I am running Mac OS X 10.9.5.
I'm struggling to install Breakdancer.
I installed cmake (3.2.3) as required, with the command line option activated (symlink in my usr/bin/
folder)
I started Breakdancer compilation as recommended:
- 1st step works fine (
cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local
) - but 2nd step (
make
) fails:
Scanning dependencies of target boost-libs
[ 1%] Creating directories for 'boost-libs'
[ 3%] Performing download step (verify and extract) for 'boost-libs'
...
Scanning dependencies of target breakdancer
[ 43%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BedWriter.cpp.o
[ 45%] Building CXX object build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BreakDancer.cpp:1:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BreakDancer.hpp:3:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/breakdancer/BasicRegion.hpp:3:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/io/Alignment.hpp:3:
In file included from /Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/common/ReadFlags.hpp:5:
/Users/lab/TOOLS_VariantAnalysis/breakdancer/build/vendor/boost/boost/include/boost/array.hpp:62:11: error:
implicit instantiation of undefined template 'std::__1::basic_string<char,
std::__1::char_traits<char>, std::__1::allocator<char> >'
T elems[N]; // fixed-size array of elements of type T
^
/Users/lab/TOOLS_VariantAnalysis/breakdancer/src/lib/common/ReadFlags.hpp:41:37: note:
in instantiation of template class
'boost::array<std::__1::basic_string<char, std::__1::char_traits<char>,
std::__1::allocator<char> >, 11>' requested here
PerFlagArray<std::string>::type strings_;
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/iosfwd:188:33: note:
template is declared here
class _LIBCPP_TYPE_VIS_ONLY basic_string;
^
1 error generated.
make[2]: *** [build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/BreakDancer.cpp.o] Error 1
make[1]: *** [build/src/lib/breakdancer/CMakeFiles/breakdancer.dir/all] Error 2
make: *** [all] Error 2
Does anyone have a suggestion to solve this out ?
Fabrice
No problem. I'd love to know if the changes worked for you or not. I hope they do!