Bug 405631 – sci-biology/ncbi-tools++ version bump request

• Product: Gentoo Linux
• Status: RESOLVED OBSOLETE

[Description Joel Berendzen 2012-02-24 17:21:06 UTC]

ncbi-tools++ has moved to a new version and version numbering scheme (7.0.0) as of June, 2011.

ncbi-tools++-2010.06.15-r1 no longer compiles because of dependencies on libpng14 which is no longer in portage, despite the patch for libpng15.

The e-build needs some dependencies added, as documented in another bug report.

I'd like to request a version bump.

Reproducible: Always

[Comment 1 Justin Lecher (RETIRED) 2012-02-24 17:35:37 UTC]

boohoo :D
I will take a look into that bump. I have a nearly complete patch for the complete dependency tracking. Hope I will find time soonish

[Comment 2 Joel Berendzen 2012-02-24 17:58:44 UTC]

(In reply to comment #1)
> boohoo :D
> I will take a look into that bump. I have a nearly complete patch for the
> complete dependency tracking. Hope I will find time soonish

Thanks, Justin.  Personally, I think the EMBOSS mess for which you are the stuckee is higher-priority and harder to workaround.

[Comment 3 Justin Lecher (RETIRED) 2014-01-01 19:09:25 UTC]

There is a half working ebuild in the sci overlay. Anybody is free to contribute there.

[Comment 4 Pacho Ramos 2014-04-06 11:04:04 UTC]

Since this is still blocking gnutls-3 stabilization, maybe we should either put that overlay version in the tree or point people to use that one and lastrite the one in main tree :/

What do you think?

[Comment 5 Justin Lecher (RETIRED) 2014-04-06 11:09:47 UTC]

(In reply to Pacho Ramos from comment #4)
> Since this is still blocking gnutls-3 stabilization, maybe we should either
> put that overlay version in the tree or point people to use that one and
> lastrite the one in main tree :/
> 
> What do you think?

If we lastrite this one, we will also quite some other packages. The version in the overlay is not really prime time. And I have no time to work on that at the moment. That's the status.

The main issue is, that the package is huge, uses a custom buildsystem with weirdest dep tracking and misuses autotools --with options. If you/someone could look into the ebuild in the sci overlay we ca rescue the package.

[Comment 6 Joel Berendzen 2014-04-10 23:10:10 UTC]

(In reply to Justin Lecher from comment #5)
> (In reply to Pacho Ramos from comment #4)
> > Since this is still blocking gnutls-3 stabilization, maybe we should either
> > put that overlay version in the tree or point people to use that one and
> > lastrite the one in main tree :/
> > 
> > What do you think?
> 
> If we lastrite this one, we will also quite some other packages. The version
> in the overlay is not really prime time. And I have no time to work on that
> at the moment. That's the status.
> 
> The main issue is, that the package is huge, uses a custom buildsystem with
> weirdest dep tracking and misuses autotools --with options. If you/someone
> could look into the ebuild in the sci overlay we ca rescue the package.

Agreed, this package is both too unwieldy to fix quickly and too important to ignore.  Among the software this package provides is BLAST, which has been estimated from citation counts to be the most widely-used scientific software in existence.  

I don't have the time for it either, unfortunately.  This and EMBOSS both need some serious attention from someone.

[Comment 7 Robin Johnson 2014-08-03 20:35:18 UTC]

ncbi-tools++ was removed from the tree it seems, so these bugs aren't relevant anymore.