Package: cytofkit

Version: 1.13.2

Command: rm -rf cytofkit.buildbin-libdir && mkdir cytofkit.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cytofkit_1.13.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cytofkit.buildbin-libdir

StartedAt: 2018-10-29 04:59:14 -0400 (Mon, 29 Oct 2018)

EndedAt: 2018-10-29 05:00:43 -0400 (Mon, 29 Oct 2018)

EllapsedTime: 88.9 seconds

RetCode: 0

Status:  OK

PackageFile: cytofkit_1.13.2.tgz

PackageFileSize: 5.404 MiB

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### Running command:
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###   rm -rf cytofkit.buildbin-libdir && mkdir cytofkit.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cytofkit_1.13.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R cytofkit.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cytofkit.buildbin-libdir cytofkit_1.13.2.tar.gz'
>>>>>>> 

* installing *source* package ‘cytofkit’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c jaccard_coeff.cpp -o jaccard_coeff.o
clang++ -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 cytofkit.so RcppExports.o jaccard_coeff.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/cytofkit.buildbin-libdir/cytofkit/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were declared in NAMESPACE but not found
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: S3 method ‘xts::as.xts.data.table’ was declared in NAMESPACE but not found
Warning: S3 methods ‘ggplot2::autoplot.zoo’, ‘ggplot2::fortify.zoo’ were declared in NAMESPACE but not found
Warning: Package 'cytofkit' is deprecated and will be removed from Bioconductor
  version 3.9
* DONE (cytofkit)


>>>>>>> 
>>>>>>> FIXING LINKS FOR cytofkit.buildbin-libdir/cytofkit/libs//cytofkit.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "cytofkit.buildbin-libdir/cytofkit/libs//cytofkit.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "cytofkit.buildbin-libdir/cytofkit/libs//cytofkit.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "cytofkit.buildbin-libdir/cytofkit/libs//cytofkit.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "cytofkit.buildbin-libdir/cytofkit/libs//cytofkit.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "cytofkit.buildbin-libdir/cytofkit/libs//cytofkit.so"