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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                       56.374  2.508  59.384
PlotDimRed                        53.485  3.332  57.287
UpdateMetaclusters                16.678  1.166  17.859
PlotOutliers                      16.110  0.879  17.042
PlotMarker                        15.908  0.998  16.967
PlotStars                         13.252  0.974  14.264
FlowSOM                           12.765  0.871  13.664
GroupStats                        12.606  0.977  13.610
PlotGroups                        11.088  1.129  12.241
AddAnnotation                      9.316  0.690  10.118
query_multiple                     8.953  0.487   9.452
QueryMultiple                      8.433  0.563   9.023
GetFlowJoLabels                    7.840  0.869   8.737
Plot2DScatters                     7.939  0.732   8.748
PlotManualBars                     7.389  0.795   8.239
PlotNumbers                        7.300  0.810   8.128
PlotVariable                       6.882  0.919   7.825
QueryStarPlot                      6.935  0.495   7.435
PlotPies                           6.568  0.842   7.432
CountGroups                        6.724  0.616   7.417
PlotNode                           6.688  0.652   7.366
SaveClustersToFCS                  5.910  0.928   6.902
TestOutliers                       5.887  0.744   6.642
PlotLabels                         5.943  0.685   6.645
MetaclusterMFIs                    5.707  0.749   6.490
UpdateNodeSize                     6.071  0.356   6.432
PlotFlowSOM                        5.747  0.658   6.452
MetaclusterCVs                     5.408  0.804   6.287
NClusters                          5.507  0.680   6.247
GetMetaclusters                    4.964  0.803   5.866
GetFeatures                        5.352  0.406   5.761
print.FlowSOM                      4.894  0.718   5.620
GetMFIs                            4.969  0.573   5.551
NMetaclusters                      4.877  0.665   5.581
GetMetaclusterCVs                  4.828  0.664   5.496
GetPercentages                     4.850  0.621   5.500
GetMetaclusterMFIs                 4.852  0.565   5.506
PlotOverview2D                     4.809  0.566   5.403
GetMetaclusterPercentagesPositive  4.856  0.512   5.391
GetClusters                        4.620  0.652   5.300
GetClusterPercentagesPositive      4.680  0.561   5.327
GetClusterMFIs                     4.680  0.546   5.373
GetCounts                          4.459  0.557   5.027
* 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)