[Debian-med-packaging] Bug#848543: src:lambda-align: New version available

[Andreas Tille]

Package: src:lambda-align
Severity: normal

Hi Sascha,

I tried to upgrade lambda-align to latest upstream version in Git.
Unfortunately the build failed with:

...
/build/lambda-align-1.9.1/src/lambda.cpp:298:36:   required from 'int argConv4(LambdaOptions&, const TOutFormat&, const seqan::BlastTabularSpecSelector<h>&, const seqan::BlastProgramSelector<p>&, const TRedAlph&, const TScoreExtension&) [with TOutFormat = seqan::Tag<seqan::BlastTabular_>; TRedAlph = seqan::SimpleType<unsigned char, seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >; TScoreExtension = seqan::Tag<seqan::AffineGaps_>; seqan::BlastTabularSpec h = (seqan::BlastTabularSpec)1u; seqan::BlastProgram p = (seqan::BlastProgram)4u]'
/build/lambda-align-1.9.1/src/lambda.cpp:269:24:   required from 'int argConv3(LambdaOptions&, const TOutFormat&, const seqan::BlastTabularSpecSelector<h>&, const seqan::BlastProgramSelector<p>&, const TRedAlph&) [with TOutFormat = seqan::Tag<seqan::BlastTabular_>; TRedAlph = seqan::SimpleType<unsigned char, seqan::ReducedAminoAcid_<seqan::Tag<seqan::Murphy10_> > >; seqan::BlastTabularSpec h = (seqan::BlastTabularSpec)1u; seqan::BlastProgram p = (seqan::BlastProgram)4u]'
/build/lambda-align-1.9.1/src/lambda.cpp:224:28:   required from 'int argConv2(LambdaOptions&, const TOutFormat&, const seqan::BlastTabularSpecSelector<h>&, const seqan::BlastProgramSelector<p>&) [with TOutFormat = seqan::Tag<seqan::BlastTabular_>; seqan::BlastTabularSpec h = (seqan::BlastTabularSpec)1u; seqan::BlastProgram p = (seqan::BlastProgram)4u]'
/build/lambda-align-1.9.1/src/lambda.cpp:194:28:   required from 'int argConv1(LambdaOptions&, const TOutFormat&, const seqan::BlastTabularSpecSelector<h>&) [with TOutFormat = seqan::Tag<seqan::BlastTabular_>; seqan::BlastTabularSpec h = (seqan::BlastTabularSpec)1u]'
/build/lambda-align-1.9.1/src/lambda.cpp:152:104:   required from here
/build/lambda-align-1.9.1/src/lambda.hpp:2065:36: error: '_prepareAndRunSimdAlignment' was not declared in this scope
/build/lambda-align-1.9.1/src/options.hpp: In function 'void getCwd(TString&) [with TString = std::__cxx11::basic_string<char>]':
...

Could you please take over?

Kind regards

       Andreas.


-- System Information:
Debian Release: 8.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)