polipo 1.0.4.1-2 2012-11-22 19:14

2012-11-28 Thread Bart Martens
Hi Rolf,

I had a look at this package:
http://mentors.debian.net/package/polipo

Looks like a good maintenance update, and uploading this to experimental seems
the best choice since there are still important bugs open that could be fixed
in wheezy via unstable.  How is progress on bugs 610199, 655851 and 684742 ?
Any chance to get them fixed in wheezy ?

Regards,

Bart Martens


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Bug#681167: marked as done (RFS: cellml-api/20120711-1 [ITP])

2012-11-28 Thread Debian Bug Tracking System
Your message dated Wed, 28 Nov 2012 16:20:27 +
with message-id 
and subject line closing RFS: cellml-api/20120711-1 [ITP]
has caused the Debian Bug report #681167,
regarding RFS: cellml-api/20120711-1 [ITP]
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
681167: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=681167
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---

Package: sponsorship-requests
CC: debian-scie...@lists.debian.org
CC: debian-mentors@lists.debian.org

The CellML API (upstream website: http://cellml-api.sf.net/) is an 
application programming interface, along with a complete reference 
implementation, for manipulating and processing mathematical models in 
the CellML format (http://www.cellml.org/). It is tri-licensed under the 
GPL / LGPL and MPL licenses (i.e. can be used under any one of the three).


This packaging enables all the main features of the API implementation:
  * Core library for manipulating arbitrary CellML mathematical models. 
This includes a W3C DOM and W3C MathML DOM implementation.

  * RDF processing library for processing CellML metadata.
  * CellML Variable Association Service to simplify working with models 
where the same variable is split across multiple components (possibly 
imported from multiple files).
  * CellML Units Simplification and Expansion Service, for processing 
physical units as required by the CellML specifications.
  * MathML to Language Export Service, for converting MathML 
mathematical expressions into text in a customisable way.
  * CellML Code Generation Service, for converting from CellML models 
into imperative code for solving systems of differential-algebraic 
equations described in the model.
  * CellML Integration Service, for running numerical simulations 
described in CellML models with SUNDIALS IDA.
  * Text Language for the Input of CellML Models Service, for 
converting to and from a plain-text format, to facilitate the input and 
display of CellML models by and to end users.
  * CellML Language Export Definition Service, for processing XML files 
that describe how to translate a CellML model into imperative code in a 
particular language.
  * SED-ML Processing Service, for manipulating simulation experiment 
descriptions in Simulation Experiment Description Markup Language 
(http://sedml.org)
  * SED-ML Running Service, for running simulation experiments 
described in SED-ML.
  * Documentation generated from the IDL files and supplementary 
documentation files by Doxygen.

  * Java bindings.
  * Development package with C++ headers and libraries.

Packages are up on mentors.d.n:
  http://mentors.debian.net/package/cellml-api
Repository containing the debian directory is up at:
  git://git.debian.org/git/debian-science/packages/cellml-api.git

Package quality: The package is Lintian clean except for spurious 
warnings about hardening (hardening is enabled, but some of the shared 
objects don't use anything from glibc that can be hardened, and so 
trigger false positive warnings) and 'shlib-calls-exit' (which is caused 
by the use of a C++ flex scanner). The docs package also has a 
duplicate-files warning, but this is a consequence of using Doxygen.


In addition, I have manually checked the package for compliance with the 
Debian Science policy, and believe it complies.


Best wishes,
Andrew Miller



--- End Message ---
--- Begin Message ---
Package cellml-api has been removed from mentors.--- End Message ---


Processed: prime-phylo: block ITP 684039 by RFS 694632

2012-11-28 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> block 684039 by 694632
Bug #684039 [wnpp] ITP: prime-phylo -- Bayesian estimation of gene trees taking 
the species tree into account
684039 was not blocked by any bugs.
684039 was not blocking any bugs.
Added blocking bug(s) of 684039: 694632
> stop
Stopping processing here.

Please contact me if you need assistance.
-- 
684039: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=684039
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems


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Bug#694632: RFS: prime-phylo/1.0.10-1 [NEW]

2012-11-28 Thread Erik Sjölund
Package: sponsorship-requests
Severity: wishlist

Dear mentors,

I am looking for a sponsor for my new package "prime-phylo"

* Package name: prime-phylo
  Version : 1.0.10-1
  Upstream Author : Lars Arvestad, Bengt
Sennblad and others
* URL : http://prime.sbc.su.se
* License : GPL-3
  Programming Lang: C++
  Section : science

It builds the binary package:

  prime-phylo - bayesian estimation of gene trees taking the species
tree into account

To access further information about this package, please visit the
following URL:

http://mentors.debian.net/package/prime-phylo


Alternatively, one can download the package with dget using this command:

  dget -x 
http://mentors.debian.net/debian/pool/main/p/prime-phylo/prime-phylo_1.0.10-1.dsc

The URL for the upstream project homepage is: http://prime.sbc.su.se

The upstream name PrIME is an acronym for Probabilistic Integrated
Models of Evolution.
The package supports inference of evolutionary parameters in a
Bayesian framework using
Markov chain Monte Carlo simulation. A distinguishing feature of PrIME
is that the species
tree is taken into account when analyzing gene trees.

A scientific description of PrIME has been published in this scientific paper:
  Åkerborg, Ö., Sennblad, B., Arvestad, L., & Lagergren, J. (2009).
  Simultaneous Bayesian gene tree reconstruction and reconciliation analysis.
  Proceedings of the National Academy of Sciences, 106(14), 5714-5719.
  doi:10.1073/pnas.0806251106
  
http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=ref&cmd=prlinks&dbfrom=pubmed&id=19299507

There are some existing Debian packages that provide some of the
functionality also given by prime-phylo:

  fastdnaml
  fasttree
  phyml
  raxml
  tree-puzzle

but none provide the same functionality.

I previously sent an ITP bug report for prime-phylo
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=684039

Should I have replied to that bug report instead of sending this one?
(This is my first package submission)

Cheers,
Erik Sjölund


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