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### Running command:
###
###   /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                       64.034  2.557 101.446
PlotDimRed                        57.729  2.995  90.081
PlotOutliers                      34.022  0.981  48.524
PlotMarker                        21.077  1.157  31.062
UpdateMetaclusters                19.074  1.306  26.653
PlotStars                         16.343  1.076  24.598
FlowSOM                           14.366  1.212  21.923
GroupStats                        14.532  0.995  24.208
PlotGroups                        13.805  1.113  20.835
Plot2DScatters                    12.052  0.798  20.008
query_multiple                    11.826  0.514  16.991
QueryMultiple                     11.335  0.487  16.764
AddAnnotation                     10.181  0.726  15.488
PlotManualBars                     9.810  0.812  14.657
PlotVariable                       9.454  0.842  14.191
GetFlowJoLabels                    9.070  0.733  13.996
QueryStarPlot                      8.842  0.406  13.080
PlotNode                           8.419  0.770  12.703
PlotPies                           8.293  0.736  12.479
PlotNumbers                        7.988  0.835  12.324
CountGroups                        7.909  0.704  13.159
SaveClustersToFCS                  7.258  0.935  11.344
PlotFlowSOM                        7.045  0.787  11.029
PlotLabels                         6.714  0.750  10.192
print.FlowSOM                      6.273  0.886   9.861
MetaclusterMFIs                    6.182  0.924   9.683
PlotOverview2D                     6.378  0.704   9.791
NClusters                          6.184  0.883   9.852
NMetaclusters                      6.182  0.853  10.366
UpdateNodeSize                     6.759  0.222   9.659
GetFeatures                        6.390  0.567  10.322
TestOutliers                       6.030  0.684   9.177
GetCounts                          5.857  0.652  10.022
GetPercentages                     5.680  0.752   9.543
GetMFIs                            5.656  0.705   8.854
GetMetaclusters                    5.574  0.759   8.755
MetaclusterCVs                     5.577  0.664   8.744
GetMetaclusterMFIs                 5.555  0.625   8.588
GetMetaclusterCVs                  5.569  0.607   8.836
GetClusters                        5.379  0.669   9.310
GetMetaclusterPercentagesPositive  5.334  0.652   8.340
GetClusterPercentagesPositive      5.244  0.612   8.037
GetClusterMFIs                     5.236  0.519   7.763
NewData                            4.844  0.603   8.475
MetaClustering                     4.740  0.656   8.095
FlowSOMSubset                      4.727  0.447   7.246
ReadInput                          3.636  0.665   6.032
* 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)