data61 / gossamer

Gossamer bioinformatics suite
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Try ubuntu trusty #7

Open axman6 opened 7 years ago

axman6 commented 7 years ago

Working in this branch until I can get travis working.

This is probably a dead end, once we find a proper fix I'll delete this, but it might be a good place to experiment in the mean time

axman6 commented 7 years ago

@Deguerre I think I've got travis working as far as I can without delving into the C++ side of things, if you get a few minutes would you mind having a look at the failing build on travis? Excerpt from the build:

Linking CXX static library libelectusapp.a
[ 30%] Built target electusapp
Scanning dependencies of target electus
[ 30%] Building CXX object src/CMakeFiles/electus.dir/electus.cc.o
Linking CXX executable electus
libgosslib.a(PhysicalFileFactory.cc.o): In function `boost::filesystem::copy_file(boost::filesystem::path const&, boost::filesystem::path const&)':
PhysicalFileFactory.cc:(.text._ZN5boost10filesystem9copy_fileERKNS0_4pathES3_[_ZN5boost10filesystem9copy_fileERKNS0_4pathES3_]+0x24): undefined reference to `boost::filesystem::detail::copy_file(boost::filesystem::path const&, boost::filesystem::path const&, boost::filesystem::copy_option, boost::system::error_code*)'
collect2: error: ld returned 1 exit status
make[2]: *** [src/electus] Error 1
make[1]: *** [src/CMakeFiles/electus.dir/all] Error 2
make: *** [all] Error 2
The command "make && make test" exited with 2.

Once this is all sorted, I'll add the covered build status icon to the README =)

Deguerre commented 7 years ago

That is precisely the issue I had building on Ubuntu 14. The default boost is build with the old (pre-C++11) ABI.