Package: BiocParallel

Version: 1.18.1

Command: rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocParallel_1.18.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BiocParallel.buildbin-libdir

StartedAt: 2019-10-16 08:13:53 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 08:14:16 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 23.5 seconds

RetCode: 0

Status:  OK

PackageFile: BiocParallel_1.18.1.tgz

PackageFileSize: 1.046 MiB

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### Running command:
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###   rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocParallel_1.18.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R BiocParallel.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.18.1.tar.gz'
>>>>>>> 

* installing *source* package ‘BiocParallel’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for shm_open in -lrt... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c ipcmutex.cpp -o ipcmutex.o
In file included from ipcmutex.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/uuid/uuid_generators.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/uuid/random_generator.hpp:17:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/mersenne_twister.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/seed_impl.hpp:26:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/const_mod.hpp:23:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/large_arithmetic.hpp:19:
In file included from /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/random/detail/integer_log2.hpp:19:
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/pending/integer_log2.hpp:7:1: warning: This header is deprecated. Use  instead. [-W#pragma-messages]
BOOST_HEADER_DEPRECATED("");
^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/header_deprecated.hpp:23:37: note: expanded from macro 'BOOST_HEADER_DEPRECATED'
# define BOOST_HEADER_DEPRECATED(a) BOOST_PRAGMA_MESSAGE("This header is deprecated. Use " a " instead.")
                                    ^
/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include/boost/config/pragma_message.hpp:24:34: note: expanded from macro 'BOOST_PRAGMA_MESSAGE'
# define BOOST_PRAGMA_MESSAGE(x) _Pragma(BOOST_STRINGIZE(message(x)))
                                 ^
:177:2: note: expanded from here
 message("This header is deprecated. Use " "" " instead.")
 ^
1 warning generated.
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 BiocParallel.so ipcmutex.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/BiocParallel.buildbin-libdir/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel)


>>>>>>> 
>>>>>>> FIXING LINKS FOR BiocParallel.buildbin-libdir/BiocParallel/libs//BiocParallel.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" "BiocParallel.buildbin-libdir/BiocParallel/libs//BiocParallel.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "BiocParallel.buildbin-libdir/BiocParallel/libs//BiocParallel.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" "BiocParallel.buildbin-libdir/BiocParallel/libs//BiocParallel.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "BiocParallel.buildbin-libdir/BiocParallel/libs//BiocParallel.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "BiocParallel.buildbin-libdir/BiocParallel/libs//BiocParallel.so"