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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                       57.575  2.416  60.312
PlotDimRed                        52.073  2.801  55.147
PlotMarker                        17.080  1.093  18.202
UpdateMetaclusters                16.022  1.266  17.317
PlotOutliers                      16.268  0.686  16.987
PlotStars                         12.832  0.969  13.837
FlowSOM                           12.694  1.067  13.980
GroupStats                        12.239  0.862  13.132
PlotGroups                        10.274  1.026  11.328
query_multiple                     9.262  0.590   9.902
QueryMultiple                      8.816  0.472   9.293
AddAnnotation                      8.733  0.515   9.256
GetFlowJoLabels                    7.870  0.791   8.669
Plot2DScatters                     7.978  0.647   8.669
PlotPies                           7.269  0.804   8.083
CountGroups                        7.266  0.653   7.954
PlotNode                           7.078  0.606   7.711
PlotManualBars                     6.966  0.649   7.650
QueryStarPlot                      7.115  0.478   7.637
PlotVariable                       6.763  0.679   7.473
PlotNumbers                        6.636  0.742   7.400
SaveClustersToFCS                  5.766  0.708   6.483
PlotLabels                         5.726  0.643   6.380
UpdateNodeSize                     5.828  0.325   6.159
PlotFlowSOM                        5.490  0.638   6.165
NClusters                          5.415  0.679   6.103
GetFeatures                        5.446  0.409   5.862
NMetaclusters                      5.158  0.655   5.836
TestOutliers                       5.178  0.591   5.790
print.FlowSOM                      5.002  0.727   5.735
PlotOverview2D                     5.129  0.595   5.734
GetCounts                          4.975  0.633   5.626
MetaclusterCVs                     4.914  0.592   5.520
GetMFIs                            4.877  0.609   5.540
GetMetaclusterCVs                  4.832  0.622   5.467
GetMetaclusters                    4.808  0.614   5.437
GetPercentages                     4.854  0.568   5.428
GetMetaclusterMFIs                 4.557  0.668   5.267
MetaclusterMFIs                    4.642  0.579   5.258
GetMetaclusterPercentagesPositive  4.607  0.574   5.202
GetClusterPercentagesPositive      4.702  0.450   5.173
GetClusterMFIs                     4.596  0.523   5.155
GetClusters                        4.565  0.529   5.119
* 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)