Source compile error about intarna

[martin-raden]

Hi @anselmic
it seems your compiler is a bit more stringent on the shared variables.
The quick fix is to remove "queryNumber" from the list of shared variables in line 233 of the IntaRNA.cpp file.
I will update the sources respectively soon.
Please let me know if this did the trick!
Thanks,
Martin

[anselmic]

Hi @martin-raden

Thank you for the quick answer. The quick fix worked for IntaRNA.o.
However, it seems I have problem linking the boost libraries. I have tried with different versions and freshly installed ones, but without luck.
Any suggestion is appreciated.

make[3]: Entering directory '/root/src/IntaRNA-3.3.1/src/bin'
CXX IntaRNA.o
CXX CommandLineParsing.o
CXXLD IntaRNA
IntaRNA.o: In function CommandLineParsing::getFullFilename(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, IntaRNA::RnaSequence const*, IntaRNA::RnaSequence const*) const': IntaRNA.cpp:(.text._ZNK18CommandLineParsing15getFullFilenameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKN7IntaRNA11RnaSequenceESB_[_ZNK18CommandLineParsing15getFullFilenameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKN7IntaRNA11RnaSequenceESB_]+0x3aa): undefined reference to boost::filesystem::path::extension_v3() const'
CommandLineParsing.o: In function CommandLineParsing::validate_outputTarget(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': CommandLineParsing.cpp:(.text._ZN18CommandLineParsing21validate_outputTargetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_[_ZN18CommandLineParsing21validate_outputTargetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_]+0x148): undefined reference to boost::filesystem::path::find_parent_path_size() const'
CommandLineParsing.cpp:(.text.ZN18CommandLineParsing21validate_outputTargetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7[ZN18CommandLineParsing21validate_outputTargetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7]+0x3fb): undefined reference to boost::filesystem::path::find_parent_path_size() const' CommandLineParsing.cpp:(.text._ZN18CommandLineParsing21validate_outputTargetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_[_ZN18CommandLineParsing21validate_outputTargetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_]+0x538): undefined reference to boost::filesystem::path::find_parent_path_size() const'
collect2: error: ld returned 1 exit status
make[3]: *** [Makefile:467: IntaRNA] Error 1
make[3]: Leaving directory '/root/src/IntaRNA-3.3.1/src/bin'
make[2]: *** [Makefile:577: all-recursive] Error 1
make[2]: Leaving directory '/root/src/IntaRNA-3.3.1/src'
make[1]: *** [Makefile:436: all] Error 2
make[1]: Leaving directory '/root/src/IntaRNA-3.3.1/src'
make: *** [Makefile:423: all-recursive] Error 1

[anselmic]

It compiled with --with-boost-libdir=...

[martin-raden]

👌