PVM is no longer maintained, and hasn't been for quite some time. The use case for when PVM is relevant is when RAM on individual machines was closer to 16M. Given that we have $5 computers with 256MB, I find it reasonable to tell such users to upgrade.As for interpro-scan, most of the documents got updated for the project and it is easier to set up locally. However, there is still a large amount of work that goes into updates every few days to a few weeks and users should rely on the service rather than a package. If you do want to have the package, you need a employee charged with it's regular updates and development because of how involved and federated that particular program set is.On Fri, Jan 4, 2019 at 10:41 AM Steffen Möller <steffen_moeller@gmx.de> wrote: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
>