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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                       57.634  2.683  60.519
PlotDimRed                        52.486  2.613  55.430
PlotMarker                        16.990  1.164  18.235
PlotOutliers                      16.901  0.664  17.588
UpdateMetaclusters                15.697  1.163  16.926
PlotStars                         13.444  1.145  14.718
FlowSOM                           13.082  1.097  14.367
GroupStats                        12.211  0.983  13.295
PlotGroups                        10.586  0.987  11.617
query_multiple                     9.383  0.422   9.824
QueryMultiple                      9.027  0.485   9.531
AddAnnotation                      8.800  0.429   9.239
GetFlowJoLabels                    7.774  0.763   8.550
PlotManualBars                     7.533  0.714   8.287
PlotVariable                       7.162  0.755   7.937
PlotNumbers                        6.977  0.689   7.682
Plot2DScatters                     6.983  0.574   7.585
PlotNode                           6.789  0.697   7.500
QueryStarPlot                      6.878  0.397   7.283
PlotPies                           6.395  0.835   7.245
CountGroups                        6.372  0.627   7.030
NClusters                          5.666  0.956   6.658
SaveClustersToFCS                  5.720  0.724   6.450
TestOutliers                       5.653  0.742   6.400
PlotFlowSOM                        5.723  0.666   6.403
NMetaclusters                      5.499  0.796   6.402
GetMetaclusterMFIs                 5.536  0.582   6.130
MetaclusterMFIs                    5.383  0.686   6.091
GetMetaclusterCVs                  5.272  0.732   6.026
GetPercentages                     5.321  0.640   5.983
PlotLabels                         5.410  0.546   5.975
UpdateNodeSize                     5.608  0.239   5.849
print.FlowSOM                      4.886  0.799   5.691
GetFeatures                        5.243  0.384   5.653
PlotOverview2D                     4.820  0.670   5.512
GetMFIs                            4.869  0.554   5.432
GetMetaclusterPercentagesPositive  4.822  0.592   5.422
GetMetaclusters                    4.859  0.523   5.404
GetClusters                        4.496  0.592   5.102
GetClusterMFIs                     4.475  0.598   5.082
GetClusterPercentagesPositive      4.474  0.557   5.038
* 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)