Bug#730902: avarice: diff for NMU version 2.11-1.1

2013-12-22 Thread Shaun Jackman
Hi David,

Thanks for fixing this bug in avarice. Please do go ahead with the NMU.

avarice is up for adoption. See the RFA here: http://bugs.debian.org/732433
Would you like to adopt avarice?

Cheers,
Shaun

-- 
http://sjackman.ca

On 2013-Dec-22 at 10:39:11 , David Prévot (taf...@debian.org) wrote:

tags 730902 + patch  
thanks  

Dear maintainer,  

I've prepared an NMU for avarice (versioned as 2.11-1.1) and  
uploaded it to DELAYED/2. Please feel free to tell me if I  
should delay it longer.  

Regards.  

David  
- avarice-2.11-1.1-nmu.diff, 921 bytes
- signature.asc, 501 bytes

Bug#732430: RM: pptview -- RoM, no rdepends

2013-12-17 Thread Shaun Jackman
Package: ftp.debian.org
Severity: normal

Hi,

Please remove pptview. It's quite dated (circa 1997), and there are
better free alternatives now. It has two open Ubuntu bugs.

installation fails for amd64
https://bugs.launchpad.net/ubuntu/+source/pptview/+bug/909447

PowerPoint viewer version 97 can't open OpenXML PPSX presentations
https://bugs.launchpad.net/ubuntu/+source/pptview/+bug/1242369

Thanks,
Shaun


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Bug#732431: RM: pocketpc-cab -- RoM, unmaintained upstream

2013-12-17 Thread Shaun Jackman
Package: ftp.debian.org
Severity: normal

Hi,

Please remove pocketpc-cab. I'm the upstream developer and the Debian
package maintainer, and it hasn't been maintained in many years.

Thanks,
Shaun


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Bug#732430: Fwd: Remove or Fix Debian‘s pptview

2013-12-17 Thread Shaun Jackman
From: Ma Xiaojun damage3...@gmail.com
Date: 17 December 2013 07:51
Subject: Remove or Fix Debian‘s pptview
To: sjack...@debian.org

Hi,

pptview is actually a pretty smart work. It offers a high level of
desktop integration, it somehow conforms to FHS, ...

However, it also have multiple issues today.

* The version is dated by today's standard:
https://bugs.launchpad.net/ubuntu/+source/pptview/+bug/1242369

* Suggested openoffice.org-impress no longer exist

* If there is a pptview, where is docview or xlsview?

I guess the simplest resolution is simply remove it. So users won't be
disappointed by it. If people want viewers from MSFT they should go
for winetricks or CrossOver or whatever wine frontends.

Regards,
Ma Xiaojun


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Bug#732433: RFA: avarice -- use GDB with Atmel's JTAG ICE for the AVR

2013-12-17 Thread Shaun Jackman
Package: wnpp

Please adopt avarice. A new upstream version is available: 2.13.
http://avarice.sourceforge.net/

Thanks,
Shaun


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Bug#702440: closed by Charles Plessy ple...@debian.org (Bug#702440: fixed in abyss 1.3.6-1)

2013-09-08 Thread Shaun Jackman
Fantastic. Thanks for the GCC 4.8 patch. We'll merge it upstream.

On 7 September 2013 20:21, Debian Bug Tracking System
ow...@bugs.debian.org wrote:
 This is an automatic notification regarding your Bug report
 which was filed against the abyss package:

 #702440: New upstream release available

 It has been closed by Charles Plessy ple...@debian.org.

 Their explanation is attached below along with your original report.
 If this explanation is unsatisfactory and you have not received a
 better one in a separate message then please contact Charles Plessy 
 ple...@debian.org by
 replying to this email.


 --
 702440: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=702440
 Debian Bug Tracking System
 Contact ow...@bugs.debian.org with problems


 -- Forwarded message --
 From: Charles Plessy ple...@debian.org
 To: 702440-cl...@bugs.debian.org
 Cc:
 Date: Sun, 08 Sep 2013 03:18:19 +
 Subject: Bug#702440: fixed in abyss 1.3.6-1
 Source: abyss
 Source-Version: 1.3.6-1

 We believe that the bug you reported is fixed in the latest version of
 abyss, which is due to be installed in the Debian FTP archive.

 A summary of the changes between this version and the previous one is
 attached.

 Thank you for reporting the bug, which will now be closed.  If you
 have further comments please address them to 702...@bugs.debian.org,
 and the maintainer will reopen the bug report if appropriate.

 Debian distribution maintenance software
 pp.
 Charles Plessy ple...@debian.org (supplier of updated abyss package)

 (This message was generated automatically at their request; if you
 believe that there is a problem with it please contact the archive
 administrators by mailing ftpmas...@ftp-master.debian.org)


 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA256

 Format: 1.8
 Date: Sun, 08 Sep 2013 11:36:44 +0900
 Source: abyss
 Binary: abyss
 Architecture: source amd64
 Version: 1.3.6-1
 Distribution: unstable
 Urgency: low
 Maintainer: Debian Med Packaging Team 
 debian-med-packag...@lists.alioth.debian.org
 Changed-By: Charles Plessy ple...@debian.org
 Description:
  abyss  - de novo, parallel, sequence assembler for short reads
 Closes: 702440 722072
 Changes:
  abyss (1.3.6-1) unstable; urgency=low
  .
* Team upload (Closes: #722072).
e05ee57 Imported Upstream version 1.3.5
b391f1f Imported Upstream version 1.3.6 (Closes: #702440)
7edc28b Signal the use of git-buildpackage with this configuration file.
a3beaac Normalised source package control file with config-model-edit.
dd86394 Conforms with Policy version 3.9.4.
71d42ad Normalised VCS URLs.
 Checksums-Sha1:
  bf4e40f2c8b5257f9cf65487aa8e62df6e26cf03 2039 abyss_1.3.6-1.dsc
  ac5004972c90cedfb116b307dcf051fb30b7a102 678880 abyss_1.3.6.orig.tar.gz
  672132adba821fb326a0d97905b9d2a090269053 11516 abyss_1.3.6-1.debian.tar.gz
  f1301a6d7f7f3ab961264c4e11d3058ad282381d 867230 abyss_1.3.6-1_amd64.deb
 Checksums-Sha256:
  300b63319b5422eb5b46253135e8e8405e3ad39c5b1822d978f07be86a8985ff 2039 
 abyss_1.3.6-1.dsc
  4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 678880 
 abyss_1.3.6.orig.tar.gz
  8246ebd6c9ba9539ddad05450f7be0bbab5dd6cdb0d8dff2f7a5f54b136b2139 11516 
 abyss_1.3.6-1.debian.tar.gz
  921ca17052122d1aa45bd5c732fd8d14508f88fde8db4ef2c0b6cf624a449938 867230 
 abyss_1.3.6-1_amd64.deb
 Files:
  2f8a23a6373dcee6b6d1cd02b7a40478 2039 non-free/science optional 
 abyss_1.3.6-1.dsc
  4182c24de5b74a1294fc8f9a452ae743 678880 non-free/science optional 
 abyss_1.3.6.orig.tar.gz
  cdf33bfd6ae35dc2482c46545ebdbb4b 11516 non-free/science optional 
 abyss_1.3.6-1.debian.tar.gz
  ee386cc32f08ec888b10f7430ed09565 867230 non-free/science optional 
 abyss_1.3.6-1_amd64.deb

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 -END PGP SIGNATURE-

 -- Forwarded message --
 From: Shaun Jackman sjack...@gmail.com
 To: Submit@BTS sub...@bugs.debian.org
 Cc:
 Date: Wed, 6 Mar 2013 07:50:30 -0800
 Subject: New upstream release available
 Package: abyss
 Priority: wishlist

 ABySS 1.3.5 is available.

 Cheers,
 Shaun




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Bug#702440: New upstream release available

2013-08-15 Thread Shaun Jackman
Hi Andreas,


  


My home machine is running OS X and I use Homebrew to manage packages, and 
at work I don't have root access on the Linux servers, so I use Linuxbrew to 
manage packages. To maintain a Debian package, there's a little extra effort 
required to fire up a VM. I opened the bug report to document that a new 
version of ABySS is available. If you have time to update the package, that's 
great, otherwise it'll wait until I find some time to do it.


  


Thanks for the bug report. It's an easy one line fix (delete the offending 
line) and will definitely be included in the next release of ABySS. Here's a 
link to the upstream bug report.


  



  https://github.com/bcgsc/abyss/issues/26



  




Cheers,

Shaun

—
http://about.me/sjackman

On Wed, Aug 14, 2013 at 4:58 PM, Andreas Tille andr...@fam-tille.de
wrote:

 Hi Shaun,
 I wonder if there is any reason that you did just files a bug report
 about a new version and did not simply uploaded the package as you
 formerly did.  Could you please drop the Debian Med team some note if
 something prevents you from doing so.
 BTW, I checked the latest version and injected it into the Git
 repository but I realised that it does not build because of:
 g++ -DHAVE_CONFIG_H -I. -I..  -I.. -I../Common -I../DataLayer -I.  
 -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 
 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security 
 -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo 
 './'`DotWriter.cpp
 In file included from DotWriter.cpp:5:0:
 ../Graph/ContigGraphAlgorithms.h: In function 'OutIt assemble_if(Graph, 
 OutIt, Predicate)':
 ../Graph/ContigGraphAlgorithms.h:202:44: error: typedef 'vertex_descriptor' 
 locally defined but not used [-Werror=unused-local-typedefs]
   typedef typename Graph::vertex_descriptor vertex_descriptor;
 ^
 cc1plus: all warnings being treated as errors
 make[3]: *** [libassembly_a-DotWriter.o] Error 1
 make[3]: Leaving directory `/tmp/buildd/abyss-1.3.6/Assembly'
 make[2]: *** [all-recursive] Error 1
 make[2]: Leaving directory `/tmp/buildd/abyss-1.3.6'
 make[1]: *** [all] Error 2
 make[1]: Leaving directory `/tmp/buildd/abyss-1.3.6'
 dh_auto_build: make -j1 returned exit code 2
 Since you are upstream dealing with things like this would be way
 simpler if you just fix these things upstream rather than leaving us
 poor packagers alone with patching.
 Kind regards
Andras.
 -- 
 http://fam-tille.de

Bug#702440: New upstream release available

2013-03-06 Thread Shaun Jackman
Package: abyss
Priority: wishlist

ABySS 1.3.5 is available.

