##############################################################################
##############################################################################
###
### 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                       73.185  0.382  73.676
PlotDimRed                        67.219  0.144  67.526
PlotOutliers                      41.539  0.108  41.783
PlotMarker                        22.193  0.072  22.337
UpdateMetaclusters                21.663  0.139  21.870
PlotStars                         18.181  0.051  18.282
GroupStats                        16.409  0.044  16.503
FlowSOM                           15.003  0.140  15.186
PlotGroups                        14.990  0.027  15.067
Plot2DScatters                    12.843  0.035  12.919
query_multiple                    12.815  0.016  12.867
QueryMultiple                     12.774  0.028  12.840
AddAnnotation                     11.628  0.375  12.042
PlotManualBars                    10.841  0.012  10.885
PlotNode                           9.493  0.016   9.539
QueryStarPlot                      9.368  0.048   9.445
GetFlowJoLabels                    8.821  0.119   8.970
PlotNumbers                        8.660  0.016   8.706
PlotVariable                       8.168  0.068   8.256
PlotPies                           8.149  0.044   8.216
UpdateNodeSize                     8.165  0.024   8.209
CountGroups                        7.617  0.100   7.740
PlotFlowSOM                        7.053  0.032   7.108
GetFeatures                        6.805  0.016   6.840
MetaclusterMFIs                    6.724  0.020   6.766
SaveClustersToFCS                  6.698  0.016   6.734
PlotOverview2D                     6.537  0.064   6.623
PlotLabels                         6.586  0.007   6.614
NClusters                          6.407  0.016   6.440
NMetaclusters                      6.310  0.020   6.348
TestOutliers                       6.230  0.004   6.253
MetaclusterCVs                     5.745  0.056   5.818
GetMetaclusterCVs                  5.556  0.008   5.582
GetMFIs                            5.460  0.012   5.490
print.FlowSOM                      5.439  0.028   5.480
GetCounts                          5.438  0.004   5.457
GetMetaclusterMFIs                 5.381  0.060   5.459
GetPercentages                     5.377  0.008   5.402
GetMetaclusterPercentagesPositive  5.277  0.024   5.319
GetMetaclusters                    5.273  0.004   5.294
FlowSOMSubset                      5.140  0.036   5.191
GetClusterPercentagesPositive      5.153  0.000   5.166
GetClusterMFIs                     5.079  0.040   5.132
GetClusters                        5.074  0.012   5.099
* 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)