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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 12.7.5
* 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                       93.001  2.631 114.270
PlotDimRed                        75.037  2.395  89.828
PlotOutliers                      39.372  0.774  47.873
UpdateMetaclusters                32.555  1.066  38.137
PlotMarker                        32.573  0.999  37.405
PlotStars                         27.834  0.878  31.793
GroupStats                        26.309  0.792  31.308
FlowSOM                           22.606  0.921  27.309
PlotGroups                        22.576  0.888  26.664
AddAnnotation                     17.192  0.683  21.147
QueryMultiple                     17.370  0.491  20.158
query_multiple                    17.320  0.454  19.945
Plot2DScatters                    16.153  0.612  18.937
PlotManualBars                    15.086  0.639  18.363
GetFlowJoLabels                   13.857  0.671  16.863
PlotNode                          13.369  0.596  15.739
PlotNumbers                       12.555  0.601  14.536
QueryStarPlot                     12.690  0.337  14.612
PlotVariable                      12.276  0.589  14.556
GetFeatures                       12.385  0.365  14.794
CountGroups                       11.837  0.562  14.201
PlotPies                          11.534  0.637  13.407
UpdateNodeSize                    11.826  0.207  12.748
PlotFlowSOM                       10.487  0.534  12.452
SaveClustersToFCS                  9.734  0.609  11.673
PlotLabels                         9.717  0.533  12.155
NClusters                          9.594  0.615  12.448
MetaclusterMFIs                    9.613  0.520  12.017
NMetaclusters                      9.317  0.565  11.641
TestOutliers                       8.890  0.561  10.493
FlowSOMSubset                      8.781  0.388  10.716
MetaclusterCVs                     8.536  0.502  11.000
GetMetaclusterPercentagesPositive  8.418  0.572  10.875
GetMFIs                            8.097  0.545   9.869
PlotOverview2D                     8.155  0.470   9.503
GetMetaclusterCVs                  8.116  0.502  10.522
GetMetaclusters                    7.981  0.607  10.072
GetPercentages                     7.995  0.520   9.953
print.FlowSOM                      7.884  0.539   9.236
GetMetaclusterMFIs                 7.940  0.479   9.901
GetCounts                          7.667  0.455   9.333
GetClusterMFIs                     7.613  0.445   9.433
GetClusterPercentagesPositive      7.634  0.390   9.307
GetClusters                        7.582  0.439   9.326
NewData                            7.471  0.337   9.078
ReadInput                          6.668  0.422   8.037
MetaClustering                     6.542  0.392   8.381
metaClustering_consensus           5.315  0.404   6.485
* 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)