Cheers,
Shaun


Bug#605421: pptview: Please make sure to reduce the dependencies

2011-12-03 Thread Shaun Jackman
pptview is a PE32 executable, so wine is necessary.

Cheers,
Shaun

On 29 November 2010 12:13, Frenchn00b frenchn...@yahoo.com wrote:
 Package: pptview
 Severity: important

 Non non-substancial needed dependencies are in the deb file.

 wine dependencies, could you avoid that too please ?


 a# apt-get install abiword pptview
 Reading package lists... Done
 Building dependency tree
 Reading state information... Done
 abiword is already the newest version.
 The following extra packages will be installed:
  cups-bsd libwine libwine-alsa libwine-cms libwine-gl libwine-gphoto2 
 libwine-ldap libwine-print libwine-sane wine wine-bin wine-utils
 Suggested packages:
  wine-doc openoffice.org-impress binfmt-support ttf-mscorefonts-installer 
 avscan klamav clamav
 The following NEW packages will be installed:
  cups-bsd libwine libwine-alsa libwine-cms libwine-gl libwine-gphoto2 
 libwine-ldap libwine-print libwine-sane pptview wine wine-bin wine-utils
 0 upgraded, 13 newly installed, 0 to remove and 59 not upgraded.
 Need to get 12.9MB of archives.
 After this operation, 57.0MB of additional disk space will be used.
 Do you want to continue [Y/n]? y

 best regards

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

 Kernel: Linux 2.6.32-5-686 (SMP w/2 CPU cores)
 Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
 Shell: /bin/sh linked to /bin/dash





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Bug#644925: ITP: jellyfish -- count k-mers of DNA

2011-10-10 Thread Shaun Jackman
Package: wnpp
Severity: wishlist

Package name: jellyfish
Version: 1.1.2
Upstream author: Guillaume Marçais gmarc...@umd.edu
License: GPL-3+
Description: count k-mers of DNA
 JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
 DNA. A k-mer is a substring of length k, and counting the occurrences
 of all such substrings is a central step in many analyses of DNA
 sequence. JELLYFISH can count k-mers using an order of magnitude less
 memory and an order of magnitude faster than other k-mer counting
 packages by using an efficient encoding of a hash table and by
 exploiting the compare-and-swap CPU instruction to increase
 parallelism.
 .
 JELLYFISH is a command-line program that reads FASTA and multi-FASTA
 files containing DNA sequences. It outputs its k-mer counts in an
 binary format, which can be translated into a human-readable text
 format using the jellyfish dump command.
 .
 If you use JELLYFISH in your research, please cite:
 Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for
 efficient parallel counting of occurrences of k-mers. Bioinformatics
 (2011) 27(6): 764-770 (first published online January 7, 2011)
 doi:10.1093/bioinformatics/btr011



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Bug#631534: ITP: ABySS -- de novo, parallel, short-read assembler

2011-06-24 Thread Shaun Jackman
Package: wnpp
Severity: wishlist

Package name: abyss
Version: 1.2.7
Upstream Author: sjack...@bcgsc.ca
URL: http://www.bcgsc.ca/platform/bioinfo/software/abyss
License: free for academic use
Description: a de novo, parallel, paired-end sequence assembler
 ABySS is a de novo, parallel, paired-end sequence assembler that is
 designed for short reads. It may be used to assemble genome or
 transcriptome sequence data.  Parallelization is achieved using MPI,
 OpenMP and pthread.
 .
 To cite your use of ABySS, please reference
 ABySS: A parallel assembler for short read sequence data. Simpson JT,
 Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research,
 2009-June.



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Bug#619201: New upstream release available

2011-03-21 Thread Shaun Jackman
Package: picard-tools
Priority: wishlist

Picard 1.41 is available.

Cheers,
Shaun



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Bug#616002: bzip2 does not work with nohup

2011-03-01 Thread Shaun Jackman
Package: bzip2
Version: 1.0.5-6

When running bzip2 inside nohup, bzip2 exits when the terminal closes.
Here are the steps to reproduce the issue:

1. open a terminal
2. nohup bzip2 foo 
3. close the terminal
4. open a terminal
5. cat nohup.out
bzip2: Control-C or similar caught, quitting.
bzip2: Deleting output file ABySS_assembly_A.fa.bz2, if it exists.

It's possible that this bug should be assigned to nohup (coreutils). I
figured bzip2 was the more likelier candidate since most all other
software works fine with nohup.

Cheers,
Shaun



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Bug#591952: RM: colt -- RoM, no rdepends

2010-08-06 Thread Shaun Jackman
Package: ftp.debian.org
Severity: normal

Hi friendly FTP master,

Please remove colt and libcolt-java. Its only reverse dependency was
igv, and igv no longer depends on libcolt-java.

Cheers,
Shaun

Hi Charles,

Should it be uploaded to say experimental, so that in the future if
somebody needs it again, they won't repackage it from scratch?

Cheers,
Shaun

On 29 July 2010 01:20, Charles Plessy ple...@debian.org wrote:
 Le Wed, Jul 28, 2010 at 11:31:51PM +, Shaun Jackman a écrit :

 +  * Remove libcolt-java from the dependencies.

 Hi Shaun,

 if you have sometimes followed my rants on -devel or -project, you know that I
 am advocating aggressive package removal, so…

 If igv does not depend on libcolt-java anymore, how about removing this 
 package
 rather than letting it be released, and therefore owe support for a couple of
 years?

 Have a nice day,

 --
 Charles



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Bug#588562: ITP: colt -- libraries for High Performance Scientific and Technical Computing in Java

2010-07-09 Thread Shaun Jackman
Package: wnpp
Severity: wishlist

Package name: colt
Version: 1.2.0
Upstream author: c...@listbox.cern.ch
URL: http://acs.lbl.gov/software/colt/
License: other
Description: libraries for High Performance Scientific and Technical
Computing in Java
Scientific and technical computing, as, for example, carried out at
CERN, is characterized by demanding problem sizes and a need for high
performance at reasonably small memory footprint. There is a
perception by many that the Java language is unsuited for such work.
However, recent trends in its evolution suggest that it may soon be a
major player in performance sensitive scientific and technical
computing. For example, IBM Watson's Ninja project showed that Java
can indeed perform BLAS matrix computations up to 90% as fast as
optimized Fortran. The Java Grande Forum Numerics Working Group
provides a focal point for information on numerical computing in Java.
With the performance gap steadily closing, Java has recently found
increased adoption in the field. The reasons include ease of use,
cross-platform nature, built-in support for multi-threading, network
friendly APIs and a healthy pool of available developers. Still, these
efforts are to a significant degree hindered by the lack of foundation
toolkits broadly available and conveniently accessible in C and
Fortran.



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Bug#585457: IGV dependencies

2010-06-15 Thread Shaun Jackman
Hi Andreas,

On 11 June 2010 00:41, Andreas Tille andr...@an3as.eu wrote:
 Hi Shaun,

 On Thu, Jun 10, 2010 at 11:55:54AM -0700, Shaun Jackman wrote:
 IGV has a lot of dependencies, and the list follows. Many of these
 dependencies are already in Debian; many others are not. Where the
 dependency is satisfied, I've given the Debian package name. Where
 it's not satisfied, I've given the upstream URL.

 thanks for your ITP which is quite interesting for Debian Med.  Will you
 consider also packaging the dependencies?  I woud suggest coordination
 with debian-j...@lists.debian.org.  Perhaps there is some work ongoing
 or some help can be given.

I'm planning on doing some dependency triage for the dependencies that
are not yet packaged for Debian:
If the dependency is for an optional feature of IGV (say a file
format) then I'll remove that feature from IGV.
If the dependency is mandatory and related to bioinformatics, I'll
consider packaging it.
If the dependency is mandatory and not related to bioinformatics, I'll
submit an RFP and ask whether debian-java would like to package it.

Cheers,
Shaun



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Bug#586015: ITP: picard-tools -- manipulate SAM and BAM files

2010-06-15 Thread Shaun Jackman
Package: wnpp
Severity: wishlist

Package name: picard-tools
Version: 1.22
Upstream Author:
URL: http://picard.sourceforge.net/
License: MIT
Description: manipulate SAM and BAM files

This Java library implements an API to manipulate SAM and BAM files.
SAM (Sequence Alignment/Map) format is a generic format for storing
large nucleotide sequence alignments.

