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 -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: http://lists.debian.org/[email protected]
