Package: diffuStats

Version: 0.104.0

Command: rm -rf diffuStats.buildbin-libdir && mkdir diffuStats.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh diffuStats_0.104.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R diffuStats.buildbin-libdir

StartedAt: 2018-10-17 01:13:40 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 01:14:34 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 54.5 seconds

RetCode: 0

Status:  OK

PackageFile: diffuStats_0.104.0.tgz

PackageFileSize: 1.429 MiB

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### Running command:
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###   rm -rf diffuStats.buildbin-libdir && mkdir diffuStats.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh diffuStats_0.104.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R diffuStats.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=diffuStats.buildbin-libdir diffuStats_0.104.0.tar.gz'
>>>>>>> 

* installing *source* package ‘diffuStats’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c diffuse_parallel.cpp -o diffuse_parallel.o
diffuse_parallel.cpp:28:48: warning: 'acquire_chunked<double>' is deprecated [-Wdeprecated-declarations]
  arma::access::rw(res.values) = arma::memory::acquire_chunked<double>(x.size() + 1);
                                               ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:9: note: 'acquire_chunked<double>' has been explicitly marked deprecated here
memory::acquire_chunked(const uword n_elem)
        ^
diffuse_parallel.cpp:32:53: warning: 'acquire_chunked<unsigned int>' is deprecated [-Wdeprecated-declarations]
  arma::access::rw(res.row_indices) = arma::memory::acquire_chunked<arma::uword>(i.size() + 1);
                                                    ^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:117:9: note: 'acquire_chunked<unsigned int>' has been explicitly marked deprecated here
memory::acquire_chunked(const uword n_elem)
        ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppParallel/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -std=gnu++11 -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 diffuStats.so RcppExports.o diffuse_parallel.o init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/diffuStats.buildbin-libdir/diffuStats/libs
** R
** data
*** moving datasets to lazyload DB
** 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
* DONE (diffuStats)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "diffuStats.buildbin-libdir/diffuStats/libs//diffuStats.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "diffuStats.buildbin-libdir/diffuStats/libs//diffuStats.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "diffuStats.buildbin-libdir/diffuStats/libs//diffuStats.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "diffuStats.buildbin-libdir/diffuStats/libs//diffuStats.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "diffuStats.buildbin-libdir/diffuStats/libs//diffuStats.so"