Cheers,
Shaun



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Bug#585457: ITP: igv -- Integrative Genomics Viewer

2010-06-10 Thread Shaun Jackman
Package: wnpp
Severity: wishlist

Package name: igv
Version: 1.4.2
Upstream Author: igv-h...@broadinstitute.org
URL: http://www.broadinstitute.org/igv
License: LGPL
Description: Integrative Genomics Viewer

The Integrative Genomics Viewer (IGV) is a high-performance
visualization tool for interactive exploration of large, integrated
datasets. It supports a wide variety of data types including sequence
alignments, microarrays, and genomic annotations.

Cheers,
Shaun



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Bug#585457: IGV dependencies

2010-06-10 Thread Shaun Jackman
IGV has a lot of dependencies, and the list follows. Many of these
dependencies are already in Debian; many others are not. Where the
dependency is satisfied, I've given the Debian package name. Where
it's not satisfied, I've given the upstream URL.

Cheers,
Shaun

colt.jarhttp://acs.lbl.gov/software/colt/
commons-math-1.1.jar libcommons-math-java
concurrent.jar  libconcurrent-java
jargs.jar   libjargs-java
jhdf5.jar   libjhdf5-java
jibble.jar  libjlibeps-java
jide-action.jar http://www.jidesoft.com/
jide-common.jar 
jide-components.jar 
jide-dialogs.jar
jide-dock.jar   
jide-grids.jar  
junit-4.5.jar   junit4
jlfgr-1_0.jar   http://java.sun.com/developer/techDocs/hi/repository/
ledatastream.jarhttp://mindprod.com/products1.html#LEDATASTREAM
log4j-1.2.15.jarliblog4j1.2-java
maf.jar http://www.broadinstitute.org/genome_bio/siphy/
sam-1.08.jarhttp://picard.sourceforge.net/
swing-layout-1.0.jarlibswing-layout-java



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Bug#580277: GMAP -- Align mRNA and EST sequences to a genome

2010-05-10 Thread Shaun Jackman
Hi Charles,

On 4 May 2010 21:01, Charles Plessy ple...@debian.org wrote:
 Le Tue, May 04, 2010 at 06:30:26PM -0700, Shaun Jackman a écrit :

 I've packaged GMAP:
 Align mRNA and EST sequences to a genome
  GMAP: Genomic Mapping and Alignment Program
  GSNAP: Genomic Short-read Nucleotide Alignment Program

 The ITP is here:
 http://bugs.debian.org/580277

 The git repository is here:
 git://git.debian.org/git/debian-med/gmap.git
 http://git.debian.org/?p=debian-med/gmap.git

 Dear Shaun,

 thank you very much for helping us to stay up to date in the field of
 next-generation sequencing. Just out of curiosity, will you use the
 package yourself, or did you prepare it for a friend or a colleague?

 I had a look at your package and have the following comments:

  - It is non-free:

   ‘Distribution of this Package as part of a commercial software product 
 requires
    prior arrangement with the Developers.’

   I updated debian/control accordingly.

Thanks.

 Since this license is not compatible with
   the GPL, I recommend that you chose another license for your packaging 
 work, in
   order to avoid headaches in the future.

Can you recommend a license that is DFSG free and compatible with the
upstream license?

  - We will have to be careful when doing modifications.

   ‘Distribution of a modified version of this Package requires prior
    arrangement with the Developers.’

   I am not sure of what it means for the manpages you wrote. If you have 
 written them
   using the output of the programs as a template, they are a derivative of 
 them,
   and the above may mean that we need agreement of the upstream developpers 
 before
   redistributing them. But anyway, manpages are better to be forwarded 
 upstream. Have
   you contacted them?

I'm in contact with the upstream author, but not yet regarding the
Debian package. I'll forward the man pages upstream.

  - Location of the databases.

   I have seen ‘-DGMAPDB=\/usr/share/gmap\’ in the build logs. Does that 
 mean that the
   users will have to install their databases there, or is there a way to 
 override
   this path? In general, I think Debian users expect /usr/share to be 
 completely under
   the control of the packaging system. Perhaps another path would be better?

The default location can be overridden by a command line option (-D)
or an environment variable (GMAPDB).

How about /var/cache/gmap?
http://www.pathname.com/fhs/pub/fhs-2.3.html#VARCACHEAPPLICATIONCACHEDATA

 - Package description. How about this one:

 Description: spliced and SNP-tolerant alignment programs for mRNA and short 
 reads
  This package contains the GMAP and GSMAP programs to align biological
  sequences, and additional utilities to manage genome databases in GMAP/GSNAP
  format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
  cDNAs (complementary DNA) to reference genomes. GSNAP (Genomic Short-read
  Nucleotide Alignment Program) is a tool for aligning single and paired-end
  sequence reads as short as 14 nt and of arbitrarily long length. It can do de
  novo discovery of splice sites (including interchromosomal splicing) or use a
  datbase of known splice sites. It also tolerates known single nucleotide
  polymorphisms (SNPs) and can align bisulfite-treated DNA.

I edited and reformatted your description. How's this look?

Description: spliced and SNP-tolerant alignment for mRNA and short reads
 This package contains the programs GMAP and GSNAP as well as
 utilities to manage genome databases in GMAP/GSNAP format.
 GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
 EST, mRNA and cDNA sequences.
 GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
 aligning single and paired-end transcriptome reads.
 Both tools can use a database of
 * known splice sites and identify novel splice sites.
 * known single nucleotide polymorphisms (SNPs).
GSNAP can align bisulfite-treated DNA.

  Maybe it would be good to propose to the authors to proofread this 
 description,
  so that we are sure that I did not under- or over-estimate the possibilities
  of their programs.

I believe these claims are correct, but of course it wouldn't hurt to check.

Cheers,
Shaun



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Bug#580277: ITP: gmap -- Align mRNA and EST sequences to a genome

2010-05-04 Thread Shaun Jackman
Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org

Package name: gmap
Version: 20100309
Upstream Author: Thomas Wu t...@gene.com
URL: http://research-pub.gene.com/gmap/
License: other (DFSG)
Description: Align mRNA and EST sequences to a genome

GMAP is composed of two programs:
 GMAP: Genomic Mapping and Alignment Program
 GSNAP: Genomic Short-read Nucleotide Alignment Program

as well as a variety of utilities to support these programs.

Cheers,
Shaun



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Bug#580013: uuid-dev: Should be named libuuid-dev

2010-05-02 Thread Shaun Jackman
Package: uuid-dev

The package uuid-dev contains library and header files, and as such
should be named libuuid-dev.

Cheers,
Shaun



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Bug#565280: jtag2usb.cc:98: error: invalid conversion from 'const char*' to 'char*' [PATCH]

2010-01-24 Thread Shaun Jackman
Hi Joerg,

Attached is a patch from Nobuhiro Iwamatsu to fix a compiler error in
usb_dev_handle.

Cheers,
Shaun

-- Forwarded message --
From: Nobuhiro Iwamatsu iwama...@nigauri.org
Date: 2010/1/22
Subject: Bug#565280: FTBFS: jtag2usb.cc:98: error: invalid conversion
from 'const  char*' to 'char*'
To: 565...@bugs.debian.org


tags 565280 patch
thanks

I made the patch which revised this problem.
And I checked build and the installation of the package.
But I do not have environment working this.
Sorry.

Best regards,
 Nobuhiro

--
Nobuhiro Iwamatsu
 iwamatsu at {nigauri.org / debian.org}
 GPG ID: 40AD1FA6
diff --git a/src/jtag2usb.cc b/src/jtag2usb.cc
index 5981e57..43329dd 100644
--- a/src/jtag2usb.cc
+++ b/src/jtag2usb.cc
@@ -40,6 +40,7 @@
 #include signal.h
 #include string.h
 #include errno.h
+#include assert.h
 
 #include usb.h
 
@@ -71,6 +72,7 @@ static usb_dev_handle *opendev(const char *jtagDeviceName, emulator emu_type,
   struct usb_device *dev;
   usb_dev_handle *udev;
   char *serno, *cp2;
+  char *s;
   u_int16_t pid;
   size_t x;
 
@@ -95,7 +97,9 @@ static usb_dev_handle *opendev(const char *jtagDeviceName, emulator emu_type,
* right-to-left, so only the least significant nibbles need to be
* specified.
*/
-  if ((serno = strchr(jtagDeviceName, ':')) != NULL)
+  s = strdup(jtagDeviceName);
+  assert(s !=  NULL);
+  if ((serno = strchr(s, ':')) != NULL)
 {
   /* first, drop all colons there if any */
   cp2 = ++serno;
@@ -109,6 +113,7 @@ static usb_dev_handle *opendev(const char *jtagDeviceName, emulator emu_type,
 
   unixCheck(strlen(serno) = 12, invalid serial number \%s\, serno);
 }
+  free(s);
 
   usb_init();
 


Bug#521746: eagle: FTBFS bug not fixed yet re: libxrender.so.1 and amd64 [fix attached]

2009-11-10 Thread Shaun Jackman
It sounds like the solution is to move ia32-libs to Build-Depends
then. I'll do that. I'll also e-mail the maintainer of ia32-libs and
see whether he agrees.

