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BUILD BIN report for contiBAIT on merida1

This page was generated on 2019-04-16 11:59:18 -0400 (Tue, 16 Apr 2019).

Package 322/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
contiBAIT 1.10.1
Kieran O'Neill
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/contiBAIT
Branch: RELEASE_3_8
Last Commit: 750bd27
Last Changed Date: 2019-01-04 13:26:34 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: contiBAIT
Version: 1.10.1
Command: rm -rf contiBAIT.buildbin-libdir && mkdir contiBAIT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh contiBAIT_1.10.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R contiBAIT.buildbin-libdir
StartedAt: 2019-04-16 03:53:18 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:54:44 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 86.2 seconds
RetCode: 0
Status:  OK 
PackageFile: contiBAIT_1.10.1.tgz
PackageFileSize: 4.326 MiB

Command output

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### Running command:
###
###   rm -rf contiBAIT.buildbin-libdir && mkdir contiBAIT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh contiBAIT_1.10.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R contiBAIT.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=contiBAIT.buildbin-libdir contiBAIT_1.10.1.tar.gz'
>>>>>>> 

* installing *source* package ‘contiBAIT’ ...
** libs
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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c buildLinkageGroups.cpp -o buildLinkageGroups.o
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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c computeSim.cpp -o computeSim.o
In file included from computeSim.cpp:3:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/dynamic_bitset.hpp:15:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/dynamic_bitset/dynamic_bitset.hpp:47:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/move.hpp:30:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/iterator.hpp:27:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/iterator_traits.hpp:29:1: warning: inline namespaces are a C++11 feature [-Wc++11-inline-namespace]
BOOST_MOVE_STD_NS_BEG
^
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include/boost/move/detail/std_ns_begin.hpp:18:34: note: expanded from macro 'BOOST_MOVE_STD_NS_BEG'
   #define BOOST_MOVE_STD_NS_BEG _LIBCPP_BEGIN_NAMESPACE_STD
                                 ^
/usr/local/clang4/bin/../include/c++/v1/__config:388:52: note: expanded from macro '_LIBCPP_BEGIN_NAMESPACE_STD'
#define _LIBCPP_BEGIN_NAMESPACE_STD namespace std {inline namespace _LIBCPP_NAMESPACE {
                                                   ^
1 warning 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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c orderContigsGreedy.cpp -o orderContigsGreedy.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 contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.8-bioc/meat/contiBAIT.buildbin-libdir/contiBAIT/libs
** R
** data
** 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 (contiBAIT)


>>>>>>> 
>>>>>>> FIXING LINKS FOR contiBAIT.buildbin-libdir/contiBAIT/libs//contiBAIT.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" "contiBAIT.buildbin-libdir/contiBAIT/libs//contiBAIT.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "contiBAIT.buildbin-libdir/contiBAIT/libs//contiBAIT.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" "contiBAIT.buildbin-libdir/contiBAIT/libs//contiBAIT.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "contiBAIT.buildbin-libdir/contiBAIT/libs//contiBAIT.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "contiBAIT.buildbin-libdir/contiBAIT/libs//contiBAIT.so"