Processed: tagging as pending bugs that are closed by packages in NEW

2012-11-04 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> # Sunday 4 November  07:03:21 UTC 2012
> # Tagging as pending bugs that are closed by packages in NEW
> # http://ftp-master.debian.org/new.html
> #
> # Source package in NEW: libltc
> tags 692102 + pending
Bug #692102 [wnpp] ITP: libltc -- linear timecode library
Added tag(s) pending.
> # Source package in NEW: libboost-geometry-utils-perl
> tags 689649 + pending
Bug #689649 [wnpp] RFP: libboost-geometry-utils-perl -- Bindings for the Boost 
Geometry library
Added tag(s) pending.
> # Source package in NEW: libmath-clipper-perl
> tags 689650 + pending
Bug #689650 [wnpp] RFP: libmath-clipper-perl -- Perl module for polygon 
clipping in 2D
Added tag(s) pending.
>
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Bug#620067: ITA: python-pipeline -- iterator pipelines for Python

2012-11-04 Thread Denis Doria

Changing the bug from O to ITA, since I have the intention do adopt it.

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Processed: ITP: double-conversion -- routines to convert IEEE doubles to and from strings

2012-11-04 Thread Debian Bug Tracking System
Processing control commands:

> block 691912 by -1
Bug #691912 [wnpp] ITP: julia -- high-level, high-performance dynamic 
programming language for technical computing
691912 was not blocked by any bugs.
691912 was not blocking any bugs.
Added blocking bug(s) of 691912: 692264

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Bug#692264: ITP: double-conversion -- routines to convert IEEE doubles to and from strings

2012-11-04 Thread Sébastien Villemot

Package: wnpp
Severity: wishlist
Owner: "Sébastien Villemot" 
User: debian-scie...@lists.debian.org
Usertags: field..mathematics
Control: block 691912 by -1

* Package name: double-conversion
  Version : 1.1.1-1
  Upstream Author : Florian Loitsch 
* URL : http://double-conversion.googlecode.com
* License : BSD
  Programming Lang: C++
  Description : routines to convert IEEE floats to and from strings

The library provides routines to convert IEEE single and double floats
to and from string representations. It offers at lot of flexibility with
respect to the conversion format: shortest, fixed, precision or
exponential representation; decimal, octal or hexadecimal basis; control
over number of digits, leading/trailing zeros and spaces.

The library consists of efficient conversion routines that have been
extracted from the V8 JavaScript engine. The code has been refactored
and improved so that it can be used more easily in other projects.

-- 
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: :' :Debian Developer
`. `' http://www.dynare.org/sebastien
  `-  GPG Key: 4096R/381A7594


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Description: PGP signature


Bug#692238: Packaging Ray for Debian Med

2012-11-04 Thread Sébastien Boisvert

Hi,

On 11/04/2012 04:42 AM, Charles Plessy wrote:

Le Sun, Nov 04, 2012 at 01:04:37AM -0400, Sébastien Boisvert a écrit :

OK, so the things in my pristine-tar branch are not good at all !

I checked the pristine-tar branch of debian-med/bwa.git, and it contains
delta between orig tarballs.
But is the first orig tarball stored somewhere ?


The binary delta is between the original tarball and the collection of Git
objects corresponding to its content.



Oh I understand now.
pristine-tar/x.y.z-R is something applied to upstream/x.y.z in order to
produce package_x.y.z-R.orig.tar.bz2.

Why not just pick the upstream tarball then ?
Because you save on storage ?


Usually, we import the tarball with the git-buildpackage helper, which takes
care of pristine-tar.
In your case, you already have an upstream branch with
tags corresponding to version numbers of releases.


But with the debian/ directory, which is not in my tarball.


 The command 'pristine-tar
commit' should therefore help you to populate a pristine-tar branch, if you
want.



Thanks !

I did
  pristine-tar commit ~/debian-med/ray_2.1.0.orig.tar.bz2

I don't need to put any tag for branch pristine-tar, right ?


If I understand well, the Git repository on Alioth is a clone of RayGit, on top
of which you have added RayPlatform ?


Yes, the master branch contain basically a dump of Ray-v2.1.0.tar.bz2, with 
debian/ added
too. This is equivalent to having "RayGit" and "RayPlatformGit" and then adding 
debian/.


In that case, a pristine-tar binary
delta would contain a full copy of RayPlatform.


But what's the workflow when upstream RayPlatformGit changes too ?

Do we "pull" it inside branch upstream ?

I guess I will use

  pristine-tar commit ~/debian-med/ray_x.y.z.orig.tar.bz2

when we ship a new release ?



But given the size (856 here),
it may not be a problem if the number or releases is limited.


So far, we ship around 3 to 6 releases per year. The bz2 tarball size is 330 KB.

So size is not an issue.