Thanks for the bug report and solution, Scott. Cheers,
Shaun



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Bug#521746: eagle: FTBFS bug not fixed yet re: libxrender.so.1 and amd64 [fix attached]

2009-11-09 Thread Shaun Jackman
Bug #360358 asked me to replace the ia32-libs-dev in Build-Depends
with libc6-dev-i386, which is the current state:
http://bugs.debian.org/360358

This page says that ia32-libs-dev only exists on ia64 (not amd64):
http://packages.debian.org/sid/ia32-libs-dev

Though ia32-libs is available on amd64:
http://packages.debian.org/sid/ia32-libs

and depends on these libraries::
  libc6-i386 (= 2.9-18) [amd64]
  GNU C Library: 32-bit shared libraries for AMD64
  lib32asound2 [amd64]
  shared library for ALSA applications (32 bit)
  lib32gcc1
  GCC support library (32 bit Version)
  lib32ncurses5 [amd64]
  shared libraries for terminal handling (32-bit)
  lib32stdc++6 [amd64]
  The GNU Standard C++ Library v3 (32 bit Version)
  lib32z1 [amd64]
  compression library - 32 bit runtime

Perhaps one of these should be in Build-Depends. What exactly was the
error message you saw when building eagle?

Cheers,
Shaun



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Bug#546237: eagle: Eagle exits with segmentation fault

2009-10-19 Thread Shaun Jackman
Great! Glad to hear it.

Cheers,
Shaun

2009/10/19 Johan Folkesson j...@tem00.org:
 Thanks! It works perfect!

 Cheers
 Johan

 Shaun Jackman wrote:

 Hi Johan,

 Here's the workaround:
 cp /usr/lib/eagle/bin/eagle ~/.eagle/bin/

 Then run eagle normally. It shouldn't crash any longer. I'm working on
 a fix for the Debian package.

 Cheers,
 Shaun






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Bug#546237: eagle: Eagle exits with segmentation fault

2009-10-18 Thread Shaun Jackman
Hi Johan,

Here's the workaround:
cp /usr/lib/eagle/bin/eagle ~/.eagle/bin/

Then run eagle normally. It shouldn't crash any longer. I'm working on
a fix for the Debian package.

Cheers,
Shaun



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Bug#521746: [Fwd: eagle and libXfixes dependency]

2009-10-05 Thread Shaun Jackman
2009/9/1 Klaus Schmidinger klaus.schmidin...@cadsoft.de:
 On 08/27/09 15:48, Ed Robledo wrote:
 From: Shaun Jackman sjack...@gmail.com

 The ChangeLog states that...
 The Linux version of EAGLE no longer uses libXinerama and libXfixes,
 because these libraries are not available on all systems.

 Yet eagle still depends on libXfixes:
 $ ldd bin/eagle |grep libXfixes
         libXfixes.so.3 = /usr/lib/libXfixes.so.3 (0xb7a4a000)

 Hello Shaun,

 actually EAGLE should use xfixes on systems that provide it,
 and not use it if not present.

 I assume your system doesn't have xfixes. Is there an error
 message if you start EAGLE?

 Best regards
 Klaus Schmidinger

Hi Klaus,

You're right; eagle does not depend on libXfixes. ldd reported that it
depended on libXfixes.so.3, but it's not a direct dependency. Eagle
depends on libXcursor.so.1, which, on Debian, depends on
libXfixes.so.3.

Cheers,
Shaun



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Bug#546237: eagle: Eagle exits with segmentation fault

2009-10-05 Thread Shaun Jackman
Hi,

Can you try starting eagle like so:
exec -a /usr/share/eagle/bin/eagle /usr/lib/eagle/bin/eagle

and like so:
exec -a ~/.eagle/bin/eagle /usr/lib/eagle/bin/eagle

Cheers,
Shaun

2009/9/11 jcfolke jfn-nes...@tem00.org:
 Package: eagle
 Version: 5.6.0-1
 Severity: important

 I can start eagle in two ways, either by clicking program-programming-eagle 
 (or typing eagle in a terminal) or by /usr/lib/eagle/bin/eagle in a terminal.

 If i start it the first way, the program starts, i can create a PCB, draw a 
 wire but if i try to edit the wire, the program crashes.

 If i start the second way, i get dialogs complaining that a lot of 
 directories are missing like /usr/lib/eagle/lbr etc. If i click 'no' on every 
 of this dialogs that are appearing, the program starts and i can draw and 
 edit as many wires as i like without the application crashing. However, if i 
 start it this way there are no libraries etc.

 I guess you would need more information, so please tell me if there is 
 something i can do.

 Best Regards



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Bug#545758: closed by Charles Plessy ple...@debian.org (Re: [Debian-med-packaging] Bug#545758: samtools: New upstream release)

2009-09-14 Thread Shaun Jackman
Thanks, Charles.



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Bug#545758: samtools: New upstream release

2009-09-08 Thread Shaun Jackman
Package: samtools
Severity: wishlist

A new upstream release, 0.1.6, of samtools is available.

Cheers,
Shaun



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Bug#543800: zlibc: Include a script in /usr/bin

2009-08-26 Thread Shaun Jackman
Package: zlibc
Severity: wishlist

I prefer to use zlibc with a script rather than /etc/ld.so.preload:

== /usr/bin/zlibc ==
#!/bin/bash
LD_PRELOAD=/lib/uncompress.so exec $...@%.gz}
== /usr/bin/zlibc ==

$ zlibc wc /usr/share/dict/connectives.gz
150 150 706 /usr/share/dict/connectives

A user may create an alias to a shorter name, such as `z', if they
wish. I find this very useful.

Cheers,
Shaun



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Bug#515015: azureus incorrectly depends on openjdk-6-jre

2009-07-12 Thread Shaun Jackman
Hi Zachary,

Azureus depends on openjdk-6-jre primarily to exclude the GNU java
interpreter, which for some unknown reason does not work with Azureus.
Since, as far as I know, Sun's java interpreter is not in the Debian
archive, I didn't add an explicit alternative for it. I don't however
see any harm in adding an alternative. What's the name of the Sun java
interpreter package?

Cheers,
Shaun

2009/7/10 Zachary Palmer zep_deb...@bahj.com:
 Package: azureus
 Version: 3.1.1.0-4
 Followup-For: Bug #515015


 In order to correct this, azureus should be made to depend upon
 java6-runtime, right?  Then, one could use either OpenJDK's JRE or the
 Sun JRE to run Azureus.



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Bug#535868: eagle: bashism in /bin/sh script

2009-07-05 Thread Shaun Jackman
The bashism used here is 'exec -a', which is used to set argv[0] (the
program path) when executing a binary. This trick is necessary,
because the program in question looks for files in the directory
dirname(argv[0]). Does dash have a way to achieve the same? If not,
I'll change the interpreter of this script to /bin/bash.

Cheers,
Shaun

2009/7/5 Raphael Geissert atom...@gmail.com:
 Package: eagle
 Severity: important
 Version: 5.4.0-3
 User: debian-rele...@lists.debian.org
 Usertags: goal-dash

 Hello maintainer,

 While performing an archive wide checkbashisms (from the 'devscripts' package)
 check I've found your package containing a /bin/sh script making use
 of a bashism.

 checkbashisms' output:
 possible bashism in ./usr/bin/eagle line 13 (exec -c/-l/-a name):
         exec -a /usr/share/eagle/bin/eagle /usr/lib/eagle/bin/eagle $@
 possible bashism in ./usr/bin/eagle line 24 (exec -c/-l/-a name):
 exec -a ~/.eagle/bin/eagle /usr/lib/eagle/bin/eagle $@


 Not using bash (or a Debian Policy conformant shell interpreter which doesn't
 provide such an extra feature) as /bin/sh is likely to lead to errors or
 unexpected behaviours.
 Please be aware that although bash is currently the default /bin/sh there was
 a release goal for Lenny to make dash the default /bin/sh[1], and has been
 proposed for squeeze as well[2][3].

 If you want more information about dash as /bin/sh, you can read:
 http://lists.debian.org/debian-release/2008/01/msg00189.html

 For more information supporting this goal please refer to Debian Policy,
 section 10.4, at:
 http://www.debian.org/doc/debian-policy/ch-files.html#s-scripts

 Hints about how to fix bashisms:
 Sometimes these bugs are already fixed in Ubuntu, look at the PTS.
 If not already fixed you can read:
 https://wiki.ubuntu.com/DashAsBinSh

 If you still don't know how to fix the bashisms don't hesitate to reply to
 this email, or tag the bug as 'help'.

 [1]http://release.debian.org/lenny/goals.txt
 [2]http://lists.debian.org/debian-release/2009/04/msg00133.html
 [3]http://lists.debian.org/debian-devel/2009/06/msg00767.html

 Thank you,
 Raphael Geissert






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Bug#534131: nvidia-glx-legacy-96xx: New version available

2009-06-21 Thread Shaun Jackman
Package: nvidia-glx-legacy-96xx
Severity: wishlist

nvidia-glx-legacy-96xx Version: 96.43.11 is released.

http://us.download.nvidia.com/XFree86/Linux-x86/96.43.11/NVIDIA-Linux-x86-96.43.11-pkg1.run

Thanks,
Shaun



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Bug#521746: FTBFS: couldn't find library libXrender.so.1

2009-06-17 Thread Shaun Jackman
Hi Johann,

2009/5/22 Johann Glaser johann.gla...@gmx.at:
 Eagle starting from version 5.3 should not require libXinerama and
 libXfixes any more. See http://www.cadsoftusa.com/version50.htm.en and
 scroll down to Version 5.3.

I see this comment in the changelog:

Version 5.3
Platforms
* The Linux version of EAGLE no longer uses libXinerama and libXfixes,
because these libraries are not available on all systems.

Yet the executable still links to libXfixes, though not to libXinerama.

