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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FlowSOM_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.16.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                    user system elapsed
FlowSOMmary                       90.736  2.617  96.532
PlotDimRed                        73.186  2.662  77.403
PlotOutliers                      39.795  1.012  41.484
PlotMarker                        32.499  1.460  34.799
UpdateMetaclusters                31.833  1.334  35.549
PlotStars                         27.834  1.138  31.842
GroupStats                        25.830  1.119  28.112
PlotGroups                        22.403  1.152  24.688
FlowSOM                           22.127  1.211  24.459
QueryMultiple                     17.328  0.524  18.298
query_multiple                    17.025  0.474  17.831
AddAnnotation                     16.505  0.925  18.192
Plot2DScatters                    16.139  0.761  18.037
PlotManualBars                    14.644  0.846  15.741
GetFlowJoLabels                   13.613  0.688  14.714
PlotNode                          12.991  0.804  14.656
PlotNumbers                       12.156  1.136  13.704
QueryStarPlot                     12.551  0.365  13.168
PlotVariable                      11.815  0.845  12.928
GetFeatures                       12.122  0.462  13.101
PlotPies                          11.353  0.942  13.512
CountGroups                       11.345  0.831  12.953
UpdateNodeSize                    11.923  0.208  12.653
PlotFlowSOM                       10.478  0.838  12.048
SaveClustersToFCS                  9.576  0.753  10.919
NMetaclusters                      9.117  1.005  10.675
NClusters                          9.027  1.064  10.295
PlotLabels                         9.304  0.749  10.219
MetaclusterMFIs                    8.949  1.067  10.347
TestOutliers                       8.884  0.691  10.431
FlowSOMSubset                      8.276  0.586   8.980
GetPercentages                     7.925  0.890   9.438
GetMetaclusterPercentagesPositive  7.811  0.981   8.906
PlotOverview2D                     7.931  0.772   8.905
MetaclusterCVs                     7.852  0.803   8.988
GetMetaclusters                    7.725  0.888   8.769
print.FlowSOM                      7.761  0.811   9.050
GetMFIs                            7.664  0.879   8.607
GetMetaclusterMFIs                 7.741  0.791   8.605
GetMetaclusterCVs                  7.674  0.736   8.454
GetClusters                        7.535  0.664   8.680
GetCounts                          7.611  0.585   8.457
NewData                            7.437  0.641   8.389
GetClusterPercentagesPositive      7.446  0.396   8.295
GetClusterMFIs                     7.380  0.435   8.179
MetaClustering                     6.628  0.729   7.559
ReadInput                          6.562  0.744   7.571
metaClustering_consensus           5.501  0.669   6.416
PlotSD                             4.214  0.126   5.040
* 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
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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)