##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* 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                       72.804  0.318  73.258
PlotDimRed                        72.488  0.208  72.826
PlotOutliers                      43.144  0.120  43.377
PlotMarker                        23.482  0.092  23.636
UpdateMetaclusters                22.189  0.056  22.308
PlotStars                         19.187  0.016  19.260
GroupStats                        16.962  0.116  17.113
FlowSOM                           15.679  0.063  15.793
PlotGroups                        15.258  0.004  15.303
QueryMultiple                     13.282  0.047  13.372
query_multiple                    13.096  0.024  13.158
Plot2DScatters                    13.036  0.047  13.109
AddAnnotation                     12.229  0.347  12.621
PlotManualBars                    11.431  0.008  11.471
QueryStarPlot                      9.939  0.048  10.018
GetFlowJoLabels                    9.395  0.216   9.638
PlotNode                           9.209  0.020   9.253
PlotNumbers                        8.958  0.012   8.991
PlotPies                           8.763  0.020   8.810
PlotVariable                       8.575  0.012   8.610
UpdateNodeSize                     8.344  0.056   8.418
CountGroups                        8.311  0.028   8.366
PlotFlowSOM                        7.528  0.040   7.589
GetFeatures                        7.221  0.075   7.317
SaveClustersToFCS                  7.051  0.020   7.093
PlotLabels                         6.772  0.059   6.848
PlotOverview2D                     6.503  0.100   6.623
NClusters                          6.456  0.064   6.533
NMetaclusters                      6.343  0.048   6.406
MetaclusterMFIs                    6.322  0.012   6.346
TestOutliers                       6.187  0.012   6.217
GetMetaclusters                    5.855  0.080   5.946
GetMFIs                            5.881  0.028   5.921
MetaclusterCVs                     5.821  0.028   5.859
GetMetaclusterMFIs                 5.752  0.087   5.853
GetMetaclusterCVs                  5.743  0.064   5.819
GetPercentages                     5.679  0.040   5.731
print.FlowSOM                      5.696  0.016   5.728
GetClusterPercentagesPositive      5.483  0.163   5.666
GetMetaclusterPercentagesPositive  5.591  0.044   5.646
GetClusters                        5.480  0.132   5.625
GetCounts                          5.484  0.092   5.590
FlowSOMSubset                      5.507  0.032   5.556
GetClusterMFIs                     5.393  0.092   5.502
* 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.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* 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)