Bug#461402: ITP: cl-unification -- Unification framework for common lisp

2008-01-18 Thread Philipp Benner
Package: wnpp
Severity: wishlist
Owner: Philipp Benner <[EMAIL PROTECTED]>

* Package name: cl-unification
  Upstream Author : Marco Antoniotti <[EMAIL PROTECTED]>
* URL : http://common-lisp.net/project/cl-unification/
* License : BSD
  Programming Lang: Lisp
  Description : Unification framework for common lisp

The library provides a full blown unification framework for Common Lisp.

The notion of unification originated in the field of formal logic
and has been used extensively in Computer Science and
Programming Languages. Most notably, Prolog uses the full power of
unification.


-- System Information:
Debian Release: lenny/sid
  APT prefers testing
  APT policy: (990, 'testing'), (500, 'unstable'), (500, 'stable')
Architecture: powerpc (ppc)

Kernel: Linux 2.6.18
Locale: LANG=en_IE.UTF-8, LC_CTYPE=en_IE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash

-- 
Philipp Benner



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Re: Possible mass bug filing: missing shared library dependencies

2008-01-18 Thread Loïc Minier
On Thu, Jan 17, 2008, Niko Tyni wrote:
> List of binary packages by maintainer ('dd-list -b') appended. I can't
> see any chance for false positives here, but please tell me if I'm wrong.

 I didn't find a list which included Uploaders information in the
 thread; could you repost a list with maintainer or uploader -> packages
 mappings for the next round?  (dd-list -u)

 To join the fun, I fixed these packages in SVN:

> Sebastien Bacher <[EMAIL PROTECTED]>
>libgtk2.0-dev
>libpango1.0-dev
> 
> Debian GNOME Maintainers <[EMAIL PROTECTED]>
>update-manager-core
> 
> Debian multimedia packages maintainers <[EMAIL PROTECTED]>
>liba52-0.7.4-dev
> 
> Loic Minier <[EMAIL PROTECTED]>
>libglib2.0-dev
> 
> Gustavo R. Montesino <[EMAIL PROTECTED]>
>libgnomedb2-dev

 lol:

> Debian ia32-libs Team <[EMAIL PROTECTED]>
>ia32-libs-gtk

-- 
Loïc Minier


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libburnia/libisofs/cdrskin in Debian.

2008-01-18 Thread Simon Huggins
The libburn packages in Debian are severely outdated and back in June I
tried to poke various people to see what was going on.

Sean Harshburger is nowhere to be seen despite mails, bugs and so on
dating back to August 2006 so I think can be called MIA.

cdrskin has been actively maintained as a statically linked binary
package and the most active contributor in Debian on this is George
Danchev who is almost all the way through NM now just waiting on DAM.
Eduard Bloch said he didn't really have enough time to do much with the
packages back in June.

George filed an RFH on cdrskin which is #450873

I've been looking at it periodically since I suggested that we just use
the Ubuntu packages more or less as is.

Since then upstream released 0.4.0 which broke the soname (shipped with
libburn.so.0 after libburn.so.4) but SVN has fixed this (so that's what
I packaged).  Upstream also ship a Makefile.am that deliberately builds
a static cdrskin that I don't quite get but anyway.

I've created new packages for libburn and libisofs based on the Ubuntu
ones but modified.  As I said I've made cdrskin dynamically linked.
I've kept Ubuntu's use of cdbs in the hope that we can standardise on
the same packaging (or almost) in both distributions.

If uploaded, they would replace the current cdrskin and libburn source
packages in the archive and the cdrskin, libburn-1, libburn-dev,
libisofs-1 and libisofs-dev binary packages.

They are currently available at:
http://the.earth.li/~huggie/libburn/
and at least cdskin works fine for me.  It's entirely possible I did
something stupid in which case send hot patches.

I really do think Debian needs something like this for its libburn and
cdrskin as the current situation is rather sad.  I'm happy to sponsor
them in for George to maintain and to continue to do so but I'd rather
not maintain them long term.

If no one objects I'll upload them in a week or two though I'd prefer
someone who really wants to maintain them changes the maintainer and
does so.

If anyone has any better ideas, let me know though if it is "we've had
lots of really good discussion about this and we've got a plan we're
going to implement RSN" then I'm not that interested as I was told that
in June.

