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 I also tried to get rid of the outdated seqan copy but this creates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
>
>
signature.asc
Description: This is a digitally signed message part
