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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_2.14.0.tar.gz
###
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* 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                        71.650  0.168  71.909
FlowSOMmary                       67.807  0.339  68.222
PlotOutliers                      23.691  0.056  23.795
UpdateMetaclusters                21.218  0.064  21.331
PlotMarker                        20.662  0.087  20.790
PlotStars                         17.278  0.044  17.354
GroupStats                        16.566  0.036  16.644
FlowSOM                           15.540  0.147  15.746
PlotGroups                        14.337  0.020  14.383
AddAnnotation                     11.598  0.552  12.199
QueryMultiple                     11.045  0.068  11.136
query_multiple                    11.048  0.056  11.129
Plot2DScatters                    10.160  0.056  10.239
PlotManualBars                     9.862  0.012   9.895
GetFlowJoLabels                    9.138  0.168   9.334
PlotNode                           8.493  0.012   8.520
PlotVariable                       8.452  0.024   8.496
QueryStarPlot                      8.420  0.004   8.438
CountGroups                        8.186  0.068   8.282
PlotNumbers                        8.148  0.020   8.184
UpdateNodeSize                     8.052  0.023   8.095
PlotPies                           7.944  0.060   8.017
GetFeatures                        7.361  0.056   7.437
PlotFlowSOM                        7.216  0.048   7.278
SaveClustersToFCS                  6.984  0.028   7.025
PlotLabels                         6.557  0.008   6.575
MetaclusterMFIs                    6.449  0.063   6.528
NMetaclusters                      6.382  0.024   6.419
NClusters                          6.327  0.020   6.361
TestOutliers                       6.309  0.004   6.329
GetMetaclusterCVs                  5.989  0.064   6.068
PlotOverview2D                     5.918  0.008   5.936
GetMFIs                            5.832  0.055   5.902
GetPercentages                     5.820  0.052   5.888
GetMetaclusterMFIs                 5.825  0.044   5.883
MetaclusterCVs                     5.817  0.016   5.846
GetMetaclusterPercentagesPositive  5.755  0.048   5.817
GetMetaclusters                    5.700  0.076   5.803
print.FlowSOM                      5.723  0.008   5.744
FlowSOMSubset                      5.577  0.028   5.638
GetClusterMFIs                     5.402  0.079   5.495
GetCounts                          5.374  0.044   5.432
GetClusterPercentagesPositive      5.405  0.008   5.425
GetClusters                        5.368  0.020   5.400
* 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.

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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-4.4.3/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)