[Debian-med-packaging] Fwd: Updating Hmmer2 request

[Fabian Klötzl]

Hi Joshua,

Thank you for wanting to improve Hmmer for Debian users. However, I see
a few issues with your request. Note that this is my personal opinion
and I do not speak for the Debian Med team.


On 13.04.2018 19:47, Joshua Marshall wrote:
> Hmmer2 upstream is listed at 2.4i

The current version of hmmer2 in Debian is 2.3.2+dfsg-5, see [1].
Judging from the official homepage of Hmmer [2] that is indeed the
latest release.

> I have a few cleanups and fixes […] fix a few uninitialized variables

Most of these look minor, if not even superfluous [4, 5].

> which enable pthreads by default, remove support for PVM

Could you please go into detail, why you think this change is
necessary/an improvement?

> adding a default suffix of '2'

Debian already does that, I think [3]. And if not, renaming binaries
between two releases of a package will break existing workflows and
confuse a lot of users.

> So with that, I'd like to make the request to update to 2.5j.  Humor me
> if something with this is incorrect.  I think all guidelines are being
> met for posting.
> 

There are basically two ways to incorporate your changes into Debian. 1)
We could declare upstream as dead (even though they are not) and use
your repository as the "new official version". 2) We pile your changes
on top of the last public release 2.3.2. For this we require small patch
files each implementing one of the fixes you mentioned above. Having
just one big commit (your words) is problematic.

My favourite solution would be 2). I am looking forward to receiving
your patches.

Best,
Fabian


1: https://tracker.debian.org/pkg/hmmer2
2: http://hmmer.org/download.html
3: https://salsa.debian.org/med-team/hmmer2/blob/master/debian/rules#L33
4:
https://github.com/MichiganTech/hmmer/commit/4a9327d49cd25129ebef313f19db6d1034bd3d21#diff-92b08d78ee5212675b1339a03afc95ddR1451
5:
https://github.com/MichiganTech/hmmer/commit/4a9327d49cd25129ebef313f19db6d1034bd3d21#diff-ee177e329d3820670951a24d5ad0b521R985