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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_2.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/FlowSOM.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.6.0’
* 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
* 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 R 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 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 ... OK
* 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                       41.134  2.226  43.670
PlotDimRed                        35.302  2.382  37.960
PlotMarker                        15.641  1.439  17.190
UpdateMetaclusters                15.092  1.725  16.911
PlotStars                         12.653  1.359  14.108
PlotGroups                        10.822  1.387  12.281
GroupStats                        11.042  1.133  12.248
FlowSOM                           10.366  1.385  11.852
AddAnnotation                      8.284  0.682   9.010
query_multiple                     8.023  0.563   8.620
QueryMultiple                      7.615  0.691   8.386
Plot2DScatters                     7.105  1.067   8.226
GetFlowJoLabels                    7.346  0.776   8.173
PlotManualBars                     6.839  1.092   8.028
PlotFlowSOM                        5.852  1.105   7.018
PlotVariable                       5.799  1.137   7.000
PlotNode                           5.977  0.844   6.890
PlotPies                           5.805  0.949   6.796
PlotNumbers                        5.459  1.003   6.502
QueryStarPlot                      5.849  0.470   6.355
SaveClustersToFCS                  5.110  1.199   6.363
CountGroups                        5.523  0.782   6.336
TestOutliers                       4.755  1.042   5.858
NClusters                          4.577  1.125   5.874
MetaclusterMFIs                    4.552  1.143   5.739
NMetaclusters                      4.520  1.102   5.655
PlotLabels                         4.668  0.885   5.588
GetMetaclusterPercentagesPositive  4.536  0.893   5.451
print.FlowSOM                      4.342  1.058   5.449
GetFeatures                        4.905  0.459   5.401
UpdateNodeSize                     4.896  0.375   5.314
GetMetaclusters                    4.327  0.894   5.253
FlowSOMSubset                      4.647  0.494   5.175
GetMFIs                            4.321  0.709   5.061
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c som.c -o som.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/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)