Cheers,
Shaun

$ ldd bin/eagle |grep X
libXrender.so.1 = /usr/lib/libXrender.so.1 (0xb7f5)
libXrandr.so.2 = /usr/lib/libXrandr.so.2 (0xb7f49000)
libXcursor.so.1 = /usr/lib/libXcursor.so.1 (0xb7f4)
libXft.so.2 = /usr/lib/libXft.so.2 (0xb7f2d000)
libXext.so.6 = /usr/lib/libXext.so.6 (0xb7e7e000)
libX11.so.6 = /usr/lib/libX11.so.6 (0xb7d6)
libXi.so.6 = /usr/lib/libXi.so.6 (0xb7d54000)
libXfixes.so.3 = /usr/lib/libXfixes.so.3 (0xb7a52000)
libXau.so.6 = /usr/lib/libXau.so.6 (0xb7a29000)
libXdmcp.so.6 = /usr/lib/libXdmcp.so.6 (0xb7a0a000)



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Bug#532846: swt-gtk: New upstream release 3.4.2

2009-06-12 Thread Shaun Jackman
Package: swt-gtk
Severity: wishlist

swt-gtk 3.4.2 is available.

Cheers,
Shaun



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Bug#528961: bluez-utils: Cannot connect to bluetooth keyboard

2009-05-16 Thread Shaun Jackman
Package: bluez-utils
Version: 3.36-3
Severity: important

I cannot connect to an Apple bluetooth keyboard using hidd:

$ sudo hidd --search
Searching ...
Connecting to device 00:1F:5B:FC:77:F9
Can't create HID control channel: Connection timed out
$ sudo hidd --connect 00:1F:5B:FC:77:F9
Can't create HID control channel: Connection timed out

I can ping the device using l2ping.

Cheers,
Shaun



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Bug#521901: marked as done (avarice: FTBFS: current binutils static libs need -lz)

2009-05-06 Thread Shaun Jackman
Hi Phillip,

Thanks for finding and uploading this fix.

Cheers,
Shaun

009/5/6 Debian Bug Tracking System ow...@bugs.debian.org:
 Closes: 521901
 Changes:
  avarice (2.9-1.1) unstable; urgency=low
  .
   * Non-maintainer upload.
   * Fix FTBFS because of missing zlib import.  Add zlib1g-dev as a
 Build-Depency.  (Closes: #521901)
   * Added a Build-Conflicts on binutils-multiarch as that diverts
 the static archive of libbfd away.



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Bug#520597: [Pkg-openmpi-maintainers] Bug#520597: openmpi: New release 1.3.1 available

2009-03-23 Thread Shaun Jackman
Hi Manuel,

Is Open MPI 1.3.1 not binary compatible with Open MPI 1.3?

Cheers,
Shaun



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Bug#520597: openmpi: New release 1.3.1 available

2009-03-21 Thread Shaun Jackman
Package: openmpi
Severity: wishlist



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Bug#520598: sparsehash: ext/hash_fun.h not found

2009-03-21 Thread Shaun Jackman
Package: sparsehash
Severity: serious

google/sparse_hash_set includes ext/hash_fun.h, which is not found:

configure:6326: checking google/sparse_hash_set usability
configure:6338: g++ -c -g -O2  -I/usr/lib/openmpi/include conftest.cc 5
In file included from conftest.cc:76:
/usr/include/google/sparse_hash_set:88:60: error: ext/hash_fun.h: No
such file or directory
In file included from conftest.cc:76:
/usr/include/google/sparse_hash_set:96: error: expected type-specifier



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Bug#520599: sparsehash: New release 1.4

2009-03-21 Thread Shaun Jackman
Package: sparsehash
Severity: wishlist

http://code.google.com/p/google-sparsehash/
http://google-sparsehash.googlecode.com/files/sparsehash-1.4.tar.gz



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Bug#519874: RM: pocketpc-binutils

2009-03-16 Thread Shaun Jackman
2009/3/16 Frank Lichtenheld dj...@debian.org:
 On Sun, Mar 15, 2009 at 01:35:55PM -0700, Shaun Jackman wrote:
 Please remove the source package pocketpc-binutils. I've also
 requested the removal of its only reverse dependency pocketpc-gcc.
 These toolchains are based on an obsolete version of GCC.

 There is an additional reverse-dependency: pocketpc-sdk

Shaun Jackman wrote...
 The Pocket PC toolchain has been essentially unmaintained for a long
 time. I haven't had a Pocket PC device in years. I've requested that
 the pocketpc toolchain be removed from the Debian's unstable archive.
 The packages will still be available in etch and lenny.

 The bug numbers requesting removal from the archive are 519874,
 519875, and 519877 for the packages pocketpc-binutils, pocketpc-gas
 and pocketpc-gcc. You are the maintainer of the package pocketpc-sdk.
 Should I request its removal as well?

2009/3/15 Eric House eeho...@eehouse.org:
 I think so.

 Just FYI, last week I started filling out an ITP for the cegcc toolchain.
 After using it for two years and shipping a release with it I finally
 managed to build the damn thing and so ought to be able to get it into
 Debian.  The upstream is active and supportive of my packaging it, so it
 seems a worthy successor.

 --Eric



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Bug#519874: RM: pocketpc-binutils

2009-03-15 Thread Shaun Jackman
Package: ftp.debian.org

Please remove the source package pocketpc-binutils. I've also
requested the removal of its only reverse dependency pocketpc-gcc.
These toolchains are based on an obsolete version of GCC.

Thanks,
Shaun



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Bug#519877: RM: pocketpc-gcc

2009-03-15 Thread Shaun Jackman
Package: ftp.debian.org

Please remove the source package pocketpc-gcc.This toolchain is based
on an obsolete version of GCC. It has no reverse dependencies.

Thanks,
Shaun



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Bug#519875: RM: pocketpc-gas

2009-03-15 Thread Shaun Jackman
Package: ftp.debian.org

Please remove the source package pocketpc-gas from the archive. This
toolchain is based on an obsolete version of GCC. I've also requested
the removal of its reverse dependencies, pocketpc-binutils and
pocketpc-gcc.

Thanks,
Shaun



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Bug#426305: Bug#426304: closed by César Gómez Martín cesar.go...@gmail.com (Bug#426304: fixed in lcab 1.0b12-3)

2009-03-15 Thread Shaun Jackman
Hi César,

Would you care to adopt pocketpc-cab?

Cheers,
Shaun

2008/1/27 César Gómez Martín cesar.go...@gmail.com:
 Hello, I don't mind to adopt pocketpc-cab but I will not be able to
 test it in a Pocket PC because I don't have one...

 Best regards,
 César.

 On Jan 27, 2008 10:03 PM, Shaun Jackman sjack...@gmail.com wrote:
 Thanks for adopting lcab. Do you have any interest in adopting
 pocketpc-cab, which creates CAB files for the Pocket PC platform?

 Cheers,
 Shaun

 On Jan 27, 2008 11:09 AM, Debian Bug Tracking System
 ow...@bugs.debian.org wrote:
  This is an automatic notification regarding your Bug report
  which was filed against the wnpp package:
 
  #426304: ITA: lcab -- create cabinet (.cab) archives
 
  It has been closed by César Gómez Martín cesar.go...@gmail.com.



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Bug#518441: wireshark-dev: Please include asn2wrs.py

2009-03-05 Thread Shaun Jackman
Package: wireshark-dev

Please include the script tools/asn2wrs.py in the package wireshark-dev.

Thanks,
Shaun



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Bug#516255: Azureus adoption

2009-02-25 Thread Shaun Jackman
Hi Adnan,

Thanks for your interest in adopting Azureus/Vuze. It can be a pretty
tough package to maintain. I've also learned the hard way that it is
best to be a daily (or at least regular) user of a package you
maintain. It can be a fair bit of work, and it can be embittering if
you're not sharing in the benefits of using the program.

If you feel you're up to it, you can start by preparing an upload of
SWT 3.4.1, which I've found easier to maintain than Vuze, although it
has its own quirks as well. If that goes well for you, you can prepare
an upload of Vuze 4.1.0.2.

You can track how upstream versions differ from Debian's versions here:
http://qa.debian.org/developer.php?login=sjack...@debian.org

I don't see you in the Debian new maintainer queue:
https://nm.debian.org/nmlist.php
How is your application progressing?

Cheers,
Shaun

2009/2/24 Adnan Hodzic ad...@foolcontrol.org:
 Hello,

 For quite some time I've been keeping an eye on a packages for
 adoption waiting for my perfect package and today I just saw that
 Azureus is up for adoption :)

 http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=516255

 I haven't used Azureus in years, but I remember I really used to love
 it back in the day. I'm in my process of learning Java and in my
 process of becoming official Debian Developer :)

 So being able to package/maintain Azureus within Debian would be just great!

 This would be my first Debian package, but if I'm eligible for this
 task I'd love to do it.

 Regards,

 Adnan

 --

 Laurence J. Peter  - If two wrongs don't make a right, try three.




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Bug#516252: eagle: FTBFS on amd64

2009-02-19 Thread Shaun Jackman
Package: eagle
Version: 5.4.0-1
Severity: important
Submitter: Jindrich Makovicka makov...@gmail.com

It would be nice to have a package for x86-64 also. It seems that it
suffices to remove dh_strip from the rules file to make the amd64
version build. As the closed source binaries are stripped anyway, it
should be ok to remove this line.

