##############################################################################
##############################################################################
###
### 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_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-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 ‘2.15.0’
* 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
PlotDimRed                        81.510  0.140  81.757
FlowSOMmary                       77.443  0.255  77.736
PlotOutliers                      25.075  0.032  25.143
PlotMarker                        22.276  0.032  22.340
UpdateMetaclusters                21.975  0.080  22.099
PlotStars                         18.624  0.080  18.735
GroupStats                        17.712  0.108  17.857
FlowSOM                           16.776  0.100  16.907
PlotGroups                        15.437  0.016  15.475
QueryMultiple                     12.364  0.032  12.422
AddAnnotation                     11.856  0.100  11.981
query_multiple                    11.669  0.024  11.713
Plot2DScatters                    10.712  0.056  10.789
PlotManualBars                    10.567  0.040  10.626
GetFlowJoLabels                    9.682  0.191   9.890
PlotNumbers                        9.205  0.040   9.256
PlotNode                           9.124  0.048   9.183
QueryStarPlot                      9.097  0.008   9.125
PlotVariable                       8.947  0.048   9.013
CountGroups                        8.634  0.036   8.685
PlotPies                           8.586  0.008   8.606
UpdateNodeSize                     8.238  0.016   8.270
PlotFlowSOM                        7.957  0.024   7.996
SaveClustersToFCS                  7.579  0.020   7.616
GetFeatures                        7.311  0.084   7.405
PlotLabels                         7.242  0.036   7.287
MetaclusterMFIs                    7.029  0.016   7.059
NClusters                          7.020  0.020   7.054
NMetaclusters                      6.899  0.060   6.971
TestOutliers                       6.761  0.048   6.822
GetMetaclusterCVs                  6.329  0.092   6.430
GetPercentages                     6.365  0.024   6.402
PlotOverview2D                     6.338  0.047   6.395
GetMFIs                            6.314  0.048   6.372
MetaclusterCVs                     6.312  0.035   6.360
GetMetaclusterPercentagesPositive  6.274  0.040   6.328
GetMetaclusters                    6.208  0.084   6.304
GetMetaclusterMFIs                 6.206  0.028   6.243
print.FlowSOM                      6.220  0.008   6.240
GetClusters                        6.109  0.020   6.138
GetCounts                          5.817  0.104   5.929
FlowSOMSubset                      5.811  0.024   5.846
GetClusterPercentagesPositive      5.781  0.016   5.806
GetClusterMFIs                     5.672  0.064   5.745
NewData                            5.519  0.008   5.536
* 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-3.21-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-devel_2025-02-19/site-library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.15.0’
** 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/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)