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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_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/FlowSOM.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.8.0’
* 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 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 ... NOTE
PlotManualBars: no visible binding for global variable ‘MC’
PlotManualBars: no visible binding for global variable ‘Manual’
Undefined global functions or variables:
  MC Manual
* 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                       93.362  2.326 124.937
PlotDimRed                        74.261  2.595 101.373
PlotOutliers                      34.918  0.750  45.317
UpdateMetaclusters                32.541  1.092  43.055
PlotMarker                        32.219  0.999  43.130
PlotStars                         27.892  0.817  36.760
GroupStats                        26.006  0.906  36.077
PlotGroups                        22.238  0.812  32.355
FlowSOM                           22.081  0.893  30.750
QueryMultiple                     17.164  0.416  21.952
AddAnnotation                     16.916  0.659  23.360
query_multiple                    17.027  0.428  21.676
PlotManualBars                    15.661  0.684  21.944
Plot2DScatters                    15.613  0.715  21.307
GetFlowJoLabels                   13.656  0.843  24.739
PlotNode                          12.815  0.636  17.867
QueryStarPlot                     13.060  0.296  17.597
PlotVariable                      12.165  0.622  15.723
PlotNumbers                       11.967  0.572  16.377
PlotPies                          11.788  0.590  15.690
GetFeatures                       12.000  0.365  15.172
UpdateNodeSize                    11.980  0.270  16.115
CountGroups                       11.084  0.548  15.022
PlotFlowSOM                       10.618  0.642  14.657
SaveClustersToFCS                  9.678  0.812  14.276
NClusters                          9.656  0.685  14.295
NMetaclusters                      9.153  0.762  14.217
PlotLabels                         9.303  0.481  13.174
MetaclusterMFIs                    9.090  0.619  12.989
TestOutliers                       8.847  0.649  11.851
GetMetaclusterPercentagesPositive  8.266  0.483  11.546
FlowSOMSubset                      8.236  0.338  11.496
PlotOverview2D                     8.015  0.538  10.804
MetaclusterCVs                     7.940  0.549  11.123
GetMetaclusterCVs                  7.944  0.521  11.521
GetMFIs                            7.871  0.592  13.115
GetMetaclusterMFIs                 7.905  0.470  11.055
GetPercentages                     7.868  0.501  10.772
GetMetaclusters                    7.869  0.478  10.952
print.FlowSOM                      7.813  0.503  10.717
GetClusterMFIs                     7.605  0.480  11.277
GetClusterPercentagesPositive      7.520  0.423  10.612
GetCounts                          7.533  0.398  10.190
GetClusters                        7.482  0.439  10.674
NewData                            7.373  0.429  10.987
ReadInput                          6.640  0.516   9.559
MetaClustering                     6.450  0.527   9.779
metaClustering_consensus           5.653  0.366   8.071
PlotSD                             4.111  0.105   5.539
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-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/4.3-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 -single_module -multiply_defined suppress -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/4.3-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)