Regards,
Jindrich Makovicka



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Bug#516255: RFA: azureus -- BitTorrent client

2009-02-19 Thread Shaun Jackman
Package: wnpp

Azureus is a BitTorrent client. The upstream package has been renamed
to Vuze and now has a focus on distributing and playing multimedia
content.

Azureus is implemented in Java and uses SWT, the cross-platform widget
toolkit for Java used primarily by the Eclipse IDE.

Eclipse packages the SWT libraries (see the source package eclipse and
the binary package libswt3.2-gtk-java), but these tend to be too out
of date to compile Azureus. For this reason, I maintain a separate
copy of SWT for GTK (see the source package swt-gtk and the binary
package libswt-gtk-3.4-java). The adopter of Azureus would need to
also adopt SWT.

Cheers,
Shaun



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Bug#515215: sparsehash: Rename package to libsparsehash-dev

2009-02-14 Thread Shaun Jackman
Package: sparsehash

Since this package is a library and contains header files, it would be
better named libsparsehash-dev.

Cheers,
Shaun



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Bug#509878: Selecting the `Classic Interface' from the command line

2008-12-30 Thread Shaun Jackman
Is it possible to select the `Classic Interface' from the command line?

Thanks,
Shaun



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Bug#509879: NMU for azureus

2008-12-29 Thread Shaun Jackman
Hi David,

Vuze is the dummy package, and azureus is the substantial package.
Vuze depends on azureus and additional packages required to run the
novel Vuze GUI. Those dependencies are not necessary when using the
classical GUI of Azureus. Azureus suggests vuze. Perhaps this should
be Recommends. Otherwise, before Lenny is released, I don't see making
any major changes. If the user wishes to run the Vuze GUI, the user
may install the package vuze, which includes all the necessary
dependencies. if the user wishes to run the Azureus GUI and minimize
dependencies, the user may install the package azureus.

The primary issue is that if the user wishes to run the Vuze GUI but
installs the azureus package, the user will see library exceptions
rather than a useful error message.

If anything, I think these bugs simply require better documentation
describing the difference between the azureus and vuze packages.

Cheers,
Shaun

2008/12/28 David Paleino d.pale...@gmail.com:
 Hello Shawn,
 do you plan fixing #509878 and #509878? I can prepare a NMU if you don't have
 time.
 Also, I saw that debian/control lists azureus and vuze: wouldn't it be
 better to make azureus a transitional dummy package depending on vuze, and 
 make
 vuze be the real package? Currently vuze only has:

 $ apt-file list vuze
 vuze: /usr/share/doc/vuze/changelog.Debian.gz
 vuze: /usr/share/doc/vuze/copyright
 $

 And azureus is not a separate tool, AFAICS, to justify two binary packages 
 (and
 one just containing useless docs)

 Kindly,
 David



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Bug#509878: azureus: Missing dependency on libswt-cairo-gtk-3.4-jni

2008-12-29 Thread Shaun Jackman
package azureus
merge 509878 509879
retitle 509878 azureus: `Unable to load graphics library' if Vuze GUI
is selected
tag 509878 confirmed
thanks

If the Vuze GUI is selected, and the azureus package is installed
instead of the vuze package, the user will see the above-mentioned
error message.



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Bug#324776: pocketpc packages

2008-12-13 Thread Shaun Jackman
Hi Justin,

I haven't used these packages in some time. I no longer have a Pocket
PC device, so I cannot test your work. The packages are based on
now-outdated versions of binutils and gcc, but updating those should
be straight forward. There's a separate package for pocketpc-gas,
because gas 2.13 was the last version (at the time) with which I was
able to produce a working DLL. Perhaps that bug's been fixed now. The
majority of the patches are to newlib to add a POSIX compatibility
layer that calls the underlying Pocket PC kernel system calls. Fire
any other questions my way.

Cheers,
Shaun

2008/12/12 Justin Card jc...@atnex.net:
 Hi Shaun,

 I am just getting into pocketpc development, and would be interested in
 taking over and adopting your debian PocketPC packages.  (Albeit slowly,
 as I am just getting started with packaging.)

 Would you be willing to answer some questions as they arise, and
 possibly sponsor my package submissions as I get started?

 Thanks,
 Justin Card



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Bug#421711: Font problem in Qtiplot and Eagle 5.2 solved

2008-11-21 Thread Shaun Jackman
From: Gudjon I. Gudjonsson [EMAIL PROTECTED]

Hi
  On my font problems 6 months birthday :) I managed to solve it. The trick
was adding a symbolic link in
/etc/fonts/conf.d/
70-no-bitmaps.conf - ../conf.avail/70-no-bitmaps.conf
and running
dpkg-reconfigure fontconfig

Since it took me 6 months to fix it, I define it as non-trivial. But you do
perhaps know a better way to solve it than I do.

Cheers
Gudjon



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Bug#506513: RFA: eagle -- Printed circuit board design tool

2008-11-21 Thread Shaun Jackman
Package: wnpp

I haven't designed a circuit board in some time, and this package
would be better maintained by someone who uses the software regularly.
A new upstream release, version 5.3, is available.

Cheers,
Shaun



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Bug#506514: RM: seda

2008-11-21 Thread Shaun Jackman
Package: ftp.debian.org

Please remove the source package seda (binary package libseda-java)
from the unstable archive. It is a Java library and has no reverse
dependencies. The stable version of Azureus (2.5.0.0+0-1) did depend
on it, but recent versions do not.

Thanks,
Shaun



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Bug#421711: Font problem in Qtiplot and Eagle 5.2 solved

2008-11-16 Thread Shaun Jackman
From: Gudjon I. Gudjonsson [EMAIL PROTECTED]

Hi
  On my font problems 6 months birthday :) I managed to solve it. The trick
was adding a symbolic link in
/etc/fonts/conf.d/
70-no-bitmaps.conf - ../conf.avail/70-no-bitmaps.conf
and running
dpkg-reconfigure fontconfig

Since it took me 6 months to fix it, I define it as non-trivial. But you do
perhaps know a better way to solve it than I do.

Cheers
Gudjon



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Bug#505820: New version available

2008-11-15 Thread Shaun Jackman
Package: maq
Severity: wishlist

maq 0.7.1 is available.



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Bug#495514: Patch for #495514

2008-08-22 Thread Shaun Jackman
On 8/19/08, Sebastien Delafond [EMAIL PROTECTED] wrote:
...
 Anyway, I'm sure Shaun now has enough datapoints to decide what sort
 of solution he'd like to implement. I've removed all my past NMU
 uploads from DELAYED/7, and uploaded a single -3.1 that regroups all
 the fixes needed for my solution to the problem. The debdiff attached
 to this email represents those changes.

Hi Sebastien and Peter,

Thanks for your work. I'm away on my honeymoon though, and so won't be
able to help out. If, amongst yourslves, you're able to arrive at a
consensus as to the best solution, please NMU as necessary.

Cheers,
Shaun



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Bug#494705: RFA: monotone-viz - visualize a monotone repository

2008-08-11 Thread Shaun Jackman
Package: wnpp

Due to a change of job, I am not using this tool as regularly as I
used to. This package we would be better maintained by someone who
does. There is one outstanding release-critical bug.

Cheers,
Shaun



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Bug#316772: Removing neutrino?

2008-08-08 Thread Shaun Jackman
Removing neutrino is fine by me. The package gnomad2 is a suitable alternative.

Cheers,
Shaun

On Fri, Aug 8, 2008 at 11:31 AM, Frank Lichtenheld [EMAIL PROTECTED] wrote:
 severity 316772 serious
 thanks

 Hi,

 neutrino has been orphaned for a very long time now and I am evaluating
 whether a request for removal should be finally filed.

 You are receiving this mail because:
  - your name showed up somewhere in the history of the package
  - I think that you might be interested for some reason
  - or you maintain a related/similar package

 Are you interested in adopting this package? Do you know potential adopters?
 If so, please could you forward them this mail, Ccing the BTS and me?

 If there is no action from anyone, I'll request the removal of this package
 from Debian after a month.

 Thank you,
 --
 Frank Lichtenheld [EMAIL PROTECTED]
 www: http://www.djpig.de/




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Bug#441947: Debian Bug report logs - #441947 ITA: freeguide -- Displays TV listings

2008-07-28 Thread Shaun Jackman
On Fri, Jul 25, 2008 at 7:37 PM, Daniel Watkins
[EMAIL PROTECTED] wrote:
...
 I have received some feedback on that package from other sources, and
 it is now significantly different.  I have uploaded the new package to
 my webspace, at http://packages.daniel-watkins.co.uk, and would
 appreciate some feedback on it.

Since you've added openjdk to the dependencies, can the package move to main?

The first line of the copyright file should mention that you adopted
the package and the date.

Looks good to me! It's all yours now.

Cheers,
Shaun



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Bug#492789: freeguide: New upstream release (0.10.8)

2008-07-28 Thread Shaun Jackman
Package: freeguide
Severity: wishlist

From:  [EMAIL PROTECTED]
Date: Mon, Jul 28, 2008 at 1:41 PM
Subject: [fmII] FreeGuide TV Guide 0.10.8 released (Default branch)

This email is to inform you about the release of version '0.10.8' of
'FreeGuide TV Guide' through freshmeat.net. All URLs and other useful
information can be found at

   http://freshmeat.net/projects/freeguide-tv/

The changes in this release are as follows:
This release displays an error message when Choose channels goes
wrong. The install tarball script now has correct absolute paths.
Support for the Swedish grabber was fixed. The Windows installer was
updated to include XMLTV 0.5.52.

