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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 (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* 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 15.0.0 (clang-1500.0.40.1)’
* 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                       64.439  2.632  97.995
PlotDimRed                        57.094  2.713  84.669
PlotOutliers                      34.028  0.992  47.925
PlotMarker                        21.497  1.079  31.534
UpdateMetaclusters                18.967  1.184  28.109
PlotStars                         16.256  0.961  23.780
FlowSOM                           14.483  1.302  23.894
GroupStats                        14.577  0.988  22.053
PlotGroups                        13.057  0.923  19.857
QueryMultiple                     11.649  0.483  17.025
Plot2DScatters                    11.208  0.838  17.001
query_multiple                    11.365  0.443  16.703
AddAnnotation                     10.207  0.744  15.434
PlotManualBars                     9.875  0.748  14.801
PlotPies                           9.320  0.761  13.668
GetFlowJoLabels                    8.815  0.725  13.365
PlotFlowSOM                        8.086  0.782  12.677
PlotNode                           8.173  0.695  12.359
QueryStarPlot                      8.506  0.358  12.718
PlotVariable                       8.173  0.657  12.275
CountGroups                        7.936  0.746  12.224
PlotNumbers                        7.999  0.668  12.128
SaveClustersToFCS                  6.539  0.774  10.321
PlotLabels                         6.657  0.636  10.277
PlotOverview2D                     6.599  0.603   9.911
NClusters                          6.153  0.891   9.751
UpdateNodeSize                     6.814  0.225  10.007
NMetaclusters                      6.169  0.858  10.013
MetaclusterMFIs                    6.164  0.840   9.916
print.FlowSOM                      6.110  0.746   9.653
GetFeatures                        6.271  0.521   9.681
TestOutliers                       6.059  0.681   9.309
GetMetaclusterMFIs                 6.008  0.686   9.204
GetMFIs                            5.647  0.677   9.256
GetPercentages                     5.630  0.683   8.928
MetaclusterCVs                     5.621  0.680   9.264
GetMetaclusterPercentagesPositive  5.526  0.683   8.866
GetMetaclusterCVs                  5.556  0.641   8.728
GetMetaclusters                    5.538  0.641   8.640
GetClusterPercentagesPositive      5.379  0.598   9.307
GetClusterMFIs                     5.360  0.602   8.986
NewData                            5.309  0.559   8.380
GetClusters                        5.292  0.572   8.950
FlowSOMSubset                      5.170  0.526   8.702
GetCounts                          5.161  0.527   9.013
ReadInput                          4.300  0.629   6.757
MetaClustering                     3.636  0.592   5.868
metaClustering_consensus           3.519  0.479   5.636
* 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-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.18.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/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)