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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 4.4.2 (2024-10-31)
* 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                       56.861  2.482  59.742
PlotDimRed                        52.949  3.167  56.354
PlotMarker                        16.519  1.247  17.799
UpdateMetaclusters                16.179  1.133  17.332
PlotOutliers                      15.829  0.620  16.506
PlotStars                         13.932  0.906  14.871
FlowSOM                           12.795  1.083  14.075
GroupStats                        12.185  0.920  13.124
PlotGroups                        10.917  1.009  11.950
query_multiple                     9.158  0.655   9.832
QueryMultiple                      8.914  0.588   9.526
AddAnnotation                      8.809  0.565   9.381
GetFlowJoLabels                    7.961  0.839   8.817
Plot2DScatters                     8.042  0.715   8.767
CountGroups                        7.339  0.630   8.035
PlotManualBars                     7.049  0.705   7.789
PlotNode                           6.651  0.706   7.366
PlotNumbers                        6.531  0.712   7.258
PlotVariable                       6.302  0.710   7.041
SaveClustersToFCS                  6.234  0.734   6.980
QueryStarPlot                      6.410  0.480   6.956
PlotPies                           6.151  0.710   6.910
PlotLabels                         5.505  0.637   6.159
PlotFlowSOM                        5.486  0.631   6.138
GetMetaclusterCVs                  5.346  0.701   6.072
NMetaclusters                      5.370  0.628   6.004
UpdateNodeSize                     5.695  0.277   5.983
MetaclusterCVs                     5.326  0.601   5.981
TestOutliers                       5.253  0.673   5.955
GetFeatures                        5.448  0.454   5.907
MetaclusterMFIs                    5.124  0.572   5.741
GetMFIs                            4.852  0.774   5.640
print.FlowSOM                      4.904  0.694   5.635
PlotOverview2D                     4.996  0.583   5.593
GetMetaclusters                    4.854  0.704   5.571
NClusters                          4.908  0.608   5.599
GetPercentages                     4.879  0.568   5.463
GetMetaclusterMFIs                 4.723  0.626   5.353
GetCounts                          4.710  0.620   5.453
GetClusterMFIs                     4.702  0.554   5.319
GetClusters                        4.574  0.546   5.148
GetMetaclusterPercentagesPositive  4.403  0.707   5.145
GetClusterPercentagesPositive      4.668  0.420   5.140
* 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)