Hello Joshua,
I would be much of a fan to see interpro-scan redistributed with Debian.
Andreas' concern is that nobody understands what happened. We have
Hammer2 in our distribution https://packages.debian.org/sid/hmmer2 and
if your work is plain compatible then I don't see why it should not
substitute it. Is there a way to keep hmmer2-pvm? There are not too
many on https://qa.debian.org/popcon.php?package=hmmer2 using it but I
would not want to ruin established services anywhere with an apt-get update.
Best,
Steffen
On 04.01.19 16:25, Joshua Marshall wrote:
> Hello all,
>
> In Spring 2018 I was working on packaging interpro-scan for some
> work. There were a number of packages which has some build or test
> failures which I worked on. Of these, Hmmer needed some more
> attention. Originally, this was an upstream request to tweak their
> autoconf but that went bizarrely bad. At that point, I went in to fix
> up a decade's worth of technical debt. Of these were removal of
> Parallel Virtual Machine support, adjusting buffer sizes upwards for
> memory found on modern systems, hard code enabling of pthreads,
> renaming executable to hmmer2 in the build to not conflict with hmmer
> or hmmer3 to allow for parallel installation, and simplification of
> the configuration header. All unit tests pass. There is a need for
> parallel installation of hmmer2 and hmmer3 because hmmer2 works on a
> global genome scale, while hmmer3 is build to only operate on parts of
> the genome.
>
> This should have do change in behavior or output in any way except for
> removal of PVM support and minor runtime changes. This change set
> should be viewed strictly as a technical debt clean up.
>
> On Fri, Jan 4, 2019 at 1:11 AM Andreas Tille <andreas@fam-tille.de
> <mailto:andreas@fam-tille.de>> wrote:
>
> Hi Joshua,
>
> On Thu, Jan 03, 2019 at 04:45:33PM -0500, Joshua Marshall wrote:
> > Is now a better time to bring up my Hmmer 2 fork?
>
> Please shortly describe the purpose of your fork the changes you
> did on the list and than we can (probably/hopefully) replace the
> existing hmmer2 package by your fork. I'm *not* a hmmer2 user
> (nor do I have the slightest idea what hmmer2 is doing - I'm not
> a biologist) so it makes no sense to discuss this just with me.
> Thus I'm posting this on the list.
>
> For other readers here are some links to previous posts about
> this issue:
>
> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066203.html
> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066757.html
> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-October/066762.html
> https://alioth-lists.debian.net/pipermail/debian-med-packaging/2018-November/066997.html
>
> My prefered way to deal with this would be to point the debian/watch
> file of hmmer2 to
>
> https://github.com/anadon/hmmer2/releases
>
> and package the latest release from there (instead of applying huge
> patches that nobody can read or maintain) but please document the
> relation to the official hmmer2, your fork/continuation and hmmer3
> at an easily accessible place.
>
> Kind regards
>
> Andreas.
>
> > On Sun, Oct 28, 2018 at 4:47 PM jrmarsha <jrmarsha@mtu.edu
> <mailto:jrmarsha@mtu.edu>> wrote:
> >
> > > I'm sorry.
> > >
> > > On 10/28/18 4:15 PM, Andreas Tille wrote:
> > > > Hi,
> > > >
> > > > the list is archived:
> > > >
> > > > https://lists.debian.org/debian-med/2018/10/threads.html
> > > >
> > > > Please do not expect always prompt responses - sometimes
> volunteers
> > > > have other things to do.
> > > >
> > > > Kind regards
> > > >
> > > > Andreas.
> > > >
> > > > On Sun, Oct 28, 2018 at 09:03:27AM -0400, jrmarsha wrote:
> > > >> Hello,
> > > >>
> > > >>
> > > >> I've tried sending a few messages but I've gotten no
> response. Are they
> > > >> making it to the debian-med mailing list.
> > > >>
> > > >>
> > >
>
> --
> http://fam-tille.de
>