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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_2.12.0.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 12.7.6
* 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                       94.713  2.808 119.130
PlotDimRed                        75.710  2.635  93.560
PlotOutliers                      39.919  0.833  48.537
PlotMarker                        33.708  1.038  39.917
UpdateMetaclusters                33.244  1.019  39.967
PlotStars                         28.111  0.808  32.762
GroupStats                        26.639  0.816  32.730
FlowSOM                           22.684  0.882  26.689
PlotGroups                        22.626  0.819  26.592
QueryMultiple                     17.821  0.468  20.709
AddAnnotation                     17.334  0.687  21.994
query_multiple                    17.353  0.461  19.087
Plot2DScatters                    16.417  0.623  20.042
PlotManualBars                    15.161  0.634  18.671
GetFlowJoLabels                   14.039  0.598  17.478
PlotNode                          13.095  0.545  15.080
PlotVariable                      12.944  0.648  15.704
QueryStarPlot                     12.998  0.314  14.790
PlotNumbers                       12.332  0.597  14.820
GetFeatures                       12.537  0.384  15.236
UpdateNodeSize                    12.364  0.226  14.305
PlotPies                          11.889  0.523  14.148
CountGroups                       11.712  0.568  13.900
PlotFlowSOM                       10.603  0.512  12.810
SaveClustersToFCS                  9.934  0.588  11.641
PlotLabels                         9.697  0.526  11.939
NMetaclusters                      9.605  0.567  12.252
MetaclusterMFIs                    9.314  0.617  12.172
NClusters                          9.271  0.583  11.798
TestOutliers                       8.963  0.484  10.924
FlowSOMSubset                      8.542  0.384  10.422
GetMetaclusterMFIs                 8.362  0.515  10.643
PlotOverview2D                     8.369  0.485  10.121
GetMetaclusterCVs                  8.090  0.600  10.460
GetMetaclusters                    8.110  0.579  10.321
MetaclusterCVs                     8.133  0.529   9.914
GetPercentages                     8.122  0.523  10.270
GetMFIs                            8.123  0.485  10.657
GetMetaclusterPercentagesPositive  8.056  0.514  10.099
print.FlowSOM                      7.923  0.534   9.103
GetClusterMFIs                     7.757  0.452   9.010
GetClusterPercentagesPositive      7.821  0.378   9.827
GetClusters                        7.746  0.434   9.687
GetCounts                          7.793  0.363   9.628
NewData                            7.561  0.379   9.385
ReadInput                          6.796  0.421   8.048
MetaClustering                     6.655  0.449   8.772
metaClustering_consensus           5.355  0.387   6.298
* 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)