Debian Bug report logs - #451193
RFP: vienna-rna -- RNA sequence analysis

Package: wnpp; Maintainer for wnpp is wnpp@debian.org;

Reported by: Steffen Moeller <steffen_moeller@gmx.de>

Date: Wed, 14 Nov 2007 01:03:01 UTC

Severity: wishlist

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Report forwarded to debian-bugs-dist@lists.debian.org, debian-devel@lists.debian.org, <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>:
Bug#451193; Package wnpp. Full text and rfc822 format available.

Acknowledgement sent to Steffen Moeller <steffen_moeller@gmx.de>:
New Bug report received and forwarded. Copy sent to debian-devel@lists.debian.org, <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>. Full text and rfc822 format available.

Message #5 received at submit@bugs.debian.org (full text, mbox):

From: Steffen Moeller <steffen_moeller@gmx.de>
To: Debian Bug Tracking System <submit@bugs.debian.org>
Subject: ITP: vienna-rna -- RNA sequence analysis
Date: Wed, 14 Nov 2007 02:01:22 +0100
Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <steffen_moeller@gmx.de>

* Package name    : vienna-rna
  Version         : 1.6.5
  Upstream Author : Ivo Hofacker
* URL             : http://www.tbi.univie.ac.at/~ivo/RNA/
* License         : non-free but redistributable
  Programming Lang: C
  Description     : RNA sequence analysis

The Vienna RNA Package consists of a C code library and several
stand-alone programs for the prediction and comparison of RNA secondary
structures.

An early version of the packaging is available via the subversion
repository of Debian-Med at debian-med.alioth.debian.org.




Information forwarded to debian-bugs-dist@lists.debian.org, <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>:
Bug#451193; Package wnpp. Full text and rfc822 format available.

Acknowledgement sent to charles-debian-nospam@plessy.org:
Extra info received and forwarded to list. Copy sent to <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>. Full text and rfc822 format available.

Message #10 received at 451193@bugs.debian.org (full text, mbox):

From: Charles Plessy <charles-debian-nospam@plessy.org>
To: 451193@bugs.debian.org
Cc: debian-med@lists.debian.org
Subject: Thoughts on the Vienna RNA package
Date: Wed, 14 Nov 2007 20:02:04 +0900
Hi all,

I had a look at the Vienna package, and here are a few thoughts about
the work to be done.

- It uses a patched version of Readseq. Maybe we should consider to
  build Vienna on Debian's readseq, possibly by adopting its patches if
  they are not disruptive. By the way, we could incorporate the Debian
  package for readseq in our repository, if its current maintainer
  agrees.

- The Vienna package provides libraries that other programs use. For
  instance, MiRanda, a sofware to discover targets of micro RNAs uses
  Vienna's RNAlib.

- Emboss provides some wrappers so we shoud probably package them as
  well.

- There are some build issues such as the Makefile in the Kinfold
  directory that has no distclean rule. Probably some autoconf mastery
  can solve the problem.

- The vienna-rna source package should probably be split into multiple
  binary packages, for instance RNAforester which is a distinct work.

- I do not have the impression that some commercial licences are sold,
  so maybe we have a chance of obtaining a relicencing ?

Have a nice day,

-- 
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan




Information forwarded to debian-bugs-dist@lists.debian.org, <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>:
Bug#451193; Package wnpp. Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <tillea@rki.de>:
Extra info received and forwarded to list. Copy sent to <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>. Full text and rfc822 format available.

Message #15 received at 451193@bugs.debian.org (full text, mbox):

From: Andreas Tille <tillea@rki.de>
To: Debian Med Project List <debian-med@lists.debian.org>
Cc: 451193@bugs.debian.org, Michael Schmitz <schmitz@debian.org>
Subject: ReadSeq (Was: Thoughts on the Vienna RNA package)
Date: Wed, 14 Nov 2007 13:20:06 +0100 (CET)
On Wed, 14 Nov 2007, Charles Plessy wrote:

> - It uses a patched version of Readseq. Maybe we should consider to
>  build Vienna on Debian's readseq, possibly by adopting its patches if
>  they are not disruptive. By the way, we could incorporate the Debian
>  package for readseq in our repository, if its current maintainer
>  agrees.

As a former maintainer of readseq I would like to clarify the situation
from my point of view:

  1. When I took over readseq in Nov 2001 the progress of rewriting
     it in Java which leaded to readseq2 [1] was nearly finished.
     The development on readseq1 (as it is packaged in Debian) was
     stopped according to the authors even at this time.

  2. I continued maintaining this upstream orphaned software because
     it was used by some users and a precondition for an other
     package of mine (arb).

  3. If anybody has reasonable patches we are probably free to do
     whatever we want (including becoming "upstream") because it
     is in public domain.  I would regard this as quite reasonable
     but we should discuss this plan with upstream anyway (perhaps
     to place reasonable links for interested users).

