  0.052   5.961
NClusters                          5.902  0.000   5.913
GetMetaclusters                    5.864  0.032   5.910
GetMetaclusterCVs                  5.714  0.107   5.837
MetaclusterCVs                     5.779  0.028   5.820
print.FlowSOM                      5.665  0.036   5.713
GetPercentages                     5.565  0.004   5.580
GetMetaclusterPercentagesPositive  5.511  0.020   5.543
GetMFIs                            5.445  0.044   5.500
GetCounts                          5.363  0.100   5.473
GetClusterPercentagesPositive      5.263  0.172   5.442
GetClusters                        5.282  0.139   5.431
GetClusterMFIs                     5.299  0.107   5.418
FlowSOMSubset                      5.135  0.028   5.175
* 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)