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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
FlowSOMmary                       74.323  0.350  74.790
PlotDimRed                        69.902  0.156  70.206
PlotOutliers                      43.172  0.160  43.451
PlotMarker                        24.173  0.060  24.299
UpdateMetaclusters                23.064  0.112  23.239
PlotStars                         19.802  0.024  19.881
GroupStats                        17.305  0.156  17.511
FlowSOM                           15.347  0.440  16.091
PlotGroups                        15.484  0.020  15.548
query_multiple                    13.613  0.072  13.725
QueryMultiple                     13.645  0.016  13.699
Plot2DScatters                    13.160  0.079  13.278
PlotManualBars                    11.767  0.008  11.808
AddAnnotation                     11.384  0.389  12.041
QueryStarPlot                     10.143  0.052  10.223
PlotNode                           9.443  0.032   9.501
GetFlowJoLabels                    9.157  0.187   9.366
PlotNumbers                        9.247  0.024   9.297
PlotPies                           8.835  0.012   8.870
PlotVariable                       8.563  0.020   8.603
UpdateNodeSize                     8.336  0.019   8.379
CountGroups                        7.719  0.205   8.073
SaveClustersToFCS                  7.388  0.063   7.471
PlotFlowSOM                        7.369  0.043   7.430
GetFeatures                        7.182  0.120   7.322
PlotLabels                         7.120  0.016   7.161
TestOutliers                       6.711  0.016   6.745
PlotOverview2D                     6.422  0.131   6.570
NMetaclusters                      6.419  0.043   6.481
GetMetaclusters                    6.427  0.032   6.477
MetaclusterMFIs                    6.352  0.048   6.422
NClusters                          6.261  0.048   6.326
GetMetaclusterPercentagesPositive  5.881  0.116   6.016
GetMetaclusterCVs                  5.861  0.084   5.960
MetaclusterCVs                     5.813  0.076   5.904
GetPercentages                     5.837  0.031   5.886
print.FlowSOM                      5.844  0.020   5.879
GetMetaclusterMFIs                 5.800  0.040   5.857
GetClusterMFIs                     5.503  0.168   5.683
GetMFIs                            5.603  0.052   5.664
GetClusters                        5.405  0.163   5.580
GetClusterPercentagesPositive      5.403  0.124   5.538
GetCounts                          5.331  0.096   5.441
FlowSOMSubset                      5.247  0.051   5.314
NewData                            5.070  0.005   5.087
* 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)