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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_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 ... OK
* 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                       90.627  2.443  97.751
PlotDimRed                        73.911  2.912  79.472
PlotOutliers                      38.874  1.018  45.875
PlotMarker                        33.599  1.599  37.156
UpdateMetaclusters                31.869  1.370  34.535
PlotStars                         27.349  1.083  29.124
GroupStats                        26.086  1.076  27.635
FlowSOM                           22.263  1.271  24.435
PlotGroups                        22.015  1.328  23.759
AddAnnotation                     16.963  0.820  18.436
QueryMultiple                     17.206  0.505  18.539
query_multiple                    16.971  0.584  18.126
Plot2DScatters                    15.651  0.765  16.862
PlotManualBars                    14.746  1.124  16.121
GetFlowJoLabels                   13.541  0.714  14.497
PlotNode                          12.871  0.824  14.040
QueryStarPlot                     12.710  0.380  13.728
PlotVariable                      11.907  1.095  13.294
PlotNumbers                       12.015  0.930  13.231
PlotPies                          12.030  0.841  14.092
UpdateNodeSize                    12.262  0.258  13.350
GetFeatures                       11.958  0.560  12.936
CountGroups                       11.381  0.776  12.389
PlotFlowSOM                       10.325  0.707  11.597
SaveClustersToFCS                 10.026  0.864  11.412
PlotLabels                         9.422  0.649  10.260
NMetaclusters                      9.035  0.989  10.635
MetaclusterMFIs                    8.956  0.992  10.464
NClusters                          9.097  0.809  10.416
TestOutliers                       8.826  0.612   9.717
MetaclusterCVs                     8.050  1.086   9.249
PlotOverview2D                     8.091  0.696   9.202
FlowSOMSubset                      8.346  0.405   9.128
GetMetaclusterMFIs                 7.911  0.792   8.920
print.FlowSOM                      7.877  0.775   9.126
GetMetaclusters                    7.816  0.800   8.923
GetMFIs                            7.803  0.806   8.783
GetMetaclusterCVs                  7.900  0.697   8.742
GetPercentages                     7.908  0.650   9.081
GetMetaclusterPercentagesPositive  7.851  0.589   8.660
GetCounts                          7.827  0.551   8.712
GetClusterPercentagesPositive      7.619  0.579   8.546
GetClusters                        7.521  0.584   8.312
NewData                            7.495  0.587   8.260
GetClusterMFIs                     7.515  0.542   8.292
MetaClustering                     6.411  0.889   7.407
ReadInput                          6.745  0.534   7.952
metaClustering_consensus           5.599  0.645   6.581
* 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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)