  4. I handed over the package to Michael Schmitz <schmitz@debian.org>
     (Changelog entry "took over from Andreas Tille 'cuz readseq is actually
     in use at our site").  I'm a little bit unsure whether this is
     valid until today - at least the package has some lintian
     problems and IMHO definitely needs polishing.  (Michael, are
     you able and willing to work on this package?)

My suggestion is that we immediately move the packaging stuff to Debian-Med
SVN and add Michael and mayelf to Uploaders, while the maintainer should
be the Debian-Med packaging team (Michael, I hope you would not regard this
as piracy ...).

Somebody should discuss with upstream whether they prefer that we
"release new versions" of readseq1 or that we maintain a set of patches
inside Debian.  In any way if there are good reasons to patch readseq
(working nicely with another package would be such a good reason) we
should just do it inside the Debian package.

BTW, I did not packaged the Java version because of the Java issues
(5 Jears ago) and because there was no explicite need for this.  If
somebody wants to build packages for readseq2 - just go for it.

Kind regards

        Andreas.

[1] http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

-- 
http://fam-tille.de




Information forwarded to debian-bugs-dist@lists.debian.org, <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>:
Bug#451193; Package wnpp. Full text and rfc822 format available.

Acknowledgement sent to Andreas Tille <tillea@rki.de>:
Extra info received and forwarded to list. Copy sent to <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>. Full text and rfc822 format available.

Message #20 received at 451193@bugs.debian.org (full text, mbox):

From: Andreas Tille <tillea@rki.de>
To: Debian Med Project List <debian-med@lists.debian.org>
Cc: 451193@bugs.debian.org
Subject: Re: Thoughts on the Vienna RNA package
Date: Wed, 14 Nov 2007 13:26:50 +0100 (CET)
[I did not checked code or website - just relay on the information of your mail]

On Wed, 14 Nov 2007, Charles Plessy wrote:

> - It uses a patched version of Readseq. Maybe we should consider to
>  build Vienna on Debian's readseq, possibly by adopting its patches if
>  they are not disruptive. By the way, we could incorporate the Debian
>  package for readseq in our repository, if its current maintainer
>  agrees.

See my other mail about readseq.

> - The Vienna package provides libraries that other programs use. For
>  instance, MiRanda, a sofware to discover targets of micro RNAs uses
>  Vienna's RNAlib.

In this case it should definitely go into a separate binary package.
Moreover we should verify that there is not a separate upstream package
of the library.  In this case we should stick to official library and
try to ask Vienna authors to remove copys of other parties code from
their upstream tarball (see aeskulap - dcmtk issue).

> - Emboss provides some wrappers so we shoud probably package them as
>  well.

Yes.

> - There are some build issues such as the Makefile in the Kinfold
>  directory that has no distclean rule. Probably some autoconf mastery
>  can solve the problem.

I had some good experiences with autoconf - sometimes upstream is
even accepting autoconf patches, but not always.

> - The vienna-rna source package should probably be split into multiple
>  binary packages, for instance RNAforester which is a distinct work.

I'm in favour of separate binary packages if there is a good chance
that people needs only a part of the whole functionality of the
upstream project.

> - I do not have the impression that some commercial licences are sold,
>  so maybe we have a chance of obtaining a relicencing ?

Without having read the license: DFSG free meens free for everybody
and not only free for Debian.  So I might have missunderstood you
but your proposal would not help to move it from non-free to main.
Or was you talking about getting it for non-free at all?

Kind regards

       Andreas.

-- 
http://fam-tille.de




Information forwarded to debian-bugs-dist@lists.debian.org, <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>:
Bug#451193; Package wnpp. Full text and rfc822 format available.

Acknowledgement sent to Michael Schmitz <schmitz@mail.biophys.uni-duesseldorf.de>:
Extra info received and forwarded to list. Copy sent to <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>. Full text and rfc822 format available.

Message #25 received at 451193@bugs.debian.org (full text, mbox):

From: Michael Schmitz <schmitz@mail.biophys.uni-duesseldorf.de>
To: Andreas Tille <tillea@rki.de>
Cc: Debian Med Project List <debian-med@lists.debian.org>, <451193@bugs.debian.org>, Michael Schmitz <schmitz@debian.org>
Subject: Re: ReadSeq (Was: Thoughts on the Vienna RNA package)
Date: Thu, 15 Nov 2007 04:30:00 +0100 (CET)
Hi,

> > - It uses a patched version of Readseq. Maybe we should consider to
> >  build Vienna on Debian's readseq, possibly by adopting its patches if
> >  they are not disruptive. By the way, we could incorporate the Debian
> >  package for readseq in our repository, if its current maintainer
> >  agrees.
>
> As a former maintainer of readseq I would like to clarify the situation
> from my point of view:
>
>    4. I handed over the package to Michael Schmitz <schmitz@debian.org>
>       (Changelog entry "took over from Andreas Tille 'cuz readseq is actually
>       in use at our site").  I'm a little bit unsure whether this is
>       valid until today - at least the package has some lintian
>       problems and IMHO definitely needs polishing.  (Michael, are
>       you able and willing to work on this package?)

