Re: Status of Altree
Hi,
Sorry for not answering the previous mail. I exchanged a few mails
with Claire about it and then I completely forgot about it.
Claire released altree 1.2 today. This version can be packaged.
You can work from the patch in attachment if you want.
Note that this version of altree requires two new dependencies.
These are both perl packages that are wrapper to existing, already
packaged C libraries.
I wrote these perl packages and did a initial packaging that I refresh
today (so they should be ok to be uploaded). You can find the work on
these packages here:
http://git.ligforge.imag.fr/?p=users/vdanjean/bio/libgsl-perl.git;a=summary
http://git.ligforge.imag.fr/?p=users/vdanjean/bio/libtamuanova-perl.git;a=summary
Development of the perl packages themselves can be found here:
http://git.ligforge.imag.fr/?p=users/vdanjean/bio/gsl-perl.git;a=summary
http://git.ligforge.imag.fr/?p=users/vdanjean/bio/tamuanova-perl.git;a=summary
Do you want I upload libgsl-perl and libtamuanova-perl, or do you
want to do it yourself?
Regards,
Vincent
Le 22/04/2012 08:38, Andreas Tille a écrit :
> Hi again,
>
> please do not leave us alone with fixing RC bugs (#669551) in altree
> with not even give us some status information. I do not mind about
> this bug which is simple enough to fix - but I always are pretty
> unsure whether to package the latest version per version number on
>
> http://claire.bardel.free.fr/files/
>
> or whether your arguing on
>
> http://lists.debian.org/debian-med/2009/08/msg00104.html
>
> remains valid even for the 1.1.1 version. I can not imagine that
> somebody has so less time to not even answer this simple question.
>
> For the moment I changed debian/watch in a way that it hides version
> 1.1.1 from our view and I really hope that this is in your interest.
>
> Kind regards
>
> Andreas.
>
> On Mon, Mar 26, 2012 at 10:34:17AM +0200, Andreas Tille wrote:
>> Hi Vincent,
>>
>> some kind of yearly ping. It is a bit hard to handle this upgrade
>> problem because of a lack of communication. I think I understood that
>> you can not spend time on this problem however, I have suggested ways to
>> cope with this (temporary?) ENOTIME problem. Asking the Debian Perl
>> team or even Debian Med team for packaging the dependencies would not be
>> a big deal. But we need your input about the stability of the newer
>> version. Your last statement[1] about the stability of new version is a
>> bit outdated. As a hint for upstream: If you are not sure about the
>> stability of a version it is better not to release it and rather mark
>> clearly the alpha / beta status in the version string.
>>
>> Please give some reasonable advise to the Debian Med team, which could
>> be:
>>
>> 1. Update the currently avialable package of verison 1.0.1
>> (in this case I would really love if you would rename your
>> upstream tarball to 1.1.0{alpha,beta} or something like this
>> which enables us adapting the watch file to not fetch this)
>> 2. Confirm that 1.1.0 is stable and can be packaged
>> 3. Altree should be removed from Debian at all because it is
>> unmaintained.
>> 4. ???
>>
>> Kind regards
>>
>> Andreas.
>>
>> [1] http://lists.debian.org/debian-med/2009/08/msg00104.html
>>
>> On Fri, Mar 25, 2011 at 08:48:06AM +0100, Andreas Tille wrote:
>>> Hi Vincent,
>>>
>>> I have not heard for one year from you. Please give us a short update
>>> about altree. As I suggested we might ask the help of the Perl team to
>>> get the needed preconditions packaged. However, we need to know whether
>>> this is worth the effort. Your last statements about the status of
>>> altree were not completely clear to me.
>>>
>>> Kind regards
>>>
>>> Andreas.
>>>
>>>
>>> On Tue, Mar 23, 2010 at 12:39:37PM +0100, Vincent Danjean wrote:
>>>> Hi,
>>>>
>>>> On 23/03/2010 11:42, Andreas Tille wrote:
>>>>> Hi again Vincent,
>>>>>
>>>>> Update about libnanova: I had a look into your packaging[3] which seems
>>>>> OK so far and interesting for Debian Med. Unfortunately I'm missing
>>>>> information about the library at the mentioned homepage. It lists some
>>>>> information about Claire Bardel-Danjean (your wife ;-))
>>>>
>>>> Yes, and I stress her so that she answers instead of feeding the baby :-)
>>>>
>>>>> but nothing about the library and where to download potential future releases.
>>>>
>>>> Nanova (and the perl bindings NAnova) is a implementation of Nested Anova
>>>> wrote by Claire and me following an old research paper.
>>>> I ask Claire to fill the documentation in order to cite this article
>>>> but also to explain that this method does not work in all cases
>>>> (sometimes, variance estimations give negative results...)
>>>>
>>>>> Could you please clarify a bit?
>>>>
>>>> The idea would be to add some documentation (article references,
>>>> problems and perl module documentation) and make a 'official' release.
>>>> The tar.gz will somewhere on http://claire.bardel.free.fr/software.html
>>>>
>>>> Claire : do you think you can do that this week ?
>>>>
>>>> Regards,
>>>> Vincent
>>>>
>>>>> Kind regards
>>>>>
>>>>> Andreas.
>>>>>
>>>>> On Fri, Mar 19, 2010 at 10:06:04AM +0100, Andreas Tille wrote:
>>>>>> Hi Vincent,
>>>>>>
>>>>>> once you wrote on this list[1] that the new version of altree is not
>>>>>> really fit for an official package. Because there are some further new
>>>>>> versions I wonder whether you can give a status update. Moreover I
>>>>>> stumbled upon your repository of inofficial packages[2] which just
>>>>>> contains the preconditions for altree you mentioned in your mail[1]
>>>>>> (libtamuanova-perl, nanova and libnanova-perl). I wonder whether it is
>>>>>> a clever idea to make these preconditions really official packages to be
>>>>>> quick in a possible altree upgrade. We might aproach a freeze sooner or
>>>>>> later and then it is possible to late to integrate the preconditions.
