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### 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
###
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* 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
FlowSOMmary                       75.708  0.422  76.207
PlotDimRed                        72.128  0.136  72.382
PlotOutliers                      42.417  0.104  42.646
PlotMarker                        23.676  0.072  23.807
UpdateMetaclusters                22.122  0.048  22.232
PlotStars                         19.528  0.039  19.625
GroupStats                        16.785  0.084  16.908
PlotGroups                        15.737  0.028  15.806
FlowSOM                           15.489  0.096  15.625
QueryMultiple                     13.140  0.016  13.193
query_multiple                    13.100  0.048  13.184
Plot2DScatters                    12.957  0.024  13.012
AddAnnotation                     11.956  0.211  12.206
PlotManualBars                    11.309  0.008  11.347
QueryStarPlot                      9.637  0.004   9.666
GetFlowJoLabels                    9.445  0.176   9.649
PlotNode                           9.554  0.024   9.602
PlotNumbers                        8.750  0.020   8.793
PlotVariable                       8.682  0.076   8.785
PlotPies                           8.565  0.012   8.602
UpdateNodeSize                     8.376  0.040   8.439
CountGroups                        7.856  0.060   7.935
PlotFlowSOM                        7.666  0.027   7.714
GetFeatures                        7.328  0.012   7.359
PlotLabels                         7.005  0.020   7.042
SaveClustersToFCS                  6.866  0.024   6.909
NMetaclusters                      6.424  0.036   6.476
NClusters                          6.429  0.011   6.461
TestOutliers                       6.387  0.015   6.419
PlotOverview2D                     6.317  0.084   6.418
MetaclusterMFIs                    6.281  0.008   6.302
GetCounts                          5.914  0.068   5.997
GetMFIs                            5.851  0.055   5.921
GetPercentages                     5.742  0.016   5.773
GetMetaclusterCVs                  5.689  0.068   5.770
GetMetaclusters                    5.699  0.048   5.760
GetMetaclusterMFIs                 5.675  0.036   5.724
print.FlowSOM                      5.690  0.020   5.725
GetMetaclusterPercentagesPositive  5.633  0.048   5.695
GetClusterMFIs                     5.455  0.204   5.673
GetClusterPercentagesPositive      5.564  0.072   5.649
GetClusters                        5.531  0.083   5.629
MetaclusterCVs                     5.589  0.008   5.609
FlowSOMSubset                      5.252  0.040   5.305
* 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.

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