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### Running command:
###
###   /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_2.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/FlowSOM.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* 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 ‘2.18.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.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                       98.861  2.233 108.812
PlotDimRed                        73.895  2.786  81.328
PlotOutliers                      70.340  1.021  78.170
PlotMarker                        37.166  1.259  40.404
UpdateMetaclusters                34.939  1.421  40.014
PlotStars                         29.926  1.028  33.975
GroupStats                        27.710  0.831  30.958
PlotGroups                        23.576  1.080  26.039
FlowSOM                           23.397  1.207  25.769
Plot2DScatters                    21.204  0.699  23.887
QueryMultiple                     21.022  0.645  23.781
query_multiple                    20.712  0.548  22.492
AddAnnotation                     17.855  0.719  20.164
PlotManualBars                    17.398  0.872  19.083
GetFlowJoLabels                   14.463  0.818  15.923
QueryStarPlot                     14.755  0.396  15.889
PlotNode                          13.755  0.962  15.913
UpdateNodeSize                    13.950  0.355  14.766
PlotNumbers                       13.178  0.818  14.732
PlotVariable                      12.741  0.729  15.250
PlotPies                          12.445  0.731  13.971
GetFeatures                       12.035  0.478  13.118
CountGroups                       11.437  0.545  12.721
PlotFlowSOM                       11.280  0.640  12.983
PlotLabels                        10.101  0.694  11.414
SaveClustersToFCS                  9.619  0.858  11.646
NMetaclusters                      9.236  0.948  10.932
MetaclusterMFIs                    9.164  0.895  10.506
NClusters                          9.197  0.670  10.392
TestOutliers                       8.822  0.763  10.180
PlotOverview2D                     8.701  0.646   9.753
MetaclusterCVs                     8.448  0.792   9.923
GetPercentages                     8.563  0.598  10.176
FlowSOMSubset                      8.407  0.424   9.564
GetClusterPercentagesPositive      8.176  0.623   9.416
print.FlowSOM                      7.883  0.849   9.422
GetMetaclusterMFIs                 8.017  0.687   9.191
GetMetaclusters                    8.066  0.613   9.158
GetMetaclusterCVs                  8.048  0.589   9.150
GetMetaclusterPercentagesPositive  8.103  0.526   9.117
GetMFIs                            7.985  0.558   8.995
NewData                            7.934  0.496   9.271
GetCounts                          7.828  0.483   9.292
GetClusters                        7.846  0.461   9.118
GetClusterMFIs                     7.749  0.463   8.711
ReadInput                          6.631  0.652   8.426
MetaClustering                     5.846  0.509   6.537
metaClustering_consensus           5.054  0.505   5.969
* 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-3.22-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 ‘2.18.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.1.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)