Release focus:
6 - Minor bugfixes

Project added:
Mon, Dec 3rd 2001 03:20 (6 years, 7 months ago)

Project description:
FreeGuide is a TV guide program. It allows you to find programs you
are interested in quickly, and ignore the rest.

Trove categories:
[Development Status  ] 3 - Alpha
[Intended Audience   ] Developers, End Users/Desktop
[License ] OSI Approved :: GNU General Public License (GPL)
[Operating System] Microsoft :: Windows :: Windows 95/98/ME, OS
Independent, POSIX :: Linux
[Programming Language] Java
[Topic   ] Desktop Environment, Internet

If you would like to cancel subscription to releases of this project,
login to freshmeat.net and choose 'home' from the personal menubar at the
top of the page. You'll be presented with a list of projects and categories
you're subscribed to in the right column, which you may cancel by
highlighting the project or category in question and clicking the 'delete'
button.

Sincerely,
freshmeat.net



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Bug#417983: marked as forwarded (freeguide tv listing '.ser' file format is pretty much undocumented)

2008-07-26 Thread Shaun Jackman
On Sat, Jul 26, 2008 at 11:47 AM, Andy Balaam
[EMAIL PROTECTED] wrote:
...
 (**the older 'freeguide' xml files could be used to show TV
 info in 'tvtime'.)

 FreeGuide has an Export function under the file menu.  Choosing to
 export as XMLTV will produce the XML files that were previously stored
 in the .freeguide directory.

 Would an FAQ entry be good enough to mark this bug as fixed?

It seems to me that it's this export feature that the original bug
submitter was looking for. I think that we can close this bug based on
this, and perhaps add an entry to the FAQ.

Cheers,
Shaun



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Bug#417983: marked as forwarded (freeguide tv listing '.ser' file format is pretty much undocumented)

2008-07-24 Thread Shaun Jackman
On Thu, Jul 24, 2008 at 6:27 PM, Debian Bug Tracking System
[EMAIL PROTECTED] wrote:
...
 I'm unsure of how to respond to the bug report below, and thought
 that you collectively would be in a much better position to answer.  I
 would ask that you CC [EMAIL PROTECTED] in your
 responses to it, so that the Debian bug is kept up-to-date with your
 discussion.

Responses should be CC'ed to [EMAIL PROTECTED], not
[EMAIL PROTECTED]

Cheers,
Shaun



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Bug#441947: Debian Bug report logs - #441947 ITA: freeguide -- Displays TV listings

2008-07-24 Thread Shaun Jackman
On Thu, Jul 24, 2008 at 1:22 PM, Daniel Watkins
[EMAIL PROTECTED] wrote:
...
 The summer job has cooled off a little, so I probably have some time to
 devote to this.  Could you walk me through the procedure to adopt the
 package?

Hi Daniel,

Prepare a package for upload incrementing the version number and
changing the maintainer, send it to me for some proof reading, then
upload it to the server, or I sponsor your upload if you're not a
Debian developer.

Cheers,
Shaun



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Bug#491221: Solved: eagle: scrambled GUI when Composite enabled

2008-07-18 Thread Shaun Jackman
package eagle
tag 491221 patch
thanks

Thanks! I'm away this weekend, but I'll upload a fix next week.

Cheers,
Shaun

On Thu, Jul 17, 2008 at 6:12 PM, Kai-Martin [EMAIL PROTECTED] wrote:

 Closer examination of the pixel dust revealed that they are remnants of
 transparency gone wrong. Somebody in the german gnome usenet group hinted me
 to a workaround -- Set the environment variable XLIB_SKIP_ARGB_VISUALS in
 usr/bin/eagle. This resolved the issue for me:

 /--/usr/bin/eagle-
 #!/bin/sh
 if [ -z $DISPLAY ]; then
echo eagle: cannot open display
exit 1
 fi
 export XLIB_SKIP_ARGB_VISUALS=1
 exec /usr/lib/eagle/bin/eagle $@
 \-

 ---(kaimartin)---



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Bug#491201: azureus: Error initialize Mainwindow

2008-07-18 Thread Shaun Jackman
Hi Fabiano,

Does installing libswt-cairo-gtk-3.4-jni fix your issue?

Cheers,
Shaun

On Thu, Jul 17, 2008 at 8:22 AM, Fabiano Manoel de Andrade
[EMAIL PROTECTED] wrote:
 Package: azureus
 Version: 3.1.1.0-1
 Severity: important


After upgrade I get this error message:
 Error initilize Mainwindow
 Unable to load graphics library [Cairo is required]
 (java.lan.NoClassDefFoundError: Could not initialize class
 org.eclipse.swt.internal.cairo.Cairo)

With this the main window is not showed properly and the systray
 icon don't appear.
Thanks in advance.
Fabiano.

 -- System Information:
 Debian Release: lenny/sid
  APT prefers unstable
  APT policy: (900, 'unstable')
 Architecture: amd64 (x86_64)

 Kernel: Linux 2.6.25-2-amd64 (SMP w/2 CPU cores)
 Locale: LANG=pt_BR.UTF-8, LC_CTYPE=pt_BR.UTF-8 (charmap=UTF-8)
 Shell: /bin/sh linked to /bin/bash

 Versions of packages azureus depends on:
 ii  gij-4.3 [java-virtual-machine 4.3.1-6The GNU Java bytecode interpreter
 ii  java-gcj-compat [java2-runtim 1.0.78-2   Java runtime environment using 
 GIJ
 ii  java-gcj-compat-headless [jav 1.0.78-2   Java runtime environment using 
 GIJ
 ii  libcommons-cli-java   1.1-3  API for working with the command 
 l
 ii  liblog4j1.2-java  1.2.15-3   Logging library for java
 ii  libswt-gtk-3.4-java   3.4-1  Standard Widget Toolkit for GTK+ 
 J
 ii  sun-java6-jre [java2-runtime] 6-07-3 Sun Java(TM) Runtime Environment 
 (

 azureus recommends no packages.

 -- no debconf information






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Bug#490214: swt-gtk: New upstream release (3.4)

2008-07-10 Thread Shaun Jackman
Package: swt-gtk
Submitter: أحمد المحمودي [EMAIL PROTECTED]
Severity: wishlist

Hello,

 I just checked http://eclipse.org/swt, and I found that they released
 swt 3.4. Could you please make a Debian package for it ?


Bug#489445: 'azureus' renamed to 'vuze'.

2008-07-06 Thread Shaun Jackman
Hi Teodor,

On Sun, Jul 6, 2008 at 2:30 AM, Teodor [EMAIL PROTECTED] wrote:
 I recommend to upload vuze_3.1.1.0 in NEW and request removal on
 azureus from unstable for the following reasons:
 * azureus has 3 RC bugs and sooner or latter will be removed from lenny [1];
 * vuze_3.0.5.0-1 depends on two packages which are no longer available [2];

 Considering that the big blocked for azureus is the upload of
 'openjdk' I recommend to not waste time fixing azureus (probably
 package 3.0.5.2 along with some bug fixes) and go for vuze_3.1.1.0 in
 lenny (azureus being a dummy package depending on vuze).

 Thanks for your response.

 [1]  
 http://bugs.debian.org/cgi-bin/pkgreport.cgi?src=azureusarchive=nopend-exc=pending-fixedpend-exc=fixedpend-exc=donesev-inc=criticalsev-inc=gravesev-inc=seriousrepeatmerged=no
 [2]  http://packages.debian.org/sid/vuze

Vuze 3.1.1.0 built and run with surprising ease. The source zip
finally includes a build script! I'm considering uploading it as
azureus 3.1.1.0 rather than changing the package name at this point.
Not much has changed in the source code. The jar file, for example, is
still named Azureus2.jar. I don't feel that there's much to be gained
by renaming the source package to vuze.

Cheers,
Shaun



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Bug#489445: azureus: New upstream release: vuze 3.1.1.0

2008-07-05 Thread Shaun Jackman
Package: azureus
Submitter: Teodor [EMAIL PROTECTED]
Severity: wishlist

Hi,

One week ago a new major release (minor version number) of azureus was
announced [1]. From this release the upstream has decided to change
the name from 'azureus' to 'vuze'.

What can be done to have this change in time for lenny? Probably a new
source package name 'vuze' and an binary dummy package for azureus -
vuze transition.
In fact this is not the problem, but what do you now about the
packaging of openjdk? From what I've read on the BTS, depending on
openjdk being in lenny or not the implication will be for azureus/vuze
too. Do you have any ideea why is taking so long to have openjdk in
Debian?

Thanks

[1] http://azureus.sourceforge.net/



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Bug#489445: 'azureus' renamed to 'vuze'.

2008-07-05 Thread Shaun Jackman
Hi Teodor,

In just four weeks, I'm leaving on vacation for ten weeks. That being
the case, I'm not sure I want to push vuze 3.1.1.0 into the archive in
time for etch, since I won't be around to help with bugs. On the plus
side, azureus 3.0.5.0 already includes a dummy package named vuze that
depends on azureus as well as the necessary packages for the web
browser that vuze embeds. So, if someone running etch installs the
package 'vuze', they should get what they expect. On the downside,
this means I can't just package vuze 3.1.1.0 as a new package with a
new name and upload it, because it would conflict with the vuze
package in azureus 3.0.5.0. I just downloaded vuze 3.1.1.0 and I'll
see if it builds and runs without too much trouble.

