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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 4.4.1 RC (2024-06-06 r86719)
* 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 12.7.1
* 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                       51.351  2.250  53.655
PlotDimRed                        40.799  2.303  43.530
PlotMarker                        19.431  1.362  21.024
PlotOutliers                      19.530  0.866  20.616
UpdateMetaclusters                17.050  1.285  18.535
PlotStars                         15.842  1.132  17.186
GroupStats                        13.735  1.038  14.880
PlotGroups                        12.957  1.123  14.281
FlowSOM                           12.791  1.067  13.983
AddAnnotation                      9.867  0.636  10.585
QueryMultiple                      9.674  0.472  10.270
query_multiple                     9.255  0.392   9.734
Plot2DScatters                     8.794  0.769   9.701
GetFlowJoLabels                    8.174  0.654   8.900
PlotManualBars                     7.841  0.815   8.754
PlotNode                           7.447  0.783   8.333
PlotNumbers                        7.119  0.817   8.077
QueryStarPlot                      7.449  0.354   7.893
PlotVariable                       6.934  0.749   7.754
PlotPies                           6.695  0.658   7.454
PlotFlowSOM                        6.405  0.702   7.199
NClusters                          5.907  0.785   6.797
CountGroups                        6.071  0.614   6.753
MetaclusterMFIs                    5.614  0.893   6.572
SaveClustersToFCS                  5.560  0.888   6.539
PlotLabels                         5.701  0.718   6.484
NMetaclusters                      5.274  0.851   6.177
GetFeatures                        5.626  0.426   6.097
TestOutliers                       5.234  0.702   6.013
UpdateNodeSize                     5.664  0.243   5.960
MetaclusterCVs                     4.973  0.759   5.787
GetPercentages                     4.743  0.677   5.473
PlotOverview2D                     4.691  0.721   5.473
GetMetaclusterCVs                  4.650  0.756   5.466
GetMFIs                            4.666  0.624   5.346
GetMetaclusterPercentagesPositive  4.541  0.712   5.299
GetMetaclusterMFIs                 4.559  0.579   5.178
GetMetaclusters                    4.448  0.630   5.181
NewData                            4.490  0.532   5.087
print.FlowSOM                      4.126  0.831   5.003
* 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)