Re: [Seqan-dev] MarkovModel

[John Reid <j.reid@mail.cryst.bbk.ac.uk>]

Subject:

Re: [Seqan-dev] MarkovModel

From:

David Weese <weese@campus.fu-berlin.de>

Date:

Sat, 31 Oct 2009 10:10:36 +0100

To:

SeqAn Development <seqan-dev@lists.fu-berlin.de>

To:

SeqAn Development <seqan-dev@lists.fu-berlin.de>

Hi John,

you are absolutely right. I fixed that. Just make an SVN update. I
reported the Trac problem to our admins.

Ciao,
Dave

  

I did a svn update and I still have the following problem. This is the content of the ticket I could not create:

The following code does not compile with the latest svn version of seqan (rev 5003)

{{{
#include <seqan/index.h>
#include <seqan/statistical_index.h>

using namespace seqan;

int main()
{
    const size_t order = 0;
    MarkovModel< Dna5 > mm( order );
    typedef String< Dna5 > string_t;
    StringSet< string_t > X;
    mm.build( X );
    return 0;
}
}}}

With gcc 4.4.1 I get the following compilation error:
{{{
In file included from /home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index.h:35,
from src/sandbox/seqan_sandbox_markov_model.cpp:6:
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h: In member function ‘void seqan::MarkovModel<
        seqan::SimpleType<unsigned char, seqan::_Dna5>, double, const seqan::Tag<seqan::Default_> >::_computeAuxiliaryMatrices()’:
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:180:   instantiated from ‘void seqan::MarkovModel<
        seqan::SimpleType<unsigned char, seqan::_Dna5>, double, const seqan::Tag<seqan::Default_>
    >::build(seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna5>, seqan::Alloc<void> >, seqan::Owner<const seqan::Tag<seqan::Default_> > > &)’
src/sandbox/seqan_sandbox_markov_model.cpp:16:   instantiated from here
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:400: error: No match for ‘_matricialSum(
        seqan::String<double, seqan::Alloc<void> >, seqan::String<double, seqan::Alloc<void> > &, const unsigned int &)’
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:522: candidates are: seqan::String<
        TValue, seqan::Alloc<void> > seqan::_matricialSum(seqan::String<TValue, TSpec> &, seqan::String<TValue, TStringSpec> &, unsigned int)
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:403: error: invalid initialization of non-const reference of type ‘seqan::String<
        double, seqan::Alloc<void> > &’ from a temporary of type ‘seqan::String<double, seqan::Alloc<void>>’
/home/john/Dev/ThirdParty/C++/seqan-svn/projects/library/seqan/statistical_index/statistical_index_markov_model.h:485: error: in passing argument 1 of ‘seqan::String<TValue, seqan::Alloc<void> >
    seqan::_matricialProduct(seqan::String<TValue, TSpec> &, seqan::String<TValue, TStringSpec> &, unsigned int)’
}}}