 What you can
also do is generate an orig.tar.gz tarball from the Git repository on Alioth,
and then commit it in the pristine-tar branch.



I did this (see above). Thanks for the pointer.
 

This said, there is no problem on Debian's side to package RayPlatform
separately.


In RayPlatform, there is a CMakeList.txt and it can build
libRayPlatform.so.

The Makefile of ray needs a patch though:

--- a/Makefile
+++ b/Makefile
@@ -185,16 +185,16 @@ showOptions:
@touch showOptions

 # how to make Ray

-Ray: showOptions RayPlatform/libRayPlatform.a code/TheRayGenomeAssembler.a
-   $(MPICXX) $(LDFLAGS)  code/TheRayGenomeAssembler.a 
RayPlatform/libRayPlatform.a -o $@
+Ray: showOptions RayPlatform/libRayPlatform.so code/TheRayGenomeAssembler.a
+   $(MPICXX) $(LDFLAGS)  code/TheRayGenomeAssembler.a 
RayPlatform/libRayPlatform.so -o $@
@echo $(PREFIX) > PREFIX
@echo Ray > TARGETS
 
 code/TheRayGenomeAssembler.a:

@cd code; make MPICXX="$(MPICXX)" CXXFLAGS="$(CXXFLAGS)" -j $(J) all ; 
cd ..
 
-RayPlatform/libRayPlatform.a:

-   @cd RayPlatform; make MPICXX="$(MPICXX)" CXXFLAGS="$(CXXFLAGS)" -j $(J) 
; cd ..
+RayPlatform/libRayPlatform.so:
+   @cd RayPlatform; cmake .; make MPICXX="$(MPICXX)" 
CXXFLAGS="$(CXXFLAGS)" -j $(J) ; cd ..
 
 clean:

@rm -f Ray showOptions PREFIX TARGETS


$ ldd Ray
linux-vdso.so.1 =>  (0x7fff5a9ff000)
libRayPlatform.so => /home/seb/git-clones/RayPlatform/libRayPlatform.so 
(0x7f1be1752000)
libmpi_cxx.so.1 => /usr/lib64/openmpi/lib/libmpi_cxx.so.1 
(0x7f1be1538000)
libmpi.so.1 => /usr/lib64/openmpi/lib/libmpi.so.1 (0x0034d4e0)
libdl.so.2 => /lib64/libdl.so.2 (0x003d5600)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x003d5c40)
libm.so.6 => /lib64/libm.so.6 (0x003d5580)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x003d5880)
libpthread.so.0 => /lib64/libpthread.so.0 (0x003d55c0)
libc.so.6 => /lib64/libc.so.6 (0x003d5540)
libnsl.so.1 => /lib64/libnsl.so.1 (0x003d69c0)
libutil.so.1 => /lib64/libutil.so.1 (0x003d6700)
libltdl.so.7 => /lib64/libltdl.so.7 (0x003d6680)
/lib64/ld-linux-x86-64.so.2 (0x003d54c0)

But at this point I think RayPlatform should be bundled because
its API is not fully stable yet and as far as I know only Ray uses it.

If a new package comes to Debian bundled also with RayPlatform,
I will package RayPlatform and repackage ray. But we are not there yet
I think.


This is what I do with fastx-toolkit and libgtextutils.



Is libgtextutils used by other packages as well ?
 

Cheers,




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Bug#644932: ITP: ndppd -- a daemon that proxies IPv6 NDP messages

2012-11-04 Thread Olivier Berger
retitle 644932 RFP: ndppd -- a daemon that proxies IPv6 NDP messages
thanks

Instead of closing, I'm transforming it to an RFP, as I guess some may be 
interested...

Also, note that the upstream project page now seems to be : 
http://priv.nu/projects/ndppd/

The upstream author provides some unofficial packages.

Hope this helps.

Best regards,

On Wed, Oct 17, 2012 at 04:00:05PM +0200, Daniel Adolfsson wrote:
> Doh. Yeah I forgot about this.
> 
> I never managed to find a sponsor, and I haven't been looking for one
> for a while either. And I'm not going to be actively looking for one
> either, as I have other things to do. That being said, it's probably
> a good idea to close this "bug".
> 
> On 15.10.2012 18:24, Philipp Kern wrote:
> >Hi,
> >
> >On Mon, Oct 10, 2011 at 10:43:59PM +0200, Daniel Adolfsson wrote:
> >>* Package name: ndppd
> >>  Version : 0.2.1
> >>  Upstream Author : Daniel Adolfsson 
> >>* URL : http://www.tuhox.com/ndppd/
> >>* License : GPL-3+
> >>  Programming Lang: C++
> >>  Description : a daemon that proxies IPv6 NDP messages
> >>
> >>ndppd is a daemon that proxies certain IPv6 NDP messages between
> >>two or
> >>more interfaces. It currently supports proxying Neighbor
> >>Solicitation
> >>Messages and Neighbor Advertisement messages in order to allow IPv6
> >>routing without relying on linux "proxy_ndp".
> >
> >an ITP is formulating an intent to package, which means that you
> >get a
> >lock on that specific piece of software. I see that you already
> >created
> >the Debian packaging for this. What's stopping this from entering the
> >archive? A missing sponsor?
> >
> >Kind regards
> >Philipp Kern

