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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_2.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* 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 ‘2.14.0’
* 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 ... OK
* 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                        72.186  0.144  72.512
FlowSOMmary                       68.560  0.319  68.991
PlotOutliers                      23.344  0.052  23.467
PlotMarker                        20.757  0.080  20.901
UpdateMetaclusters                20.004  0.047  20.111
PlotStars                         17.293  0.036  17.383
GroupStats                        15.634  0.032  15.718
FlowSOM                           14.928  0.052  15.025
PlotGroups                        14.222  0.032  14.299
AddAnnotation                     10.868  0.140  11.039
QueryMultiple                     10.696  0.044  10.773
query_multiple                    10.669  0.020  10.719
Plot2DScatters                    10.026  0.051  10.114
PlotManualBars                     9.552  0.000   9.584
GetFlowJoLabels                    8.644  0.099   8.779
PlotNode                           8.479  0.032   8.537
QueryStarPlot                      8.478  0.004   8.510
PlotVariable                       8.125  0.012   8.162
CountGroups                        8.034  0.024   8.083
PlotNumbers                        8.000  0.012   8.035
PlotPies                           7.834  0.031   7.888
UpdateNodeSize                     7.493  0.024   7.539
PlotLabels                         7.114  0.012   7.148
PlotFlowSOM                        6.998  0.096   7.117
SaveClustersToFCS                  6.837  0.052   6.910
GetFeatures                        6.717  0.012   6.753
NMetaclusters                      6.591  0.020   6.632
NClusters                          6.210  0.028   6.262
MetaclusterMFIs                    6.219  0.008   6.248
PlotOverview2D                     6.077  0.059   6.160
TestOutliers                       6.082  0.012   6.111
print.FlowSOM                      5.959  0.016   5.993
GetMetaclusters                    5.848  0.024   5.889
GetMetaclusterCVs                  5.689  0.004   5.712
GetPercentages                     5.689  0.004   5.711
MetaclusterCVs                     5.628  0.016   5.663
GetMetaclusterPercentagesPositive  5.610  0.024   5.652
GetMFIs                            5.575  0.000   5.593
GetMetaclusterMFIs                 5.554  0.012   5.584
FlowSOMSubset                      5.422  0.020   5.458
GetClusterMFIs                     5.243  0.064   5.323
GetClusterPercentagesPositive      5.219  0.024   5.263
GetCounts                          5.198  0.004   5.219
GetClusters                        5.079  0.040   5.136
* 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-3.20-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-4.4.2/site-library’
* installing *source* package ‘FlowSOM’ ...
** 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 -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 -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-4.4.2/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)