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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_2.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.6
* 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 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                       59.566  2.838  63.042
PlotDimRed                        53.508  3.243  57.663
PlotMarker                        18.747  1.067  19.959
UpdateMetaclusters                18.147  1.087  19.369
PlotOutliers                      17.777  0.699  18.594
PlotStars                         14.414  0.842  15.363
FlowSOM                           13.608  0.961  17.104
GroupStats                        13.543  0.912  14.801
PlotGroups                        11.574  0.977  12.621
AddAnnotation                     10.091  0.683  10.964
query_multiple                    10.120  0.494  10.691
QueryMultiple                      9.725  0.538  10.368
GetFlowJoLabels                    8.690  0.649   9.449
Plot2DScatters                     8.302  0.699   9.248
PlotVariable                       8.182  0.643   8.894
PlotManualBars                     7.679  0.712   8.471
CountGroups                        7.265  0.750   9.912
PlotNode                           7.238  0.602   7.910
PlotNumbers                        7.130  0.668   7.859
PlotFlowSOM                        6.928  0.759   7.733
QueryStarPlot                      7.212  0.431   7.766
PlotPies                           6.820  0.649   7.561
SaveClustersToFCS                  6.695  0.711   7.442
NClusters                          5.965  0.777   6.809
MetaclusterMFIs                    5.970  0.666   6.788
GetMFIs                            5.862  0.636   6.671
UpdateNodeSize                     6.215  0.240   6.484
TestOutliers                       5.691  0.696   6.421
GetFeatures                        5.848  0.476   6.362
NMetaclusters                      5.628  0.671   6.361
PlotOverview2D                     5.468  0.569   6.075
print.FlowSOM                      5.305  0.716   6.070
MetaclusterCVs                     5.430  0.583   6.228
GetMetaclusterMFIs                 5.286  0.675   6.087
GetMetaclusterPercentagesPositive  5.278  0.648   5.965
GetPercentages                     5.258  0.662   5.974
GetMetaclusters                    5.222  0.655   5.913
GetCounts                          5.238  0.522   5.784
PlotLabels                         5.159  0.527   5.738
GetClusterPercentagesPositive      4.909  0.587   5.529
GetMetaclusterCVs                  4.916  0.566   5.816
FlowSOMSubset                      4.996  0.388   5.463
GetClusters                        4.799  0.492   5.356
GetClusterMFIs                     4.819  0.416   5.278
NewData                            4.523  0.508   5.061
* 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.

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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-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)