-- 
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Processed: Re: Bug#644932: ITP: ndppd -- a daemon that proxies IPv6 NDP messages

2012-11-04 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> retitle 644932 RFP: ndppd -- a daemon that proxies IPv6 NDP messages
Bug #644932 [wnpp] ITP: ndppd -- a daemon that proxies IPv6 NDP messages
Changed Bug title to 'RFP: ndppd -- a daemon that proxies IPv6 NDP messages' 
from 'ITP: ndppd -- a daemon that proxies IPv6 NDP messages'
> thanks
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Processed: RFP: ndppd -- a daemon that proxies IPv6 NDP messages

2012-11-04 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> noowner 644932
Bug #644932 [wnpp] RFP: ndppd -- a daemon that proxies IPv6 NDP messages
Removed annotation that Bug was owned by Daniel Adolfsson 
.
> stop
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Processed: tagging as pending bugs that are closed by packages in NEW

2012-11-04 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> # Sunday 4 November  19:03:15 UTC 2012
> # Tagging as pending bugs that are closed by packages in NEW
> # http://ftp-master.debian.org/new.html
> #
> # Source package in NEW: double-conversion
> tags 692264 + pending
Bug #692264 [wnpp] ITP: double-conversion -- routines to convert IEEE doubles 
to and from strings
Added tag(s) pending.
>
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Bug#692320: ITP: A tool for securing communications between a client and a DNS resolver

2012-11-04 Thread sky blue
Package: wnpp
Severity: wishlist
X-Debbugs-CC: debian-de...@lists.debian.org


Package name : dnscrypt-proxy
Version: 1.2.0
Upstream Author : Frank Denis 
URL  : http://dnscrypt.org
License: ISC
Description  : A tool for securing communications between
a client and a DNS resolver
dnscrypt-proxy provides local service which can be used directly as
your local resolver or as a DNS forwarder, encrypting and
authenticating requests using the DNSCrypt protocol and passing them
to an upstream server, by default OpenDNS who run this on their
resolvers.


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Processed: retitle 692320 to ITP: dnscrypt-proxy -- A tool for securing communications between a client and a DNS resolver

2012-11-04 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> retitle 692320 ITP: dnscrypt-proxy -- A tool for securing communications 
> between a client and a DNS resolver
Bug #692320 [wnpp] ITP: A tool for securing communications between a client and 
a DNS resolver
Changed Bug title to 'ITP: dnscrypt-proxy -- A tool for securing communications 
between a client and a DNS resolver' from 'ITP: A tool for securing 
communications between a client and a DNS resolver'
> thanks
Stopping processing here.

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Bug#692326: O: mozilla-noscript

2012-11-04 Thread arno
Package: wnpp
Severity: normal

Hi,
I have no more time to maintain mozilla-noscript. Therefore, I'd like to orphan 
it.


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Bug#692332: ITP: sga -- A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation o

2012-11-04 Thread Michael Crusoe
Package: wnpp
Severity: wishlist
Owner: "Michael R. Crusoe" 

* Package name: sga
  Version : 0.9.35
  Upstream Author : Jared Simpson 
* URL : https://github.com/jts/sga
* License : GPLv3
  Programming Lang: C++
  Description : A de novo genome assembler based on the concept of
string graphs. The major goal of SGA is to be very memory efficient, which
is achieved by using a compressed representation of DNA sequence reads.

SGA is a de novo assembler for DNA sequence reads. It is based on Gene
Myers' string graph
formulation of assembly and uses the FM-index/Burrows-Wheeler transform to
efficiently
find overlaps between sequence reads. The core algorithms are described in
this paper:

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/12/i367


Processed: O: gresolver -- graphical tool for performing DNS queries

2012-11-04 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> affects 677302 gresolver
Bug #677302 [wnpp] O: gresolver -- graphical tool for performing DNS queries
Added indication that 677302 affects gresolver
>
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Processed: O: gresolver -- graphical tool for performing DNS queries

2012-11-04 Thread Debian Bug Tracking System
Processing commands for cont...@bugs.debian.org:

> affects 677302 - gresolver
Bug #677302 [wnpp] O: gresolver -- graphical tool for performing DNS queries
Removed indication that 677302 affects gresolver
> affects 677302 src:gresolver
Bug #677302 [wnpp] O: gresolver -- graphical tool for performing DNS queries
Added indication that 677302 affects src:gresolver
>
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