Issue with make

[joshhjang]

Hi,

I downloaded via "git clone --recursive https://github.com/getzlab/rnaseqc.git". After cd to rnaseqc, I tried to use make command and got hit with this error:

"g++ -Wall -std=c++14 -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -I. -ISeqLib -ISeqLib/htslib/ -c -o src/BED.o src/BED.cpp g++: error: unrecognized command line option ‘-std=c++14’ make: *** [src/BED.o] Error 1"

Any help with this issue will be much appreciated!

PS. Also, the collapse gtf code is no longer available. Do you mind providing alternative source? Thank you!

[agraubert]

To your first question, you need to make sure your GCC version is at least 5.2. Prior versions do not include support for c++14.

To the second, we apologize for the broken link but it is now fixed. You can access the collapsing script here

[joshhjang]

Thanks so much for your help and the collapsing script! Using gcc 7.5.0, I was able to overcome the previous issue. However, I'm hit with another error:

src/GTF.o: In function `boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_match()':
GTF.cpp:(.text._ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x2c7): undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'
collect2: error: ld returned 1 exit status
make: *** [rnaseqc] Error 1

Thanks again and sorry for the inconvenience.

[agraubert]

Linker errors can be hard to pin down, but I think this could be one of three things: 1) It's possible that it's an issue with the new C++ string ABI, in which case, you can disable RNA-SeQC's usage of that feature by setting this to 0 in your Makefile. You might have to run make clean in both the rnaseqc and seqlib directories (and possibly just delete seqlib/lib). After that, try make again to rebuild it. Disabling the ABI shouldn't effect RNA-SeQC's performance 2) It's also possible that your boost libraries are not compatible with this version of the C++ standard library. This probably isn't the issue, as boost tries to maintain backwards compatibility, but maybe it's not working here. I would try reinstalling/updating your boost libraries to the latest version. 3) Lastly, you could try lowering the C++ standard library version that RNA-SeQC uses here from std++14 to std++11, but I cannot guarantee that that won't just make things worse.

If possible, I would recommend using the pre-compiled binaries that we distribute on our releases page. These should work on any Linux or OSX platform, but I understand that there are situations where compiling from source is more viable

[agraubert]

Closing due to inactivity. Feel free to comment and reopen if you're still having this problem