-- 
 ,--huggie-at-earth-dot-listuff-thing-stuff--DF5CE2B4--.
_|  "JarJar Binks^W^WSupport for CRLF<->LF translation in the kernel   |_
 | must die." - Alexander Viro |
 ` http://www.earth.li/~huggie/ ---'


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ITP: libpoe-component-ikc-perl -- Perl Inter-Kernel Communication for POE

2008-01-18 Thread Ernesto Hernandez-Novich
Package: wnpp

* Package name: libpoe-component-ikc-perl
  Version: 0.2001
  Upstream Author: Philip Gwyn <[EMAIL PROTECTED]>
* URL: http://search.cpan.org/dist/POE-Component-IKC/
* License: GPL or Perl Artistic

Description:

POE::Component::IKC provides several Inter-Kernel Communication methods for POE
that help exchanging events between POE kernels.
-- 
Ernesto Hernández-Novich - Linux 2.6.18 i686 - Unix: Live free or die!
Geek by nature, Linux by choice, Debian of course.
If you can't aptitude it, it isn't useful or doesn't exist.
GPG Key Fingerprint = 438C 49A2 A8C7 E7D7 1500 C507 96D6 A3D6 2F4C 85E3


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Re: Possible mass bug filing: missing shared library dependencies

2008-01-18 Thread Olly Betts
On 2008-01-17, Niko Tyni <[EMAIL PROTECTED]> wrote:
> Olly Betts <[EMAIL PROTECTED]>
>xapian-examples

Now fixed in SVN.  In practice, the missing dependencies will be pulled
in by the dependency of libxapian15-dev, so I don't see much practical
benefit in uploading for just this change.

Cheers,
Olly


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Bug#461486: ITP: luxrender -- rendering system for physically correct 3D image synthesis

2008-01-18 Thread Cyril Brulebois
Package: wnpp
Severity: wishlist
Owner: Cyril Brulebois <[EMAIL PROTECTED]>

* Package name: luxrender
  Version : 0.1~rc4
  Upstream Authors: PHARR Matt <[EMAIL PROTECTED]>
HUMPHREYS Greg <[EMAIL PROTECTED]>
VERGAUWEN Terrence <[EMAIL PROTECTED]>
ROMANG Jean-Francois <[EMAIL PROTECTED]>
BIENKOWSKI Peter <[EMAIL PROTECTED]>
BECH Tom <[EMAIL PROTECTED]>
et al.
* URL : http://luxrender2.org/
* License : GPL (v3 or later)
  Programming Lang: C++
  Description : rendering system for physically correct 3D image synthesis

 LuxRender is a rendering system for physically correct, unbiased 3D image
 synthesis. By calculating complex light interactions and using physically
 accurate cameras and materials, LuxRender is capable of simulating light
 exactly as in the real world.
 .
 Luxrender is directly usable by artists, with the tools and features they
 need to produce high-quality photorealistic images, especially in areas like
 architectural visualization, product design, and prototyping.
 .
 It also provides with a Blender exporter, a GUI, and a C API that allows
 programmers to use LuxRender in their own programs.

Cheers,

-- 
Cyril Brulebois

PS: Sorry if that generates a duplicate for d-d, I put the list in the
pseudoheader to ensure the bug gets Cc'd there. /me hopes reportbug will
handle that nicely.



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Usage of linda

2008-01-18 Thread Joerg Jaspert
Hi

James recently merged a little branch from me into mainline dak code,
its changelog having:

  * dak/examine_package.py (check_deb): Remove linda call. It
provides no added benefit to lintian anymore.

Iow - while you are free to use linda, NEW doesn't use it
anymore.

During the last few months I did file bugs against lintian requesting
the things linda knew that lintian did not knew. All that I noticed got
included into lintian (thanks to its maintainers), so we now live
without a linda on the ftp-master host.[1]

Note that you should check your packages with the *latest* available
lintian version. Either by checking on a system running an up2date
unstable - or by using the etch-backport of lintian that I maintain on
backports.org. That backport is also installed and kept at the latest
version on the ftp-master host. I reject based on it. :)


[1] Yay, no annoying eastereggs anymore. They arent funny if you see
them a hundred of times.. :)

-- 
bye Joerg
* maxx hat weasel seine erste packung suse gebracht, der hat mich dafür
  später zu debian gebracht
 .oO( und jetzt ist der DD.  jeder macht mal fehler.. )
 du hast 2 gemacht du warst auch noch advocate :P


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Re: Possible mass bug filing: missing shared library dependencies

2008-01-18 Thread Aaron M. Ucko
Neil Williams <[EMAIL PROTECTED]> writes:

>> Aaron M. Ucko <[EMAIL PROTECTED]>
>>libncbi6-dev
>
> (Just a sample of the -dbg and -dev packages)

This was genuinely buggy (oops), as it ships a couple of utilities
alongside the other content; I've just uploaded a fixed version.

