Hi, I am trying to make SPAdes 3.8.0 [1] (just entered unstable) build with Debian's packaged LLVM libraries instead of using the version bundled by upstream. I have made the necessary CMake changes [2] in a separate git branch [3] but run into a problem that seems to stem from within the LLVM code itself. At least I can't directly see a relation to the SPAdes code... but then again I'm better at C than C++ ;)
I was wondering if anyone could probably provide some assistance? Here's what I get: $ ./debian/rules build [...] In file included from /vagrant/spades/src/modules/pipeline/config_struct.cpp:20:0: /usr/lib/llvm-3.6/include/llvm/Support/YAMLTraits.h: In instantiation of 'typename std::enable_if<llvm::yaml::missingTraits<T>::value, void>::type llvm::yaml::yamlize(llvm::yaml::IO&, T&, bool) [with T = std::map<int, long unsigned int>; typename std::enable_if<llvm::yaml::missingTraits<T>::value, void>::type = void]': /usr/lib/llvm-3.6/include/llvm/Support/YAMLTraits.h:579:14: required from 'void llvm::yaml::IO::processKey(const char*, T&, bool) [with T = std::map<int, long unsigned int>]' /usr/lib/llvm-3.6/include/llvm/Support/YAMLTraits.h:528:5: required from 'typename std::enable_if<(! llvm::yaml::has_SequenceTraits<T>::value), void>::type llvm::yaml::IO::mapOptional(const char*, T&) [with T = std::map<int, long unsigned int>; typename std::enable_if<(! llvm::yaml::has_SequenceTraits<T>::value), void>::type = void]' /vagrant/spades/src/modules/pipeline/config_struct.cpp:41:79: required from here /usr/lib/llvm-3.6/include/llvm/Support/YAMLTraits.h:663:42: error: invalid application of 'sizeof' to incomplete type 'llvm::yaml::MissingTrait<std::map<int, long unsigned int> >' char missing_yaml_trait_for_type[sizeof(MissingTrait<T>)]; Does anyone see something obvious that I may have missed? Thanks in advance! Cheers Sascha [1] https://packages.qa.debian.org/s/spades.html [2] https://anonscm.debian.org/cgit/debian-med/spades.git/commit/?h=debian_llvm&id=94b326151eba4671dc266ac0d2198596a9363c43 [3] https://anonscm.debian.org/cgit/debian-med/spades.git/log/?h=debian_llvm -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.