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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                       64.237  2.707  98.626
PlotDimRed                        57.036  2.505  85.105
PlotOutliers                      33.141  0.920  46.997
PlotMarker                        21.790  1.194  30.558
UpdateMetaclusters                19.625  1.247  28.465
PlotStars                         17.131  1.035  25.425
FlowSOM                           14.367  1.296  23.103
GroupStats                        14.650  0.959  22.361
PlotGroups                        13.101  1.048  19.743
QueryMultiple                     12.006  0.548  17.871
query_multiple                    11.568  0.488  16.248
Plot2DScatters                    11.260  0.778  17.084
PlotManualBars                     9.757  1.073  14.777
AddAnnotation                     10.092  0.708  15.422
PlotPies                           9.315  0.749  13.751
GetFlowJoLabels                    9.007  0.804  14.343
PlotNode                           8.204  0.746  12.608
QueryStarPlot                      8.578  0.359  12.404
PlotNumbers                        8.221  0.671  12.593
PlotFlowSOM                        8.071  0.755  12.329
PlotVariable                       8.024  0.677  12.207
CountGroups                        7.854  0.741  12.228
PlotOverview2D                     7.456  0.810  11.337
PlotLabels                         6.866  0.882  10.473
SaveClustersToFCS                  6.373  0.964   9.623
NClusters                          6.229  0.919  10.076
NMetaclusters                      6.236  0.889  10.047
MetaclusterMFIs                    6.212  0.798   9.879
GetFeatures                        6.364  0.468  10.577
GetMetaclusterMFIs                 6.063  0.732   9.522
UpdateNodeSize                     6.539  0.203   9.493
TestOutliers                       5.844  0.600   8.915
GetMFIs                            5.584  0.835   8.560
print.FlowSOM                      5.685  0.699   8.693
GetMetaclusters                    5.583  0.711   8.631
MetaclusterCVs                     5.590  0.670   8.676
GetPercentages                     5.506  0.692   8.627
GetMetaclusterCVs                  5.502  0.684   8.224
GetMetaclusterPercentagesPositive  5.416  0.626   8.651
GetClusters                        5.323  0.626   8.723
GetCounts                          5.199  0.683   9.302
GetClusterMFIs                     5.279  0.515   8.455
GetClusterPercentagesPositive      5.276  0.508   8.150
FlowSOMSubset                      5.110  0.507   8.641
NewData                            4.797  0.608   7.550
ReadInput                          3.614  0.777   6.311
MetaClustering                     3.614  0.609   5.883
* 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)