I'm no longer at the lab in Duesseldorf but I could certainly continue to
work on it. The additions I put in to accomodate the use in Duesseldorf
should perhaps stay in, even though those guys mostly switched to bioperl
these days.

> My suggestion is that we immediately move the packaging stuff to Debian-Med
> SVN and add Michael and mayelf to Uploaders, while the maintainer should
> be the Debian-Med packaging team (Michael, I hope you would not regard this
> as piracy ...).

Not at all - I had pertty much forgotten about readseq.

> Somebody should discuss with upstream whether they prefer that we
> "release new versions" of readseq1 or that we maintain a set of patches
> inside Debian.  In any way if there are good reasons to patch readseq
> (working nicely with another package would be such a good reason) we
> should just do it inside the Debian package.

I believe there really is no upstream activity anymore. Patches for
supporting other packages is just what I did to it anyway, so keep
adding more (making sure it keeps working for the old test cases).

I had tried to get one of the bioinformatics guys involved as maintainer
with no success. If it comes to the worst, they will know who to blame.

	Michael





Severity set to `serious' from `wishlist' Request was from nbreen@ofb.net (Nicholas Breen) to control@bugs.debian.org. (Tue, 20 Nov 2007 03:39:03 GMT) Full text and rfc822 format available.

Information forwarded to debian-bugs-dist@lists.debian.org, <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>:
Bug#451193; Package wnpp. Full text and rfc822 format available.

Acknowledgement sent to nbreen@ofb.net (Nicholas Breen):
Extra info received and forwarded to list. Copy sent to <wnpp@debian.org>, steffen moeller <steffen_moeller@gmx.de>. Full text and rfc822 format available.

Message #32 received at 451193@bugs.debian.org (full text, mbox):

From: nbreen@ofb.net (Nicholas Breen)
To: control@bugs.debian.org, 451193@bugs.debian.org
Subject: Oops!
Date: Mon, 19 Nov 2007 19:53:14 -0800
severity 451193 wishlist
thanks

Sorry about that, I typo'ed the bug number I was aiming for (451993).





Severity set to `wishlist' from `serious' Request was from nbreen@ofb.net (Nicholas Breen) to control@bugs.debian.org. (Tue, 20 Nov 2007 03:54:04 GMT) Full text and rfc822 format available.

Information forwarded to debian-bugs-dist@lists.debian.org, wnpp@debian.org, steffen moeller <steffen_moeller@gmx.de>:
Bug#451193; Package wnpp. (Mon, 24 May 2010 09:39:20 GMT) Full text and rfc822 format available.

Acknowledgement sent to Lucas Nussbaum <lucas@debian.org>:
Extra info received and forwarded to list. Copy sent to wnpp@debian.org, steffen moeller <steffen_moeller@gmx.de>. (Mon, 24 May 2010 09:39:20 GMT) Full text and rfc822 format available.

Message #39 received at 451193@bugs.debian.org (full text, mbox):

From: Lucas Nussbaum <lucas@debian.org>
To: 451193@bugs.debian.org
Cc: control@bugs.debian.org
Subject: vienna-rna: changing back from ITP to RFP
Date: Mon, 24 May 2010 09:37:02 +0000
retitle 451193 RFP: vienna-rna -- RNA sequence analysis
noowner 451193
thanks

Hi,

This is an automatic email to change the status of vienna-rna back from ITP
(Intent to Package) to RFP (Request for Package), because this bug hasn't seen
any activity during the last 30 months.

If you are still interested in adopting vienna-rna, please send a mail to
<control@bugs.debian.org> with:

 retitle 451193 ITP: vienna-rna -- RNA sequence analysis
 owner 451193 !
 thanks

However, it is not recommended to keep ITP for a long time without acting on
the package, as it might cause other prospective maintainers to refrain from
adopting the package. It is also a good idea to document your progress on this
ITA from time to time, by mailing <451193@bugs.debian.org>.

Thank your for your interest in Debian,
-- 
Lucas, for the QA team




Changed Bug title to 'RFP: vienna-rna -- RNA sequence analysis' from 'ITP: vienna-rna -- RNA sequence analysis' Request was from Lucas Nussbaum <lucas@debian.org> to control@bugs.debian.org. (Mon, 24 May 2010 09:40:01 GMT) Full text and rfc822 format available.

Removed annotation that Bug was owned by steffen moeller <steffen_moeller@gmx.de>. Request was from Lucas Nussbaum <lucas@debian.org> to control@bugs.debian.org. (Mon, 24 May 2010 09:40:01 GMT) Full text and rfc822 format available.

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