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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_2.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FlowSOM.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.14.0’
* 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                       56.828  2.476  59.366
PlotDimRed                        52.993  2.899  56.360
PlotOutliers                      17.180  0.695  17.909
PlotMarker                        16.408  1.339  17.813
UpdateMetaclusters                15.486  1.188  16.759
PlotStars                         14.034  0.964  15.021
FlowSOM                           12.447  0.729  13.265
GroupStats                        11.682  0.831  12.659
PlotGroups                        10.507  1.005  11.557
AddAnnotation                      9.030  0.721   9.836
query_multiple                     8.974  0.484   9.485
QueryMultiple                      8.795  0.504   9.331
PlotManualBars                     8.051  0.783   8.851
Plot2DScatters                     7.963  0.669   8.654
GetFlowJoLabels                    7.911  0.573   8.551
PlotVariable                       7.008  0.805   7.908
CountGroups                        6.965  0.608   7.620
PlotNumbers                        6.851  0.716   7.594
PlotPies                           6.717  0.749   7.483
PlotNode                           6.545  0.618   7.176
QueryStarPlot                      6.782  0.375   7.160
SaveClustersToFCS                  6.159  0.749   6.917
PlotFlowSOM                        5.916  0.696   6.619
MetaclusterMFIs                    5.873  0.694   6.594
NClusters                          5.590  0.958   6.641
NMetaclusters                      5.559  0.878   6.538
PlotLabels                         5.817  0.595   6.448
UpdateNodeSize                     5.707  0.234   5.945
GetFeatures                        5.420  0.463   5.887
TestOutliers                       5.222  0.616   5.894
PlotOverview2D                     5.113  0.645   5.780
print.FlowSOM                      4.932  0.650   5.636
GetMetaclusters                    4.858  0.708   5.577
GetMetaclusterCVs                  4.910  0.626   5.551
GetPercentages                     4.905  0.578   5.492
GetMFIs                            4.821  0.656   5.510
GetMetaclusterPercentagesPositive  4.838  0.550   5.399
GetClusters                        4.826  0.538   5.401
GetMetaclusterMFIs                 4.780  0.583   5.388
MetaclusterCVs                     4.604  0.567   5.206
GetClusterPercentagesPositive      4.532  0.562   5.124
GetCounts                          4.512  0.543   5.062
* 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-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)