Package: diffuStats

Version: 1.7.0

Command: rm -rf diffuStats.buildbin-libdir && mkdir diffuStats.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh diffuStats_1.7.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R diffuStats.buildbin-libdir

StartedAt: 2020-01-16 10:47:52 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 10:48:43 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 50.8 seconds

RetCode: 0

Status:  OK

PackageFile: diffuStats_1.7.0.tgz

PackageFileSize: 1.43 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_1.7.0.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_1.7.0.tar.gz'
>>>>>>> 

* installing *source* package ‘diffuStats’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:115:1: note: 'acquire_chunked<double>' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:304:44: note: expanded from macro 'arma_deprecated'
    #define arma_deprecated __attribute__((__deprecated__))
                                           ^
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/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/memory.hpp:115:1: note: 'acquire_chunked<unsigned int>' has been explicitly marked deprecated here
arma_deprecated
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/armadillo_bits/compiler_setup.hpp:304:44: note: expanded from macro 'arma_deprecated'
    #define arma_deprecated __attribute__((__deprecated__))
                                           ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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-3.11-bioc/meat/diffuStats.buildbin-libdir/00LOCK-diffuStats/00new/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 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 (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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/Resources/lib/libquadmath.0.dylib" "diffuStats.buildbin-libdir/diffuStats/libs//diffuStats.so"