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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                       91.372  2.591  98.705
PlotDimRed                        73.285  2.850  81.633
PlotOutliers                      38.606  1.031  44.294
PlotMarker                        32.111  1.790  35.331
UpdateMetaclusters                31.486  1.299  34.387
PlotStars                         27.407  1.170  30.156
GroupStats                        25.830  1.377  29.253
FlowSOM                           22.724  1.231  26.461
PlotGroups                        21.795  1.260  23.765
AddAnnotation                     17.069  0.862  19.573
QueryMultiple                     17.062  0.519  18.644
query_multiple                    16.122  0.579  17.294
Plot2DScatters                    15.755  0.933  17.817
PlotManualBars                    14.927  0.879  16.866
GetFlowJoLabels                   13.730  0.687  15.416
PlotNode                          12.824  0.886  14.312
QueryStarPlot                     12.630  0.421  13.896
PlotNumbers                       12.030  0.989  13.726
PlotVariable                      12.117  0.885  14.081
GetFeatures                       12.132  0.636  13.280
UpdateNodeSize                    12.059  0.286  12.919
PlotPies                          11.357  0.884  12.577
CountGroups                       11.167  0.723  14.000
PlotFlowSOM                       10.435  0.798  11.754
PlotLabels                         9.947  0.763  11.444
SaveClustersToFCS                  9.572  0.805  10.958
NClusters                          9.099  1.155  10.403
NMetaclusters                      9.062  1.013  10.264
MetaclusterMFIs                    9.094  0.835  10.357
TestOutliers                       9.085  0.740  10.825
GetMetaclusterPercentagesPositive  8.187  0.852   9.467
FlowSOMSubset                      8.416  0.525   9.682
PlotOverview2D                     8.182  0.702   9.477
GetMetaclusterCVs                  7.946  0.923   9.405
GetPercentages                     7.951  0.831   9.035
GetMetaclusters                    7.890  0.798   9.166
GetMFIs                            8.014  0.670   9.921
MetaclusterCVs                     7.945  0.725   9.229
GetMetaclusterMFIs                 7.828  0.612   9.009
NewData                            7.742  0.671   8.654
print.FlowSOM                      7.450  0.811   8.755
GetClusterPercentagesPositive      7.516  0.588   8.478
GetCounts                          7.550  0.498   8.214
GetClusterMFIs                     7.525  0.429   8.313
GetClusters                        7.449  0.496   8.188
ReadInput                          6.649  0.678   7.854
MetaClustering                     6.583  0.602   7.590
metaClustering_consensus           5.256  0.393   6.127
* 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)