##############################################################################
##############################################################################
###
### 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_2.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/FlowSOM.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.4.0’
* 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
* 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 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
Plot2DScatters: no visible binding for global variable ‘Population’
Undefined global functions or variables:
  Population
* 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                       87.699  1.637  89.609
PlotDimRed                        80.088  1.443  81.736
PlotMarker                        30.055  0.834  30.978
UpdateMetaclusters                29.030  0.751  29.846
GroupStats                        25.068  0.871  26.820
FlowSOM                           21.340  1.336  23.047
PlotGroups                        20.171  0.837  21.051
AddAnnotation                     14.634  0.744  15.508
QueryMultiple                     14.624  0.263  14.914
query_multiple                    14.575  0.255  14.859
Plot2DScatters                    14.113  0.675  14.852
PlotManualBars                    14.185  0.598  14.862
GetFeatures                       12.505  0.257  12.799
PlotNode                          11.575  0.680  12.301
CountGroups                       11.409  0.808  12.439
PlotFlowSOM                       11.623  0.592  12.256
GetFlowJoLabels                   11.539  0.396  12.004
PlotStars                         11.460  0.456  11.935
PlotNumbers                       11.078  0.633  11.744
PlotPies                          10.862  0.753  11.643
QueryStarPlot                     10.638  0.197  10.861
UpdateNodeSize                    10.649  0.186  10.868
SaveClustersToFCS                  9.196  0.748   9.962
TestOutliers                       9.043  0.650   9.720
PlotLabels                         9.102  0.579   9.748
MetaclusterMFIs                    8.952  0.658   9.653
NMetaclusters                      8.758  0.529   9.324
NClusters                          8.582  0.703   9.302
PlotVariable                       8.635  0.560   9.215
FlowSOMSubset                      8.108  0.475   8.610
MetaclusterCVs                     7.842  0.594   8.788
GetMetaclusterMFIs                 7.796  0.539   8.364
GetClusterMFIs                     7.958  0.340   8.321
PlotOverview2D                     7.610  0.586   8.241
GetMetaclusterCVs                  7.560  0.541   8.127
GetPercentages                     7.466  0.550   8.035
GetCounts                          7.663  0.345   8.026
GetMFIs                            7.460  0.532   8.016
GetMetaclusters                    7.349  0.614   7.988
GetClusters                        7.562  0.356   7.951
print.FlowSOM                      7.209  0.579   7.801
GetClusterPercentagesPositive      7.413  0.344   7.772
GetMetaclusterPercentagesPositive  7.296  0.424   7.736
NewData                            7.174  0.413   7.646
MetaClustering                     5.815  0.392   6.231
ReadInput                          5.692  0.449   6.152
metaClustering_consensus           4.986  0.315   5.330
* 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-3.15-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FlowSOM
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c som.c -o som.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/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)