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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                       64.093  2.717 110.480
PlotDimRed                        57.522  3.036  95.502
PlotOutliers                      33.947  1.024  52.987
PlotMarker                        21.629  1.173  34.728
UpdateMetaclusters                19.277  1.279  30.997
PlotStars                         16.586  0.984  27.322
FlowSOM                           15.087  1.321  26.108
GroupStats                        14.797  0.965  26.249
PlotGroups                        12.572  0.945  21.034
query_multiple                    11.932  0.578  18.722
Plot2DScatters                    11.415  0.833  20.251
QueryMultiple                     11.647  0.436  18.102
AddAnnotation                     10.077  0.735  16.733
PlotManualBars                     9.774  0.848  16.035
GetFlowJoLabels                    9.053  0.734  15.495
PlotPies                           8.672  0.825  14.619
QueryStarPlot                      8.939  0.508  14.110
PlotVariable                       8.452  0.809  13.909
PlotNode                           8.201  0.732  13.863
PlotNumbers                        8.056  0.816  13.582
PlotFlowSOM                        7.646  0.890  13.343
CountGroups                        7.609  0.684  14.292
SaveClustersToFCS                  7.170  0.868  11.261
MetaclusterMFIs                    6.736  0.866  11.841
PlotOverview2D                     6.709  0.637  11.186
GetMetaclusterMFIs                 6.179  1.103  10.677
PlotLabels                         6.568  0.630  11.129
NMetaclusters                      6.268  0.906  11.767
NClusters                          6.211  0.833  11.077
GetPercentages                     6.204  0.765  11.433
UpdateNodeSize                     6.691  0.207  10.547
GetFeatures                        6.335  0.547  11.232
TestOutliers                       6.042  0.739   9.496
print.FlowSOM                      5.816  0.829   9.896
GetMetaclusterPercentagesPositive  5.691  0.783   9.770
GetCounts                          5.827  0.601  10.649
GetMetaclusterCVs                  5.693  0.732   9.978
GetMetaclusters                    5.664  0.704   9.782
GetMFIs                            5.596  0.726   9.885
MetaclusterCVs                     5.613  0.645   9.890
GetClusters                        5.350  0.664   9.782
GetClusterPercentagesPositive      5.351  0.628   9.028
GetClusterMFIs                     5.251  0.551   8.530
FlowSOMSubset                      5.078  0.499   8.543
NewData                            4.800  0.695   8.478
ReadInput                          4.238  0.700   7.389
MetaClustering                     3.523  0.578   6.775
metaClustering_consensus           3.144  0.592   5.477
* 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)