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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 Patched (2025-06-14 r88325)
* 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 13.7.5
* 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 15.0.0 (clang-1500.0.40.1)’
* 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                       60.757  2.761  64.111
PlotDimRed                        49.032  2.812  52.266
PlotOutliers                      30.596  0.966  31.674
PlotMarker                        20.255  1.224  21.653
UpdateMetaclusters                17.504  1.320  18.846
PlotStars                         16.076  1.401  17.546
FlowSOM                           14.251  1.375  16.037
GroupStats                        13.446  1.229  14.942
PlotGroups                        11.362  1.204  12.648
QueryMultiple                     10.766  0.618  11.404
query_multiple                    10.528  0.523  11.229
Plot2DScatters                     9.913  0.608  10.553
AddAnnotation                      9.467  0.893  10.458
PlotManualBars                     8.992  0.697   9.740
GetFlowJoLabels                    8.616  0.775   9.556
QueryStarPlot                      8.639  0.456   9.104
PlotNumbers                        7.666  1.009   8.721
PlotPies                           7.871  0.782   8.668
PlotNode                           7.749  0.835   8.599
PlotVariable                       7.659  0.824   8.509
CountGroups                        6.533  0.670   7.270
NClusters                          6.227  0.842   7.168
GetFeatures                        6.551  0.434   7.083
SaveClustersToFCS                  6.060  0.835   6.941
UpdateNodeSize                     6.550  0.341   6.900
PlotFlowSOM                        5.964  0.816   6.804
PlotOverview2D                     6.044  0.589   6.658
TestOutliers                       5.672  0.864   6.648
PlotLabels                         5.713  0.723   6.493
GetMetaclusterCVs                  5.180  1.044   6.326
GetMetaclusters                    5.359  0.743   6.151
GetMFIs                            5.325  0.727   6.101
GetPercentages                     5.348  0.696   6.098
print.FlowSOM                      5.210  0.737   5.987
GetMetaclusterPercentagesPositive  5.191  0.711   5.924
MetaclusterMFIs                    5.118  0.714   5.854
GetMetaclusterMFIs                 5.102  0.597   5.763
GetCounts                          4.924  0.739   5.799
MetaclusterCVs                     4.896  0.688   5.607
GetClusters                        4.893  0.663   5.634
GetClusterMFIs                     4.902  0.526   5.445
GetClusterPercentagesPositive      4.850  0.578   5.450
NMetaclusters                      4.707  0.651   5.388
FlowSOMSubset                      4.594  0.637   5.417
* 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-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.16.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.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)