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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_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.12.0’
* 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                       96.890  2.818 116.609
PlotDimRed                        77.770  2.830  98.427
PlotOutliers                      40.836  0.836  52.133
PlotMarker                        36.536  1.165  45.425
UpdateMetaclusters                35.415  1.028  40.660
PlotStars                         30.619  0.974  36.323
GroupStats                        28.028  0.945  33.488
FlowSOM                           23.993  1.012  29.510
PlotGroups                        23.906  0.928  29.249
query_multiple                    19.595  0.467  21.270
QueryMultiple                     19.394  0.483  23.275
AddAnnotation                     18.403  0.748  24.542
Plot2DScatters                    17.003  0.981  22.933
PlotManualBars                    15.722  0.719  19.852
GetFlowJoLabels                   14.528  0.653  17.789
QueryStarPlot                     14.148  0.354  16.661
PlotNode                          13.589  0.610  16.304
PlotNumbers                       12.971  0.626  16.044
PlotVariable                      12.995  0.563  15.569
GetFeatures                       12.771  0.420  15.348
UpdateNodeSize                    12.916  0.258  14.600
PlotPies                          12.279  0.618  14.930
CountGroups                       11.543  0.565  14.443
PlotFlowSOM                       11.147  0.672  14.225
PlotLabels                        10.774  0.504  13.140
SaveClustersToFCS                 10.418  0.643  12.581
NMetaclusters                      9.934  0.699  13.085
MetaclusterMFIs                    9.627  0.715  12.674
GetMetaclusterMFIs                 9.231  0.619  12.023
TestOutliers                       9.231  0.547  10.906
NClusters                          8.936  0.599  11.700
PlotOverview2D                     8.628  0.683  11.557
GetPercentages                     8.682  0.586  10.997
FlowSOMSubset                      8.659  0.373  10.254
GetMetaclusterCVs                  8.369  0.609  10.965
MetaclusterCVs                     8.333  0.610  10.857
GetMetaclusters                    8.265  0.648  10.932
GetMFIs                            8.266  0.583  10.061
GetMetaclusterPercentagesPositive  8.268  0.569  10.540
print.FlowSOM                      8.146  0.566   9.274
GetClusterPercentagesPositive      7.959  0.487  10.148
GetClusterMFIs                     7.852  0.493   9.889
GetCounts                          7.907  0.424   9.814
GetClusters                        7.817  0.432   9.698
NewData                            7.842  0.398   9.853
ReadInput                          6.913  0.448   8.473
MetaClustering                     6.682  0.409   8.542
metaClustering_consensus           5.421  0.399   6.508
PlotSD                             4.433  0.099   5.377
* 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-3.19-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)