##############################################################################
##############################################################################
###
### 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_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* 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 15.0.0 (clang-1500.0.40.1)’
* 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                       57.494  2.473  60.415
PlotDimRed                        52.797  2.972  56.119
PlotOutliers                      16.633  0.697  17.362
UpdateMetaclusters                15.973  1.262  17.257
PlotMarker                        15.170  1.040  16.264
FlowSOM                           13.303  1.062  14.488
PlotStars                         13.203  0.922  14.153
GroupStats                        12.488  0.940  13.463
PlotGroups                        10.138  1.009  11.217
AddAnnotation                      9.153  0.620   9.797
query_multiple                     9.005  0.599   9.613
QueryMultiple                      8.808  0.472   9.297
Plot2DScatters                     8.101  0.662   8.784
GetFlowJoLabels                    7.951  0.749   8.724
PlotManualBars                     7.957  0.685   8.660
PlotNode                           6.780  0.666   7.462
PlotNumbers                        6.686  0.721   7.448
QueryStarPlot                      6.886  0.457   7.366
CountGroups                        6.524  0.677   7.275
PlotVariable                       6.280  0.805   7.134
PlotLabels                         6.394  0.662   7.069
PlotPies                           6.104  0.719   6.894
NMetaclusters                      5.883  0.688   6.585
PlotFlowSOM                        5.732  0.700   6.459
TestOutliers                       5.755  0.674   6.489
SaveClustersToFCS                  5.472  0.857   6.430
PlotOverview2D                     5.509  0.639   6.165
MetaclusterMFIs                    5.417  0.730   6.156
UpdateNodeSize                     5.702  0.296   6.003
NClusters                          5.272  0.682   5.998
GetFeatures                        5.401  0.540   5.998
GetMetaclusterPercentagesPositive  5.158  0.692   5.908
print.FlowSOM                      4.953  0.739   5.706
GetMFIs                            4.974  0.703   5.686
GetMetaclusterCVs                  4.933  0.719   5.753
GetPercentages                     4.803  0.657   5.470
GetMetaclusterMFIs                 4.846  0.593   5.462
GetMetaclusters                    4.734  0.563   5.311
GetClusterMFIs                     4.734  0.533   5.298
MetaclusterCVs                     4.641  0.599   5.260
GetCounts                          4.723  0.448   5.213
GetClusterPercentagesPositive      4.679  0.469   5.185
GetClusters                        4.562  0.518   5.204
* 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-3.20-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/4.4-arm64/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c som.c -o som.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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)