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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                       61.818  2.866  67.927
PlotDimRed                        52.597  3.573  58.266
PlotOutliers                      31.047  0.747  32.251
PlotMarker                        19.759  1.208  21.482
UpdateMetaclusters                17.914  1.320  19.714
PlotStars                         15.340  0.877  16.763
FlowSOM                           13.707  0.992  15.359
GroupStats                        13.301  1.231  15.334
PlotGroups                        12.359  0.940  13.706
query_multiple                    11.061  0.615  11.848
Plot2DScatters                    10.970  0.617  11.927
QueryMultiple                     11.048  0.435  11.592
AddAnnotation                      9.714  0.652  10.891
PlotManualBars                     9.330  1.032  10.698
GetFlowJoLabels                    9.088  0.594   9.829
PlotPies                           8.799  0.678   9.637
PlotNode                           8.255  0.604   9.026
QueryStarPlot                      8.374  0.415   8.881
PlotVariable                       7.925  0.738   8.800
PlotFlowSOM                        7.287  0.903   8.547
CountGroups                        7.056  0.559   8.410
PlotNumbers                        6.967  0.570   7.719
SaveClustersToFCS                  6.801  0.706   7.650
PlotLabels                         6.129  0.997   7.392
NClusters                          5.854  1.110   7.433
MetaclusterMFIs                    5.919  1.032   7.253
PlotOverview2D                     6.228  0.591   6.905
GetFeatures                        6.449  0.350   6.935
TestOutliers                       6.186  0.560   6.841
NMetaclusters                      5.926  0.658   6.815
UpdateNodeSize                     6.256  0.286   6.568
print.FlowSOM                      5.883  0.650   6.593
GetClusterPercentagesPositive      5.531  0.550   6.512
GetMFIs                            5.300  0.733   6.142
GetPercentages                     5.337  0.604   6.095
MetaclusterCVs                     5.388  0.526   6.264
GetMetaclusterPercentagesPositive  5.278  0.588   6.063
GetClusters                        5.180  0.670   6.325
GetCounts                          5.094  0.746   6.165
GetMetaclusters                    5.232  0.566   5.897
GetMetaclusterMFIs                 5.161  0.519   5.823
GetClusterMFIs                     5.094  0.435   5.906
GetMetaclusterCVs                  4.798  0.661   5.792
NewData                            4.673  0.445   5.340
FlowSOMSubset                      4.410  0.569   5.374
* 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)