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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_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2025-10-21 r88958)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 ‘2.19.0’
* 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 14.0.3 (clang-1403.0.22.14.1)’
* 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 ... INFO
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                       52.786  2.078  55.129
PlotDimRed                        39.628  2.172  42.308
PlotOutliers                      35.782  0.892  37.147
PlotMarker                        19.956  1.117  21.437
UpdateMetaclusters                18.551  1.244  20.098
PlotStars                         16.732  0.997  18.001
GroupStats                        13.978  0.844  14.991
FlowSOM                           13.282  1.032  14.483
PlotGroups                        12.018  1.020  13.175
QueryMultiple                     11.334  0.499  12.015
Plot2DScatters                    10.430  0.684  11.259
query_multiple                    10.664  0.427  11.241
AddAnnotation                      9.971  0.654  10.738
PlotManualBars                     8.942  0.794   9.850
GetFlowJoLabels                    8.078  0.555   8.711
PlotPies                           7.838  0.765   8.737
PlotNode                           7.594  0.832   8.568
QueryStarPlot                      8.089  0.324   8.520
PlotVariable                       7.407  0.791   8.340
PlotNumbers                        7.221  0.702   8.046
CountGroups                        6.193  0.602   6.890
UpdateNodeSize                     6.467  0.277   6.830
PlotLabels                         6.034  0.644   6.760
GetFeatures                        6.057  0.468   6.601
PlotFlowSOM                        5.859  0.597   6.534
MetaclusterMFIs                    5.567  0.781   6.485
SaveClustersToFCS                  5.438  0.718   6.250
NMetaclusters                      5.291  0.746   6.110
MetaclusterCVs                     5.355  0.675   6.114
NClusters                          5.352  0.643   6.073
PlotOverview2D                     5.281  0.499   5.881
TestOutliers                       4.858  0.578   5.526
GetMFIs                            4.752  0.637   5.450
GetMetaclusterCVs                  4.601  0.625   5.304
GetMetaclusterPercentagesPositive  4.563  0.587   5.206
GetCounts                          4.677  0.461   5.188
GetPercentages                     4.547  0.587   5.208
GetMetaclusters                    4.593  0.538   5.222
GetMetaclusterMFIs                 4.541  0.552   5.153
print.FlowSOM                      4.421  0.646   5.158
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-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/4.6-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** this is package ‘FlowSOM’ version ‘2.19.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.1.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-x86_64/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)