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###
### Running command:
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###   /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_2.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.13.0’
* 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                       98.169  2.350 113.970
PlotDimRed                        78.133  2.309  88.875
PlotOutliers                      40.122  0.801  45.136
PlotMarker                        36.243  1.026  40.735
UpdateMetaclusters                34.650  1.171  39.508
PlotStars                         29.864  0.882  33.335
GroupStats                        28.260  0.868  32.129
FlowSOM                           23.657  0.921  28.304
PlotGroups                        23.540  0.855  26.683
QueryMultiple                     19.186  0.407  22.077
query_multiple                    19.154  0.437  23.205
AddAnnotation                     18.279  0.676  21.416
Plot2DScatters                    16.699  0.564  19.027
PlotManualBars                    15.275  0.596  17.392
GetFlowJoLabels                   14.292  0.540  16.223
PlotNode                          13.737  0.601  15.812
QueryStarPlot                     13.979  0.342  16.220
PlotPies                          12.872  0.878  15.573
UpdateNodeSize                    13.335  0.285  15.377
PlotNumbers                       12.894  0.638  14.728
PlotVariable                      12.596  0.648  14.828
GetFeatures                       12.539  0.317  13.776
CountGroups                       11.810  0.575  14.278
PlotFlowSOM                       11.329  0.647  13.157
PlotLabels                        10.217  0.488  11.337
SaveClustersToFCS                  9.949  0.639  12.072
MetaclusterMFIs                    9.581  0.585  11.522
NClusters                          9.495  0.646  11.117
NMetaclusters                      9.471  0.563  11.006
TestOutliers                       9.065  0.594  10.697
FlowSOMSubset                      8.930  0.369  10.700
PlotOverview2D                     8.597  0.575  11.038
GetMFIs                            8.477  0.536   9.820
MetaclusterCVs                     8.365  0.516   9.715
GetPercentages                     8.295  0.534   9.643
GetMetaclusters                    8.285  0.536   9.824
GetMetaclusterPercentagesPositive  8.298  0.498   9.924
GetMetaclusterMFIs                 8.150  0.548   9.746
print.FlowSOM                      8.167  0.489   9.890
GetMetaclusterCVs                  8.065  0.485   9.093
GetCounts                          7.863  0.343   8.957
GetClusters                        7.771  0.413   9.196
GetClusterMFIs                     7.776  0.404   9.351
NewData                            7.774  0.402   8.888
GetClusterPercentagesPositive      7.762  0.364   8.871
ReadInput                          6.913  0.411   8.681
MetaClustering                     6.742  0.442   7.892
metaClustering_consensus           5.529  0.314   6.602
PlotSD                             4.417  0.155   5.220
* 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.

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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/4.4-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)