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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                       98.935  2.548 110.173
PlotDimRed                        73.653  2.692  80.878
PlotOutliers                      70.646  1.079  78.752
PlotMarker                        36.896  1.286  40.811
UpdateMetaclusters                34.924  1.333  39.033
PlotStars                         30.212  0.963  34.039
GroupStats                        27.564  0.858  30.385
FlowSOM                           23.164  1.614  25.292
PlotGroups                        23.352  0.969  25.743
Plot2DScatters                    20.982  0.823  23.069
QueryMultiple                     20.818  0.532  22.867
query_multiple                    20.705  0.579  22.554
AddAnnotation                     18.002  0.685  21.253
PlotManualBars                    17.730  0.781  19.791
GetFlowJoLabels                   14.642  0.811  16.025
QueryStarPlot                     14.627  0.376  15.448
PlotNode                          13.727  0.757  15.250
UpdateNodeSize                    13.955  0.362  15.289
PlotNumbers                       13.140  0.710  14.513
PlotVariable                      12.849  0.839  15.152
PlotPies                          12.537  0.795  13.822
GetFeatures                       11.925  0.515  12.791
CountGroups                       11.445  0.553  12.493
PlotFlowSOM                       10.765  0.728  12.173
SaveClustersToFCS                  9.673  1.072  10.964
NClusters                          9.717  0.801  11.761
PlotLabels                         9.865  0.639  10.861
PlotOverview2D                     9.739  0.730  10.655
NMetaclusters                      9.217  0.796  10.744
MetaclusterMFIs                    9.234  0.762  10.996
TestOutliers                       8.896  0.888   9.986
GetMetaclusterMFIs                 8.442  0.712  10.177
FlowSOMSubset                      8.414  0.532   9.247
MetaclusterCVs                     7.925  0.869   9.110
GetMetaclusters                    8.043  0.742   9.307
GetMetaclusterPercentagesPositive  8.131  0.587   9.467
GetClusterMFIs                     8.184  0.530   9.448
GetMetaclusterCVs                  8.084  0.616   9.147
GetMFIs                            8.017  0.646   9.111
print.FlowSOM                      7.905  0.746   8.797
GetPercentages                     8.035  0.561   9.502
GetCounts                          7.781  0.693   9.039
GetClusters                        7.726  0.522   8.839
GetClusterPercentagesPositive      7.711  0.432   8.761
NewData                            7.419  0.508   8.529
MetaClustering                     6.870  0.686   7.820
ReadInput                          6.558  0.734   7.610
metaClustering_consensus           5.001  0.568   5.758
* 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)