Thanks for bringing it to my attention, Niko!

-- 
Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org)
http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/[EMAIL PROTECTED]


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Bug#461506: ITP: altree -- program to perform phylogeny based analyses

2008-01-18 Thread Charles Plessy
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <[EMAIL PROTECTED]>

  Package name: altree
  Version : 1.0.1
  Upstream Author : Claire Bardel <[EMAIL PROTECTED]>
  URL : http://claire.bardel.free.fr/software.html
  License : GPL
  Programming Lang: Perl
  Description : program to perform phylogeny based analyses

 This software was designed to perform phylogeny based analysis: first,
 it allows the detection of an association between a candidate gene and
 a disease, and second, it enables to make hypothesis about the
 susceptibility loci.

The package is already ready: it was prepared by Vincent Danjean, who
offered it to the Debian-Med packaging team.

http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#altree

Have a nice day,

-- 
Charles Plessy



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Bug#461504: ITP: tacg -- command line program for finding patterns in nucleic acids

2008-01-18 Thread Charles Plessy
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <[EMAIL PROTECTED]>

  Package name: tacg
  Version : 4.1.0
  Upstream Author : Harry Mangalam, tacg Informatics
  URL : http://sourceforge.net/projects/tacg
  License : GPL and others
  Programming Lang: C (tacg), Perl (CGI)
  Description : command line program for finding patterns in nucleic acids

 tacg is a character-based, command line tool for unix-like operating systems
 for pattern-matching in nucleic acids and performing some of the basic protein
 manipulations. It was originally designed for restriction enzyme analysis of
 DNA, but has been extended to other types of matching. It now handles
 degenerate sequence input in a variety of matching approaches, as well as
 patterns with errors, regular expressions and TRANSFAC-formatted matrices.
 .
 It was designed to be a grep for DNA and like the original grep, its
 capabilities have grown so that now the author has to keep calling up the help
 page to figure out which flags (now ~50) mean what. tacg is NOT a GUI
 application in any sense. However, it's existance as a strictly command-line
 tool lends itself well to Webification and wrapping by various GUI tools and
 it is now distributed with a web interface form and a Perl CGI handler.
 Additionally, it can easily be integrated into editors that support shell
 commands such as nedit.
 .
 The use of tacg may be cited as: Mangalam, HJ. (2002) tacg, a grep for DNA.
 BMC Bioinformatics. 3:8  http://www.biomedcentral.com/1471-2105/3/8

I had to apply an ugly patch in order to compile it with gcc4. Because I am not
a C programmer, I barely understand what I did, so I would appreciate comments
on the patch:

http://svn.debian.org/wsvn/debian-med/trunk/packages/tacg/trunk/debian/patches/to-build-with-gcc4.patch?op=file&rev=0&sc=0

This is a low-quality patch, but it works. The modificaiton of tacg.h was
made according to what I found on the mailing lists, and seems to make
sense. The modification of SeqFuncs.c is completely heuristic; I used the
same numbers as in tacg.h. The modification of SetFlags.c is a quick
workaround that does not solve the real problem.

Also, you can consult the full copyright file in the same repository:

http://svn.debian.org/wsvn/debian-med/trunk/packages/tacg/trunk/debian/copyright?op=file&rev=0&sc=0

I use tacg to search for oligonucleotides in sequence reads: I need to allow
mismatches, and want to detect if I (unfortunatley) cloned concatemer
artefacts. If you know a better tool, let me know !

Have a nice day,

-- 
Charles Plessy
Debian-Med packaging team
Wakō, Saitama, Japan




Bug#461510: ITP: treevolve -- simulation of evolution of DNA sequences

2008-01-18 Thread Charles Plessy
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <[EMAIL PROTECTED]>

  Package name: treevolve
  Version : 1.3.2
  Upstream Author : Andrew Rambaut & Nick Grassly
  URL : http://evolve.zoo.ox.ac.uk/software.html?id=Treevolve
  License : Not found... will enquire.
  Programming Lang: C
  Description : simulation of evolution of DNA sequences

 treevolve will simulate the evolution of DNA sequences under a
 coalescent model, which allows exponential population growth,
 population subdivision according to an island model, migration and
 recombination. In addition different periods of population dynamics
 can be enforced at different times. For example, a period of
 exponential growth can be followed by a period of stasis where the
 population is subdivided into demes. Multiple sets of such simulated
 sequence data can then be compared to sequence data sampled from a
 population of interest using suitable statistics, and various
 evolutionary hypotheses concerning the evolution of this population
 tested.
 .
 Citation: Population dynamics of HIV-1 inferred from gene sequences
 Grassly NC, Harvey PH & Holmes EC (1999) Genetics 151, 427-438.

