##############################################################################
##############################################################################
###
### 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 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* 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
FlowSOMmary                       70.724  0.335  71.182
PlotDimRed                        68.822  0.051  68.954
PlotOutliers                      22.488  0.478  23.043
PlotMarker                        20.682  0.096  20.823
UpdateMetaclusters                19.650  0.135  19.846
PlotStars                         17.100  0.183  17.336
GroupStats                        15.949  0.131  16.117
FlowSOM                           15.125  0.031  15.199
PlotGroups                        13.799  0.016  13.844
AddAnnotation                     11.148  0.479  11.661
QueryMultiple                     10.389  0.143  10.567
query_multiple                    10.512  0.004  10.546
PlotManualBars                     9.798  0.016   9.835
Plot2DScatters                     9.537  0.028   9.586
GetFlowJoLabels                    8.523  0.220   8.763
CountGroups                        8.339  0.088   8.453
PlotNode                           8.385  0.020   8.426
PlotNumbers                        8.134  0.024   8.186
QueryStarPlot                      7.991  0.080   8.095
PlotVariable                       7.642  0.128   7.792
PlotPies                           7.603  0.024   7.651
UpdateNodeSize                     7.198  0.016   7.236
GetFeatures                        6.909  0.099   7.025
PlotFlowSOM                        6.822  0.052   6.889
SaveClustersToFCS                  6.698  0.048   6.767
PlotLabels                         6.295  0.072   6.380
NMetaclusters                      6.070  0.020   6.105
NClusters                          5.960  0.048   6.022
PlotOverview2D                     5.760  0.132   5.909
MetaclusterMFIs                    5.807  0.000   5.822
TestOutliers                       5.777  0.008   5.801
GetClusterMFIs                     5.630  0.104   5.747
GetClusters                        5.206  0.503   5.722
MetaclusterCVs                     5.564  0.000   5.578
GetClusterPercentagesPositive      5.487  0.032   5.531
GetMetaclusters                    5.476  0.008   5.502
GetPercentages                     5.424  0.056   5.492
GetMFIs                            5.328  0.139   5.480
GetMetaclusterPercentagesPositive  5.383  0.068   5.468
GetMetaclusterCVs                  5.437  0.008   5.456
GetMetaclusterMFIs                 5.302  0.048   5.362
FlowSOMSubset                      5.284  0.016   5.315
print.FlowSOM                      5.263  0.016   5.292
GetCounts                          5.112  0.140   5.265
* 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-4.4.2/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/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 -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-4.4.2/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)