[Debian-med-packaging] Bug#558852: Need some help with EMBOSS, that links to too many libraries.

[Charles Plessy]

tag 558852 + help
thanks

Dear all,

I have problems with controlling how the emboss packages are linked to libraries.

As you can see in http://bugs.debian.org/558852: 

1) Some libraries that should be linked are not. In the bug report there are
   some hints on how to iteratively figure out which Makefiles to changes, but I
   am not understanding C well enough to write a clear explanation for Upstream
   when the patch will be ready.

2) Some libraries are linked, but should not. I have read the thread about
   ‘-Wl, --as-needed’, but again, I am reaching my limits in programming, and
   could not figure out if using it was appropriate or not.

Point 2) is particularly problematic. Packages that are built on the EMBOSS
ajax and nucleus libraries–the EMBASSY packages–have increased
build-dependancies (binary dependancies seem to be cleaned well by ‘-Wl,
--as-needed’).

Since version 6.3, EMBOSS depends on MySQL and PostgreSQL. This gives it the
capacity to use remote databases, in particular from ENSEMBL, and although I
did not have time to test this feature, I think that it is important enough to
be enabled by default. However, as long as the linking problem explained above
is not solved, it makes the embassy-* packages build-depend on libpq-dev and
libmysqlclient-dev, which really looks wrong.

This situation is particuarly embarassing since the embassy-* packages all have
a RC bug: EMBOSS in testing is version 6.1; in sid it is version 6.3, and the
embassy packages in testing build only against version 6.2.

Here are the possible solutions:

 - Remove the EMBASSY packages from testing.
 - Upload EMBOSS 6.2 to testing-proposed-updates.
 - Upgrade embassy packages with the latest upstream version, that builds
   against EMBOSS 6.3.

I would have a strong preference for upgrading all to 6.3 (that support SAM
format–a must in 2010) and negociate with the release team for a freeze
exception, but in that case I think that the packages really need to be high
quality, which in my opinion means fixing the emboss packages so that the
embassy packages do not need to build-depend on libpq-dev and
libmysqlclient-dev.

So I would really appreciate some help or comments from people more competent
with libraries and linking.

Have a nice day,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan