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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 4.4.1 (2024-06-14)
* 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                       59.487  3.415  65.411
PlotDimRed                        52.849  3.758  58.094
PlotOutliers                      17.228  0.914  18.357
PlotMarker                        16.890  1.186  18.258
UpdateMetaclusters                16.868  1.158  18.200
PlotStars                         14.011  1.177  15.442
FlowSOM                           12.403  1.156  14.433
GroupStats                        12.404  0.746  13.549
PlotGroups                        11.247  1.471  13.096
AddAnnotation                      9.474  0.836  10.411
query_multiple                     9.248  0.633   9.964
GetFlowJoLabels                    8.767  0.877   9.953
Plot2DScatters                     8.248  1.010   9.651
PlotManualBars                     8.077  0.645   8.789
QueryMultiple                      8.108  0.427   9.017
QueryStarPlot                      7.719  0.499   8.363
PlotNumbers                        7.280  0.708   8.060
PlotVariable                       7.216  0.767   8.185
CountGroups                        6.962  0.968   8.201
PlotPies                           6.537  1.068   7.729
PlotNode                           6.375  1.057   7.531
PlotFlowSOM                        6.270  1.140   7.517
SaveClustersToFCS                  5.956  1.221   7.238
MetaclusterMFIs                    5.838  1.049   7.160
PlotLabels                         5.965  0.859   7.038
NClusters                          5.626  1.014   6.800
NMetaclusters                      5.654  0.643   6.433
MetaclusterCVs                     5.257  0.921   6.438
UpdateNodeSize                     5.928  0.180   6.170
GetMetaclusterMFIs                 5.034  1.059   6.192
GetMetaclusterPercentagesPositive  4.997  1.076   6.240
print.FlowSOM                      5.102  0.922   6.085
TestOutliers                       5.437  0.563   6.037
GetFeatures                        5.560  0.380   6.013
GetMetaclusterCVs                  5.055  0.867   5.966
PlotOverview2D                     5.104  0.576   5.782
GetMetaclusters                    5.022  0.622   5.844
GetMFIs                            5.099  0.491   5.668
GetPercentages                     4.907  0.607   5.717
GetClusterMFIs                     4.656  0.762   5.471
GetClusterPercentagesPositive      4.675  0.716   5.495
NewData                            4.473  0.742   5.392
GetClusters                        4.583  0.524   5.156
GetCounts                          4.508  0.570   5.136
FlowSOMSubset                      4.622  0.379   5.216
* 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)