The package is already ready: it was prepared by Vincent Danjean, who
offered it to the Debian-Med packaging team.

http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treevolve

Have a nice day,

--
Charles Plessy



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Bug#461508: ITP: treeplot -- Phylogenetic tree file converter

2008-01-18 Thread Charles Plessy
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <[EMAIL PROTECTED]>

  Package name: treeplot
  Version : 0.7
  Upstream Author : Olivier Langella
  URL : http://www.pge.cnrs-gif.fr/bioinfo/treeplot/ (invalid)
  License : GPL
  Programming Lang: C++
  Description : Phylogenetic tree file converter

 Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to
 Postscript (.ps), Adobe Illustrator (.ai), Scalable Vector Graphic
 (.svg), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language
 (.hpgl), xfig file (.fig), gif image file(.gif), PBM Portable aNy Map
 file (.pnm)

The package is already ready: it was prepared by Vincent Danjean, who
offered it to the Debian-Med packaging team.

http://www-id.imag.fr/Laboratoire/Membres/Danjean_Vincent/deb.html#treeplot

Have a nice day,

-- 
Charles Plessy



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Re: Possible mass bug filing: missing shared library dependencies

2008-01-18 Thread Guillem Jover
On Thu, 2008-01-17 at 19:13:43 +0200, Niko Tyni wrote:
> After noticing a few compiled Perl module packages were missing
> ${shlibs:Depends} and/or dh_makeshlibdeps, I looked a bit into how
> widespread this issue is.

> Guillem Jover <[EMAIL PROTECTED]>
>libdirectfb-dev

Fixed in svn for 1.0.1-6.

thanks,
guillem


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Re: Future Debian package candidate web pages: present and future

2008-01-18 Thread Lucas Nussbaum
On 17/01/08 at 23:48 +0100, David Bremner wrote:
> > "Sebastian" == Sebastian Pipping <[EMAIL PROTECTED]> writes:
> Sebastian>> David Bremner wrote: 
> 
> >> I would really like some (approximate) popcon data myself,
> >> especially for orphaned packages.
> 
> Sebastian> would be cool, yes. i don't have any clue to do this
> Sebastian> yet. if you do please share your thoughts with me to
> Sebastian> speed the thing up. deal? :-)
> 
> As far as I understand it (and maybe somebody more informed can
> correct me), there is currently no fancy interface (SOAP) to the data
> on popcon.debian.org  On the other hand, it does not change that
> quickly, so grabbing a copy once a week should be reasonable.
> 
> http://qa.debian.org/popcon.php?package=whatever 
> 
> obviously has access to the data, so maybe someone on the qa team can 
> comment.

You could simply download it from http://popcon.debian.org/ and parse
it...
-- 
| Lucas Nussbaum
| [EMAIL PROTECTED]   http://www.lucas-nussbaum.net/ |
| jabber: [EMAIL PROTECTED] GPG: 1024D/023B3F4F |


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Bug#461404: ITP: leds-alix -- Source for the LEDs driver of PCEngines ALIX 2/3 boards

2008-01-18 Thread Y
Package: wnpp
Severity: wishlist
Owner: Adam Cécile (Le_Vert) <[EMAIL PROTECTED]>


* Package name: leds-alix
  Version : 0.0.1
  Upstream Author : Petr Leibman <[EMAIL PROTECTED]>
* URL : https://dev.openwrt.org/ticket/2771
* License : GPL-2
  Programming Lang: C
  Description : Source for the LEDs driver of PCEngines ALIX 2/3 boards

This package provides the source code for the leds-alix kernel module.
.
PCEngines ALIX boards (version 2/3) have three LEDs on front.
.
This driver allow you to power them on/off.

-- System Information:
Debian Release: lenny/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: i386 (i686)

Kernel: Linux 2.6.21-6-raq550 (SMP w/1 CPU core)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash