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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 4.4.2 (2024-10-31)
* 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                       91.675  2.348 101.551
PlotDimRed                        74.476  2.591  80.742
PlotOutliers                      38.440  0.907  41.474
UpdateMetaclusters                32.693  1.434  36.986
PlotMarker                        32.677  1.305  35.051
PlotStars                         28.470  1.330  32.694
GroupStats                        26.410  1.041  28.452
FlowSOM                           22.865  0.998  26.363
PlotGroups                        22.134  1.157  24.378
AddAnnotation                     17.442  0.716  19.309
QueryMultiple                     17.288  0.640  19.246
query_multiple                    16.829  0.504  17.631
Plot2DScatters                    15.773  0.908  16.973
PlotManualBars                    15.226  0.917  16.957
GetFlowJoLabels                   14.162  0.682  15.790
PlotNode                          13.264  0.995  14.692
PlotVariable                      12.180  0.938  14.127
PlotNumbers                       12.055  0.918  13.805
QueryStarPlot                     12.530  0.354  13.617
GetFeatures                       12.120  0.484  13.460
PlotPies                          11.414  1.113  12.941
UpdateNodeSize                    12.234  0.256  13.290
CountGroups                       11.628  0.591  13.635
SaveClustersToFCS                 10.054  1.043  11.613
PlotFlowSOM                       10.221  0.840  11.249
NClusters                          9.258  1.149  11.100
PlotLabels                         9.585  0.728  11.427
MetaclusterMFIs                    9.230  0.815  10.611
NMetaclusters                      9.190  0.841  10.381
TestOutliers                       8.797  0.684   9.803
print.FlowSOM                      8.179  1.001   9.358
FlowSOMSubset                      8.632  0.426   9.707
PlotOverview2D                     8.153  0.674   9.098
GetMFIs                            7.925  0.848   8.947
GetPercentages                     7.958  0.808   9.337
GetMetaclusterMFIs                 7.875  0.807   8.954
GetMetaclusters                    7.869  0.797   8.777
MetaclusterCVs                     7.955  0.684   8.982
GetMetaclusterCVs                  7.936  0.657   9.118
GetCounts                          7.900  0.670   8.864
GetMetaclusterPercentagesPositive  7.849  0.634   8.699
NewData                            7.306  0.866   8.238
GetClusters                        7.555  0.614   8.430
GetClusterPercentagesPositive      7.525  0.642   8.335
GetClusterMFIs                     7.524  0.546   8.315
ReadInput                          6.440  0.671   7.243
MetaClustering                     6.445  0.591   7.512
metaClustering_consensus           5.328  0.425   5.915
* 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)