##############################################################################
##############################################################################
###
### 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_2.18.0.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 ‘2.18.0’
* 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                        75.128  0.144  75.446
FlowSOMmary                       74.054  0.469  74.650
PlotOutliers                      43.299  0.152  43.581
PlotMarker                        24.408  0.276  24.761
UpdateMetaclusters                22.373  0.080  22.502
PlotStars                         19.514  0.120  19.678
GroupStats                        17.447  0.116  17.621
PlotGroups                        16.325  0.312  16.687
FlowSOM                           15.769  0.124  15.941
QueryMultiple                     13.318  0.016  13.366
query_multiple                    13.070  0.056  13.155
Plot2DScatters                    12.915  0.060  13.011
AddAnnotation                     12.257  0.362  12.685
PlotManualBars                    11.757  0.209  12.005
QueryStarPlot                     10.058  0.012  10.092
PlotNode                           9.916  0.096  10.042
PlotNumbers                        9.679  0.060   9.769
GetFlowJoLabels                    9.475  0.187   9.698
PlotPies                           8.984  0.052   9.062
PlotVariable                       8.622  0.048   8.689
UpdateNodeSize                     8.538  0.047   8.605
CountGroups                        7.981  0.051   8.060
GetFeatures                        7.603  0.052   7.690
PlotFlowSOM                        7.546  0.023   7.594
PlotLabels                         7.001  0.171   7.189
SaveClustersToFCS                  6.966  0.028   7.009
MetaclusterMFIs                    6.404  0.024   6.446
PlotOverview2D                     6.355  0.071   6.445
NClusters                          6.382  0.020   6.421
NMetaclusters                      6.309  0.012   6.339
TestOutliers                       6.147  0.012   6.171
GetMetaclusterCVs                  5.894  0.048   5.959
print.FlowSOM                      5.895  0.020   5.928
GetMFIs                            5.823  0.059   5.906
GetPercentages                     5.803  0.056   5.877
GetMetaclusterPercentagesPositive  5.793  0.056   5.867
MetaclusterCVs                     5.701  0.044   5.761
GetMetaclusterMFIs                 5.669  0.036   5.724
GetCounts                          5.640  0.056   5.716
GetClusters                        5.569  0.119   5.710
FlowSOMSubset                      5.640  0.028   5.685
GetClusterPercentagesPositive      5.559  0.104   5.689
GetClusterMFIs                     5.503  0.147   5.671
GetMetaclusters                    5.629  0.016   5.661
* 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 ‘2.18.0’
** 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)