##############################################################################
##############################################################################
###
### 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_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.12.0’
* 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                       95.542  2.565 127.507
PlotDimRed                        77.322  2.502 100.467
PlotOutliers                      40.842  0.764  52.744
PlotMarker                        33.546  0.980  41.748
UpdateMetaclusters                33.290  1.082  44.128
PlotStars                         29.096  0.928  36.542
GroupStats                        27.186  0.806  35.834
FlowSOM                           23.473  0.873  30.955
PlotGroups                        23.130  0.909  29.515
QueryMultiple                     18.139  0.538  23.271
AddAnnotation                     17.655  0.731  24.111
query_multiple                    17.708  0.469  22.323
Plot2DScatters                    16.622  0.577  21.603
PlotManualBars                    15.395  0.578  19.944
GetFlowJoLabels                   14.305  0.648  19.269
PlotNode                          13.670  0.545  17.184
PlotNumbers                       13.056  0.597  17.155
QueryStarPlot                     13.173  0.347  16.904
UpdateNodeSize                    13.134  0.289  16.638
PlotVariable                      12.648  0.576  16.399
GetFeatures                       12.746  0.419  16.276
CountGroups                       12.237  0.553  15.992
PlotPies                          11.915  0.602  15.154
PlotFlowSOM                       10.712  0.554  15.272
PlotLabels                        10.425  0.540  13.956
SaveClustersToFCS                 10.262  0.618  13.691
NClusters                          9.890  0.671  13.362
MetaclusterMFIs                    9.540  0.599  13.234
NMetaclusters                      9.459  0.553  12.531
TestOutliers                       9.048  0.458  11.925
FlowSOMSubset                      9.011  0.404  11.956
GetMetaclusterMFIs                 8.717  0.563  12.136
GetMetaclusterCVs                  8.291  0.552  11.369
PlotOverview2D                     8.329  0.470  10.895
GetPercentages                     8.271  0.516  11.393
GetMetaclusters                    8.217  0.534  11.034
GetMFIs                            8.221  0.509  11.508
MetaclusterCVs                     8.228  0.491  11.050
GetMetaclusterPercentagesPositive  8.228  0.465  10.920
print.FlowSOM                      8.067  0.555  10.520
GetCounts                          7.974  0.442  10.547
GetClusterMFIs                     7.829  0.472  10.582
NewData                            7.782  0.395  10.221
GetClusterPercentagesPositive      7.727  0.419  10.218
GetClusters                        7.680  0.451  10.266
ReadInput                          6.807  0.401   6.789
MetaClustering                     6.730  0.380   9.814
metaClustering_consensus           5.285  0.302   6.851
PlotSD                             4.684  0.155   5.978
* 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-3.19-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)