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


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 ‘2.14.0’
* 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                        72.610  0.140  72.869
FlowSOMmary                       70.727  0.279  71.045
PlotOutliers                      24.937  0.060  25.068
PlotMarker                        21.244  0.097  21.763
UpdateMetaclusters                20.854  0.076  21.043
PlotStars                         18.734  0.036  18.819
GroupStats                        16.926  0.040  17.004
FlowSOM                           15.325  0.032  15.394
PlotGroups                        14.962  0.012  15.008
AddAnnotation                     11.657  0.140  11.827
query_multiple                    11.622  0.028  11.739
QueryMultiple                     11.184  0.027  11.238
Plot2DScatters                    10.295  0.040  10.359
PlotManualBars                    10.191  0.021  10.237
GetFlowJoLabels                    9.135  0.080   9.235
PlotNumbers                        9.104  0.036   9.535
PlotNode                           9.038  0.028   9.097
PlotVariable                       8.862  0.048   8.930
QueryStarPlot                      8.380  0.020   8.420
CountGroups                        8.215  0.024   8.258
PlotPies                           8.220  0.008   8.244
UpdateNodeSize                     7.722  0.004   7.756
PlotFlowSOM                        7.238  0.056   7.311
MetaclusterMFIs                    7.056  0.008   7.080
SaveClustersToFCS                  7.001  0.016   7.035
NClusters                          6.908  0.040   6.962
GetFeatures                        6.925  0.008   6.946
PlotLabels                         6.776  0.036   6.827
NMetaclusters                      6.746  0.012   6.771
MetaclusterCVs                     6.484  0.019   6.519
TestOutliers                       6.418  0.012   6.444
GetMetaclusterCVs                  6.202  0.028   6.243
GetMFIs                            6.145  0.008   6.169
PlotOverview2D                     6.091  0.020   6.175
GetPercentages                     5.948  0.004   5.965
GetMetaclusters                    5.934  0.008   5.955
GetMetaclusterPercentagesPositive  5.927  0.004   5.944
print.FlowSOM                      5.901  0.024   5.976
GetMetaclusterMFIs                 5.838  0.020   5.870
FlowSOMSubset                      5.472  0.023   5.509
GetClusterPercentagesPositive      5.384  0.028   5.422
GetClusterMFIs                     5.323  0.060   5.394
GetClusters                        5.313  0.044   5.368
GetCounts                          5.283  0.012   5.303
* 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.

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


* installing to library ‘/home/biocbuild/R/R-4.4.3/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-4.4.3/include" -DNDEBUG   -I/usr/local/include    -fPIC  -g -O2  -Wall -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-4.4.3/lib -L/usr/local/lib -o FlowSOM.so som.o -L/home/biocbuild/R/R-4.4.3/lib -lR
installing to /home/biocbuild/R/R-4.4.3/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)