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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_2.18.0.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                       64.328  2.720  97.262
PlotDimRed                        56.806  2.760  84.586
PlotOutliers                      34.215  0.979  49.552
PlotMarker                        20.598  1.048  31.046
UpdateMetaclusters                19.211  1.204  28.612
PlotStars                         15.804  1.024  23.562
FlowSOM                           15.032  1.198  23.885
GroupStats                        14.468  0.939  21.920
PlotGroups                        13.028  0.982  19.832
QueryMultiple                     11.610  0.496  16.922
query_multiple                    11.655  0.423  17.207
Plot2DScatters                    11.243  0.747  16.621
PlotManualBars                    10.188  0.851  16.070
AddAnnotation                     10.287  0.722  16.366
PlotPies                           9.183  0.768  14.084
GetFlowJoLabels                    9.023  0.656  13.608
QueryStarPlot                      8.698  0.361  12.562
PlotNode                           8.199  0.784  13.010
PlotVariable                       8.126  0.775  12.539
PlotNumbers                        8.001  0.714  12.280
CountGroups                        7.589  0.714  12.113
NClusters                          6.715  0.954  10.487
PlotLabels                         6.849  0.689  10.400
PlotFlowSOM                        6.777  0.711  10.493
SaveClustersToFCS                  6.599  0.834  10.248
PlotOverview2D                     6.584  0.717  10.469
UpdateNodeSize                     6.824  0.319  10.149
NMetaclusters                      6.206  0.918   9.777
MetaclusterMFIs                    6.231  0.892   9.754
GetFeatures                        6.338  0.435   9.880
TestOutliers                       6.025  0.728   9.286
print.FlowSOM                      5.751  0.836   9.104
GetMetaclusterCVs                  5.664  0.796  10.311
GetMetaclusterPercentagesPositive  5.638  0.815   9.490
GetMetaclusterMFIs                 5.676  0.772  10.394
GetCounts                          5.819  0.605   9.607
GetMetaclusters                    5.643  0.766   9.267
GetPercentages                     5.638  0.713   8.963
MetaclusterCVs                     5.566  0.720   8.775
GetMFIs                            5.403  0.665   8.367
GetClusters                        5.377  0.587   9.474
GetClusterMFIs                     5.291  0.589   8.728
GetClusterPercentagesPositive      5.179  0.627   8.775
FlowSOMSubset                      4.887  0.551   7.330
NewData                            4.770  0.560   7.177
MetaClustering                     3.968  0.655   6.529
ReadInput                          3.466  0.545   5.526
* 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)