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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FlowSOM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FlowSOM_2.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/FlowSOM.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FlowSOM/DESCRIPTION’ ... OK
* this is package ‘FlowSOM’ version ‘2.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FlowSOM’ can be installed ... OK
* 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 R 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 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 ... OK
* 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          76.913  2.009  79.106
PlotDimRed           60.054  1.599  61.743
RelabelMetaclusters  30.179  1.453  31.662
PlotMarker           25.869  1.297  27.226
GroupStats           21.569  1.326  22.931
ReassignMetaclusters 20.625  1.109  21.763
PlotGroups           18.924  1.331  20.400
FlowSOM              17.715  1.262  19.008
AddAnnotation        13.011  0.712  13.792
QueryMultiple        13.238  0.383  13.636
query_multiple       12.579  0.320  12.929
UpdateNodeSize       11.989  0.474  12.475
PlotNode             10.505  1.204  11.724
PlotStars            10.045  0.887  10.948
QueryStarPlot         9.917  0.464  10.393
Plot2DScatters        9.332  0.698  10.058
PlotManualBars        8.561  0.672   9.261
PlotNumbers           8.291  0.831   9.135
PlotPies              8.342  0.694   9.144
GetFlowJoLabels       8.344  0.469   8.860
PlotFlowSOM           7.876  0.852   8.744
CountGroups           7.224  0.752   7.986
PlotVariable          6.001  0.691   6.700
NMetaclusters         5.790  0.887   6.689
PlotLabels            5.981  0.626   6.616
SaveClustersToFCS     5.729  0.727   6.467
print.FlowSOM         5.435  0.905   6.350
TestOutliers          5.625  0.647   6.359
GetFeatures           6.046  0.211   6.269
NClusters             5.502  0.696   6.215
MetaclusterMFIs       5.267  0.724   6.012
GetClusterMFIs        5.393  0.392   5.793
GetCounts             5.190  0.521   5.732
GetMetaclusterMFIs    5.014  0.601   5.628
GetMFIs               4.743  0.838   5.593
MetaclusterCVs        4.807  0.757   5.587
GetMetaclusters       4.970  0.512   5.492
FlowSOMSubset         5.146  0.323   5.485
GetClusters           4.798  0.493   5.296
GetMetaclusterCVs     4.462  0.686   5.156
ReadInput             4.500  0.574   5.090
GetPercentages        4.457  0.592   5.065
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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-3.13-bioc/meat/FlowSOM.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FlowSOM
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘FlowSOM’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c som.c -o som.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o FlowSOM.so som.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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)