Hello Andreas, I did a
debcheckout --user <me> git://git.debian.org/debian-med/mugsy.git \ --git-track '*' and then tried git-buildpackage -uc -us which gives me a gbp:error: upstream/1r2.3+dfsg is not a valid treeish I guess you have to do a "git push --tags". I also have two dead links in the source tree mugsyWGA -> mugsy-seqan/projects/library/apps/mugsy/gcc/mugsy synchain-mugsy -> chaining/synchain-mugsy The latter one is properly set when the build starts, the first one not, that is at least not before the build fails. dpkg-buildpackage -uc -us -b starts and I get all the errors. The first series of errors is related to the fact that mugsy-seqan/projects/library/apps/mugsy/rna_alphabet.h contains what seems to be a copy of /usr/include/seqan/basic/alphabet_residue.h with a slightly different naming scheme. Which means one can remove the line 36 #include "rna_alphabet.h" from mugsy.cpp, BUT! I do not know if the underlying code really does the same. That's why I didn't upload this change. Does the package actually provide tests? The remaining errors are primarily related to differences in the bundled seqan and the installed one (I used 1.4.1+dfsg-2). I have no idea how to fix these. Then there are also a few errors that seem to be related to the more restrictive handling of C++ with newer compilers. I happily step in again to fix these if someone else was able to correct the seqan version related errors. Best, Gert On Wed, 2015-04-15 at 09:39 +0200, Andreas Tille wrote: > Hi, > > I've got some request to package mugsy which I started in Git[1]. The > source contained several code copies. I think I sorted out the code > copy of mummer by adding the patches contained in mugsy to the Debian > packaged mummer (see my last upload). > > I also tried to get rid of the outdated seqan copy but this creates > several issues of kind > > In file included from mugsy/mugsy.cpp:36:0: > mugsy/rna_alphabet.h:183:40: error: conflicting declaration 'typedef class > seqan::SimpleType<unsigned char, seqan::_Rna> seqan::Rna' > typedef SimpleType<unsigned char,_Rna> Rna;^M > ^ > In file included from /usr/include/seqan/basic/basic_alphabet.h:90:0, > from /usr/include/seqan/basic.h:68, > from mugsy/mugsy.cpp:29: > /usr/include/seqan/basic/alphabet_residue.h:402:41: note: previous > declaration as 'typedef class seqan::SimpleType<unsigned char, seqan::Rna_> > seqan::Rna' > typedef SimpleType<unsigned char, Rna_> Rna; > ^ > In file included from mugsy/mugsy.cpp:36:0: > mugsy/rna_alphabet.h:185:20: error: redefinition of 'struct > seqan::ValueSize<seqan::SimpleType<unsigned char, seqan::Rna_> >' > template <> struct ValueSize< Rna > { enum { VALUE = 4 }; };^M > ^ > In file included from /usr/include/seqan/basic/basic_alphabet.h:90:0, > from /usr/include/seqan/basic.h:68, > from mugsy/mugsy.cpp:29: > /usr/include/seqan/basic/alphabet_residue.h:405:8: error: previous definition > of 'struct seqan::ValueSize<seqan::SimpleType<unsigned char, seqan::Rna_> >' > struct ValueSize<Rna> > ^ > In file included from mugsy/mugsy.cpp:36:0: > mugsy/rna_alphabet.h:186:20: error: redefinition of 'struct > seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::Rna_> >' > template <> struct BitsPerValue< Rna > { enum { VALUE = 2 }; };^M > ^ > ... > > > Just use git-buildpackage on [1] to see more of them. My C++ knowledge > is basically zero so I do not feel able to fix this what seems to be a > simple task for a C++ programmer. Before I'll direct this question to > debian-mentors I'd like to test whether I can get some help on our list. > > Kind regards > > Andreas. > > [1] git://anonscm.debian.org/debian-med/mugsy.git > > -- > http://fam-tille.de > >
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