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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_2.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.11.0’
* 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 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 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 ... 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                       117.595  3.255 146.521
PlotDimRed                         74.536  2.923  93.319
PlotMarker                         50.838  1.319  59.588
UpdateMetaclusters                 46.096  1.248  56.327
PlotStars                          38.080  1.013  46.825
PlotOutliers                       36.929  1.042  45.941
GroupStats                         33.985  0.986  40.040
query_multiple                     30.557  0.606  36.839
QueryMultiple                      29.793  0.593  36.445
PlotGroups                         28.456  1.010  33.896
FlowSOM                            26.454  0.973  31.918
Plot2DScatters                     22.601  0.799  28.097
AddAnnotation                      22.194  0.759  27.173
QueryStarPlot                      20.897  0.455  25.878
UpdateNodeSize                     19.168  0.332  23.372
PlotNumbers                        16.412  0.721  21.736
PlotNode                           16.352  0.761  22.074
GetFlowJoLabels                    15.932  0.732  20.652
PlotVariable                       15.294  0.741  18.397
PlotManualBars                     15.012  0.667  18.439
PlotPies                           13.599  0.636  17.135
PlotFlowSOM                        12.167  0.608  14.891
GetFeatures                        12.018  0.439  14.916
CountGroups                        11.378  0.577  14.459
PlotLabels                         10.769  0.575  13.654
SaveClustersToFCS                   9.588  0.714  12.225
NMetaclusters                       8.986  0.728  11.675
TestOutliers                        9.058  0.604  11.792
MetaclusterMFIs                     9.047  0.598  12.043
NClusters                           8.552  0.577  10.529
FlowSOMSubset                       8.413  0.475  16.275
MetaclusterCVs                      7.937  0.594  10.589
print.FlowSOM                       7.960  0.567  10.081
GetMFIs                             7.942  0.566  10.247
GetPercentages                      7.891  0.594  10.258
PlotOverview2D                      7.945  0.535   9.982
GetMetaclusters                     7.862  0.591   9.916
GetClusters                         7.881  0.547  10.646
GetMetaclusterPercentagesPositive   7.891  0.535  10.379
GetMetaclusterCVs                   7.890  0.525  10.131
GetMetaclusterMFIs                  7.860  0.543  10.432
GetClusterMFIs                      7.610  0.516  10.052
GetCounts                           7.599  0.424   9.560
GetClusterPercentagesPositive       7.535  0.462   9.796
NewData                             7.306  0.441   9.165
ReadInput                           6.584  0.487   8.420
MetaClustering                      6.423  0.394   7.929
PlotSD                              5.924  0.202   7.660
metaClustering_consensus            5.328  0.258   6.650
* 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: 1 NOTE
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)