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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_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/FlowSOM.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘2.10.0’
* 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 ... 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                       114.512  2.734 124.697
PlotDimRed                         74.506  2.535  81.618
PlotMarker                         48.978  1.179  53.684
UpdateMetaclusters                 44.136  1.318  46.887
PlotStars                          36.774  1.088  40.564
PlotOutliers                       35.741  0.816  38.173
GroupStats                         32.505  1.022  35.439
QueryMultiple                      29.141  0.520  32.024
PlotGroups                         27.352  1.029  30.448
query_multiple                     27.399  0.719  31.921
FlowSOM                            25.463  1.427  27.900
Plot2DScatters                     21.604  0.669  23.306
AddAnnotation                      21.233  0.756  22.558
QueryStarPlot                      20.280  0.383  21.489
UpdateNodeSize                     17.647  0.256  18.244
PlotNumbers                        16.087  0.799  18.751
PlotNode                           16.135  0.696  19.530
GetFlowJoLabels                    15.474  0.682  17.198
PlotVariable                       14.909  0.607  16.281
PlotManualBars                     14.686  0.748  16.672
PlotPies                           13.926  0.735  16.248
PlotFlowSOM                        12.322  0.748  13.645
GetFeatures                        12.067  0.428  13.069
CountGroups                        11.351  0.806  12.362
PlotLabels                         10.541  0.575  12.310
SaveClustersToFCS                   9.371  0.876  10.363
NMetaclusters                       8.972  0.809  10.573
MetaclusterMFIs                     9.089  0.601  10.539
NClusters                           8.988  0.636  10.212
TestOutliers                        8.524  0.581   9.211
MetaclusterCVs                      8.242  0.621   9.662
GetMetaclusterMFIs                  8.120  0.563   9.588
FlowSOMSubset                       7.967  0.549   8.691
PlotOverview2D                      7.961  0.502   8.937
print.FlowSOM                       7.597  0.820  10.367
GetPercentages                      7.812  0.587   9.351
GetMetaclusters                     7.692  0.702   8.792
GetMetaclusterPercentagesPositive   7.775  0.586   8.881
GetMFIs                             7.780  0.569   8.829
GetMetaclusterCVs                   7.797  0.548   8.770
GetCounts                           7.547  0.514   8.432
GetClusterMFIs                      7.442  0.469   8.626
GetClusterPercentagesPositive       7.421  0.477   8.345
GetClusters                         7.366  0.454   8.348
NewData                             7.244  0.466   8.035
ReadInput                           6.521  0.675   7.474
MetaClustering                      5.786  0.463   6.545
PlotSD                              5.448  0.157   6.069
metaClustering_consensus            5.069  0.348   5.808
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-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 -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)