##############################################################################
##############################################################################
###
### 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: 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 12.7.6
* 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 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                       90.977  2.549  95.723
PlotDimRed                        72.837  2.534  76.752
PlotOutliers                      38.137  1.098  40.378
PlotMarker                        32.624  1.544  35.171
UpdateMetaclusters                31.941  1.348  35.508
PlotStars                         27.803  1.179  31.462
GroupStats                        26.170  1.234  28.342
FlowSOM                           22.597  1.219  25.411
PlotGroups                        22.020  1.329  24.394
AddAnnotation                     17.002  0.843  18.311
QueryMultiple                     17.068  0.481  17.982
query_multiple                    16.934  0.541  18.026
Plot2DScatters                    15.899  1.075  17.586
PlotManualBars                    14.830  0.924  16.262
GetFlowJoLabels                   13.719  0.836  15.058
PlotNode                          12.827  0.847  14.411
PlotNumbers                       12.188  0.949  14.653
QueryStarPlot                     12.629  0.467  13.196
PlotVariable                      12.114  0.970  14.395
PlotPies                          11.860  1.151  13.409
GetFeatures                       12.186  0.469  13.317
UpdateNodeSize                    12.063  0.281  12.465
CountGroups                       11.443  0.779  12.760
PlotFlowSOM                       10.328  1.021  11.788
PlotLabels                         9.888  0.887  11.123
SaveClustersToFCS                  9.734  0.988  11.122
NClusters                          9.167  1.170  10.498
TestOutliers                       9.204  0.806  10.446
NMetaclusters                      8.961  1.039  10.118
MetaclusterMFIs                    8.612  0.927  10.414
GetMetaclusterPercentagesPositive  8.125  0.808   9.158
GetPercentages                     7.882  1.023   9.016
FlowSOMSubset                      8.411  0.451   9.348
print.FlowSOM                      7.873  0.969   8.938
GetMetaclusterCVs                  7.888  0.901   8.949
GetMetaclusterMFIs                 7.840  0.882   8.980
PlotOverview2D                     8.011  0.704   8.988
MetaclusterCVs                     8.000  0.707   9.194
GetMFIs                            7.924  0.768   8.979
GetMetaclusters                    7.778  0.776   8.769
NewData                            7.670  0.812   8.524
GetClusterPercentagesPositive      7.589  0.636   8.495
GetCounts                          7.643  0.581   8.440
GetClusters                        7.549  0.657   8.318
GetClusterMFIs                     7.525  0.547   8.354
MetaClustering                     6.583  0.994   7.761
ReadInput                          6.518  0.568   7.135
metaClustering_consensus           5.194  0.472   5.777
* 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-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)