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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                   56.567  2.432  59.199
PlotDimRed                    53.735  4.623  58.518
PlotMarker                    17.312  1.098  18.444
PlotOutliers                  16.801  0.777  17.604
UpdateMetaclusters            16.016  1.226  17.253
FlowSOM                       12.859  1.022  14.009
GroupStats                    12.388  0.867  13.268
PlotStars                     12.281  0.924  13.257
PlotGroups                    10.452  0.920  11.416
AddAnnotation                  8.812  0.501   9.319
query_multiple                 8.870  0.418   9.294
QueryMultiple                  8.626  0.538   9.211
Plot2DScatters                 7.946  0.623   8.600
GetFlowJoLabels                7.871  0.624   8.507
PlotManualBars                 7.530  0.613   8.172
PlotNode                       6.999  0.723   7.736
CountGroups                    7.087  0.566   7.676
PlotPies                       6.868  0.724   7.597
PlotVariable                   6.686  0.634   7.334
QueryStarPlot                  6.839  0.390   7.244
PlotNumbers                    6.284  0.826   7.131
PlotFlowSOM                    6.053  0.725   6.807
NClusters                      5.615  0.687   6.321
MetaclusterMFIs                5.353  0.741   6.098
PlotLabels                     5.441  0.615   6.073
SaveClustersToFCS              5.354  0.653   6.086
NMetaclusters                  5.363  0.643   6.019
GetFeatures                    5.572  0.331   5.927
GetMFIs                        5.346  0.546   5.903
TestOutliers                   5.266  0.611   5.882
UpdateNodeSize                 5.670  0.202   5.873
print.FlowSOM                  4.882  0.741   5.627
GetMetaclusterCVs              4.836  0.738   5.575
PlotOverview2D                 4.915  0.649   5.587
GetPercentages                 4.818  0.624   5.454
GetMetaclusterMFIs             4.786  0.625   5.451
MetaclusterCVs                 4.798  0.582   5.390
GetClusterPercentagesPositive  4.703  0.526   5.271
FlowSOMSubset                  4.796  0.430   5.257
GetCounts                      4.684  0.454   5.226
GetClusters                    4.643  0.454   5.125
* 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)