>>>>>>
>>>>>> Kind regards and thanks for your work on altree
>>>>>>
>>>>>> Andreas.
>>>>>>
>>>>>> [1] http://lists.debian.org/debian-med/2009/08/msg00104.html
>>>>>> [2] http://moais.imag.fr/membres/vincent.danjean/deb.html
>>>>>
>>>>> [3] http://moais.imag.fr/membres/vincent.danjean/debian/pool/main/n/nanova/nanova_1.0-2.dsc
>>>>>
>>>>
>>>>
>>>> --
>>>> Vincent Danjean Adresse: Laboratoire d'Informatique de Grenoble
>>>> Téléphone: +33 4 76 61 20 11 ENSIMAG - antenne de Montbonnot
>>>> Fax: +33 4 76 61 20 99 ZIRST 51, avenue Jean Kuntzmann
>>>> Email: Vincent.Danjean@imag.fr 38330 Montbonnot Saint Martin
>>>>
>>>
>>> --
>>> http://fam-tille.de
>>>
>>>
>>> --
>>> To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
>>> with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
>>> Archive: http://lists.debian.org/20110325074806.GC18167@an3as.eu
>>>
>>>
>>
>> --
>> http://fam-tille.de
>>
>>
>> --
>> To UNSUBSCRIBE, email to debian-med-REQUEST@lists.debian.org
>> with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
>> Archive: http://lists.debian.org/20120326083417.GD16366@an3as.eu
>>
>>
>
--
Vincent Danjean Adresse: Laboratoire d'Informatique de Grenoble
Téléphone: +33 4 76 61 20 11 ENSIMAG - antenne de Montbonnot
Fax: +33 4 76 61 20 99 ZIRST 51, avenue Jean Kuntzmann
Email: Vincent.Danjean@imag.fr 38330 Montbonnot Saint Martin
diff --git a/debian/README.Debian b/debian/README.Debian
deleted file mode 100644
index 8241eff..0000000
--- a/debian/README.Debian
+++ /dev/null
@@ -1,24 +0,0 @@
-Altree for Debian
-=================
-
-Despite the fact that at the Altree Homepage
-
- http://claire.bardel.free.fr/software.html
-
-a newer version than the Debian packaged version 1.0.1 is
-available (the download area
-
- http://claire.bardel.free.fr/files/
-
-even has version 1.1.1 while homepage says 1.1.0) the upstream author
-has asked the Debian Med team to not package this version:
-
- http://lists.debian.org/debian-med/2009/08/msg00104.html
-
-Despite frequent pings we are not really sure whether this remains
-the case and thjus we would like to ask you as the user to verify
-the newer version with your data and report back whether it might
-be helpful for you to also have the new altree version. Just send
-a bug report using `reportbug altree` to give us a notice.
-
- -- Andreas Tille <tille@debian.org> Sun, 22 Apr 2012 08:40:48 +0200
diff --git a/debian/changelog b/debian/changelog
index 7eb1a40..183c424 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+altree (1.2-1) UNRELEASED; urgency=low
+
+ * New (stable) upstream release 1.2
+ * debian/{README.Debian,watch}: No need to skip old last version 1.1.1
+ * debian/patches/*: latex bug fixed upstream
+
+ -- Vincent Danjean <vdanjean@debian.org> Sun, 22 Apr 2012 23:17:38 +0200
+
altree (1.0.1-7) unstable; urgency=low
[ Thorsten Alteholz ]
diff --git a/debian/control b/debian/control
index 417ff7c..f38877d 100644
--- a/debian/control
+++ b/debian/control
@@ -19,7 +19,7 @@ Architecture: any
Conflicts: libcutils-perl, alphy
Replaces: libcutils-perl, alphy
Provides: libcutils-perl, alphy
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, libtamuanova-perl, libgsl-perl
Suggests: altree-examples
Description: program to perform phylogeny-based association and localization analysis
ALTree was designed to perform association detection and localization of
diff --git a/debian/patches/build-with-recent-tetex.patch b/debian/patches/build-with-recent-tetex.patch
deleted file mode 100644
index 445faeb..0000000
--- a/debian/patches/build-with-recent-tetex.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Date: Sun, 22 Apr 2012 08:40:48 +0200
-Bug-Closed: http://bugs.debian.org/669551
-Description: Recent TeTeX fails to build documentation when using
- dvips option
-
---- altree-1.0.1.orig/Documentation/manual.tex
-+++ altree-1.0.1/Documentation/manual.tex
-@@ -1,4 +1,4 @@
--\documentclass[dvips, a4paper, 11pt,nocolor]{report}
-+\documentclass[a4paper, 11pt,nocolor]{report}
-
- %%%%%%%%%%%%%%%%%%%%%%%% PACKAGES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index d56f9e5..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1 +0,0 @@
-build-with-recent-tetex.patch
diff --git a/debian/watch b/debian/watch
index b2f266f..8c468d0 100644
--- a/debian/watch
+++ b/debian/watch
@@ -1,7 +1,3 @@
version=3
-# According to
-# http://lists.debian.org/debian-med/2009/08/msg00104.html
-# upstream author does not want version 1.1.1 be packaged
-opts="uversionmangle=s/1\.1\.1/0.not-for-us/" \
- http://claire.bardel.free.fr/files/altree-([\d.]+)\.tar\.gz
+http://claire.bardel.free.fr/files/altree-([\d.]+)\.tar\.gz
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