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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                       60.376  2.817  63.739
PlotDimRed                        57.498  3.078  61.253
PlotOutliers                      31.182  1.051  32.347
PlotMarker                        19.485  1.264  20.833
UpdateMetaclusters                17.442  1.291  18.845
PlotStars                         15.066  1.113  16.212
FlowSOM                           14.201  1.207  15.563
GroupStats                        13.160  0.897  14.213
PlotGroups                        12.463  1.108  13.721
query_multiple                    10.841  0.520  11.505
QueryMultiple                     10.794  0.520  11.404
Plot2DScatters                    10.338  0.687  11.316
AddAnnotation                      9.970  0.664  10.783
PlotManualBars                     8.928  0.743   9.690
GetFlowJoLabels                    8.507  0.888   9.539
QueryStarPlot                      8.556  0.564   9.215
PlotPies                           7.936  0.895   8.845
PlotNumbers                        7.718  1.105   8.895
PlotNode                           7.875  0.820   8.714
PlotVariable                       7.671  0.828   8.514
CountGroups                        6.926  0.651   7.737
PlotFlowSOM                        6.735  0.697   7.482
PlotLabels                         6.474  0.688   7.202
UpdateNodeSize                     6.720  0.324   7.057
PlotOverview2D                     6.176  0.751   6.936
SaveClustersToFCS                  6.094  0.824   6.934
NClusters                          6.166  0.711   6.896
MetaclusterMFIs                    5.958  0.802   6.805
GetFeatures                        6.262  0.363   6.651
GetClusterMFIs                     5.830  0.670   7.705
NMetaclusters                      5.623  0.839   6.499
TestOutliers                       5.475  0.733   6.252
GetMetaclusters                    5.419  0.748   6.297
GetClusters                        5.581  0.562   6.619
GetMetaclusterPercentagesPositive  5.184  0.937   6.258
GetClusterPercentagesPositive      5.667  0.454   7.412
print.FlowSOM                      5.217  0.746   5.998
GetMetaclusterMFIs                 5.112  0.793   5.924
GetMetaclusterCVs                  5.206  0.679   5.921
GetCounts                          5.254  0.510   6.525
MetaclusterCVs                     5.139  0.592   5.757
GetPercentages                     5.219  0.510   5.765
NewData                            4.662  0.738   5.555
GetMFIs                            4.707  0.621   5.361
FlowSOMSubset                      4.899  0.363   5.292
* 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)