Cheers,
Shaun

On Mon, Jun 23, 2008 at 6:08 AM, Teodor [EMAIL PROTECTED] wrote:
 Hi,

 One week ago a new major release (minor version number) of azureus was
 announced [1]. From this release the upstream has decided to change
 the name from 'azureus' to 'vuze'.

 What can be done to have this change in time for lenny? Probably a new
 source package name 'vuze' and an binary dummy package for azureus -
 vuze transition.
 In fact this is not the problem, but what do you now about the
 packaging of openjdk? From what I've read on the BTS, depending on
 openjdk being in lenny or not the implication will be for azureus/vuze
 too. Do you have any ideea why is taking so long to have openjdk in
 Debian?

 Thanks

 [1] http://azureus.sourceforge.net/




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Bug#441947: Debian Bug report logs - #441947 ITA: freeguide -- Displays TV listings

2008-07-02 Thread Shaun Jackman
 On Mon, 9 Jun 2008 15:55:59 -0700 Shaun Jackman [EMAIL PROTECTED] wrote:
 Are you still interested in adopting freeguide?
On Wed, Jul 2, 2008 at 5:11 AM, Daniel Mark Watkins
[EMAIL PROTECTED] wrote:
 I am, but it'll have to wait until mid-August as I've got a fairly
 intense summer job ongoing.

Okay. Get back to me when you're ready.

Enjoy your summer! Cheers,
Shaun



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Bug#480818: Don't build depend on libxul-dev

2008-06-24 Thread Shaun Jackman
On Mon, Jun 23, 2008 at 11:48 AM, Mike Hommey [EMAIL PROTECTED] wrote:
 On Mon, Jun 23, 2008 at 10:21:32AM -0700, Shaun Jackman wrote:
 I just uploaded SWT 3.4~rc3-1 which supports xulrunner 1.9. I usually
 avoid packaging prereleases unless I have good reason, but this seems
 like a good reason. Once it makes it through the NEW queue, this bug
 will be closed.

 Is it okay with the reverse dependencies ?

The only reverse dependency is Azureus, which I maintain, and it'll
need a trivial upload, but works fine.

Cheers,
Shaun



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Bug#480818: Don't build depend on libxul-dev

2008-06-23 Thread Shaun Jackman
On Sat, Jun 21, 2008 at 11:47 PM, Mike Hommey [EMAIL PROTECTED] wrote:
 On Sat, Jun 21, 2008 at 09:28:17AM -0700, Shaun Jackman wrote:
 Hi Mike,

 Thanks for your help so far. I'm starting to get the impression that
 modifying SWT-GTK to support xulrunner 1.9 is not a trivial amount of
 work, and that it may be a better plan until upstream supports
 xulrunner 1.9 explicitly. Since they'll be doing this work anyways,
 it's a duplication of effort for me to be doing it now, and they'll
 certainly do a better job of it than I will hacking and slashing code
 together.

 How close do you think I am to fixing this? If you'd care look at it
 yourself, the function that is failing is

 XPCOM.NS_NewLocalFile in Mozilla.create in Mozilla.java:332.
 which calls
 NS_1NewLocalFile in xpcom.cpp:94
 which calls
 NS_NewLocalFile
 which returns
 Browser: org.eclipse.swt.SWTError: XPCOM error -1041039359
 which corresponds to NS_ERROR_NOT_INITIALIZED.

 I couldn't immediately see the relation between this function and
 impl_init from mozilla-embed-single.cpp from epiphany-browser.

 Could you send your current patch against the last version of swt-gtk in
 unstable ?

Hi Mike,

I just uploaded SWT 3.4~rc3-1 which supports xulrunner 1.9. I usually
avoid packaging prereleases unless I have good reason, but this seems
like a good reason. Once it makes it through the NEW queue, this bug
will be closed.

Thanks for your help with this bug. Cheers,
Shaun



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Bug#480818: Don't build depend on libxul-dev

2008-06-21 Thread Shaun Jackman
On Fri, Jun 20, 2008 at 12:03 AM, Mike Hommey [EMAIL PROTECTED] wrote:
 Hi Mike,

 If I use pkg-config libxul-embedding, when running Azureus I get the error:
 Browser: org.eclipse.swt.SWTError: XPCOM error -1041039359
 which corresponds to NS_ERROR_NOT_INITIALIZED.

 With pkg-config libxul it almost works. The embedded browser seems to
 load because it replaces the Loading... splash screen that Azureus
 displays, but all I get is a white background. It seems to be almost
 working though. I don't see any error messages on the console.

 Where do I go from here?

 It looks like all you need is to add the xpcom initialization code. The
 embedding variant needs explicit xpcom loading. You can check how it is
 done in impl_init() in mozilla-embed-single.cpp in epiphany-browser
 source, or xulrunner_init() in mozilla.cpp in kazehakase source.
 You will need to #include gtkmozembed_glue.cpp in the source file
 doing the initialization.

Hi Mike,

Thanks for your help so far. I'm starting to get the impression that
modifying SWT-GTK to support xulrunner 1.9 is not a trivial amount of
work, and that it may be a better plan until upstream supports
xulrunner 1.9 explicitly. Since they'll be doing this work anyways,
it's a duplication of effort for me to be doing it now, and they'll
certainly do a better job of it than I will hacking and slashing code
together.

How close do you think I am to fixing this? If you'd care look at it
yourself, the function that is failing is

XPCOM.NS_NewLocalFile in Mozilla.create in Mozilla.java:332.
which calls
NS_1NewLocalFile in xpcom.cpp:94
which calls
NS_NewLocalFile
which returns
Browser: org.eclipse.swt.SWTError: XPCOM error -1041039359
which corresponds to NS_ERROR_NOT_INITIALIZED.

I couldn't immediately see the relation between this function and
impl_init from mozilla-embed-single.cpp from epiphany-browser.

Cheers,
Shaun



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Bug#480818: Don't build depend on libxul-dev

2008-06-20 Thread Shaun Jackman
On Fri, Jun 13, 2008 at 12:35 AM, Mike Hommey [EMAIL PROTECTED] wrote:
 The first obvious thing would be to ensure you use the proper includes,
 which means you need, at some point, to use pkgconfig --cflags
 libxul-embedding.

 The second thing I would do is ensure it works properly if you
 build with pkg-config --libs libxul instead of libxul-embedding.
 When testing this setup, make sure you set the LD_LIBRARY_PATH to
 /usr/lib/xulrunner-1.9, as it is necessary with what is called the
 dependent glue (which is what you get with libxul.pc).

 Once you have things working with this setup, you can switch to
 libxul-embedding, which requires some additional changes, but we'll
 see then.

Hi Mike,

If I use pkg-config libxul-embedding, when running Azureus I get the error:
Browser: org.eclipse.swt.SWTError: XPCOM error -1041039359
which corresponds to NS_ERROR_NOT_INITIALIZED.

With pkg-config libxul it almost works. The embedded browser seems to
load because it replaces the Loading... splash screen that Azureus
displays, but all I get is a white background. It seems to be almost
working though. I don't see any error messages on the console.

Where do I go from here?

Thanks,
Shaun



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Bug#480818: Don't build depend on libxul-dev

2008-06-13 Thread Shaun Jackman
Hi Mike,

Switching from using -lxpcomglue in libxul-dev to `pkg-config --libs
libxul-embedding` in xulrunner-dev yields the folowing runtime error
when running Azureus/Vuze:
java: symbol lookup error: /usr/lib/jni/libswt-mozilla-gtk-3346.so:
undefined symbol: NS_StringContainerInit2

Any suggestions before the might help speed up my troubleshooting?

I'm attempting to run Azureus/Vuze as a test, which uses
libswt-mozilla-gtk-3.3-jni, which requires xulrunner.

Thanks,
Shaun

On Mon, May 12, 2008 at 12:07 AM, Mike Hommey [EMAIL PROTECTED] wrote:
 Package: swt-gtk
 Severity: wishlist
 User: [EMAIL PROTECTED]
 Usertags: xulrunner-transition

 With the upcoming xulrunner transition, libxul-dev is going to disappear.

 I already sent instructions on what you should be doing in
 http://lists.debian.org/debian-release/2008/05/msg9.html

 This bug report is mostly to help follow the transition going.

 FYI, I will start NMUing plugins and components next week, and will break
 the remaining packages by uploading xulrunner 1.9 in unstable on May 25.

 Though help will be appreciated, I'll also prepare updated packages for
 these during this week and next.

 Cheers,

 Mike






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Bug#441947: Debian Bug report logs - #441947 ITA: freeguide -- Displays TV listings

2008-06-09 Thread Shaun Jackman
Hi Dan,

Are you still interested in adopting freeguide?

Cheers,
Shaun

On Sun, Jan 27, 2008 at 4:55 PM, Shaun Jackman [EMAIL PROTECTED] wrote:
 Thanks for your interest in adopting freeguide.

 The upstream author is interested in making it work with free tools,
 thus facilitating a move from contrib to main. After your initial
 adoption upload of the package, moving freeguide to main would be a
 worthy project.

 Cheers,
 Shaun

 Daniel Watkins [EMAIL PROTECTED] wrote...
 Hi,
 This looks like an app I'm interested in using, as well as a fairly
 easy package to maintain.  I'm in the UK and, as such, have a free
 source of TV listings.

 As a result of all the above, I'd like to take over maintaining this
 package. :)


 Cheers,
 Dan



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Bug#470845: marked as done (missing amd64?)

2008-05-30 Thread Shaun Jackman
 From: Jim Paris [EMAIL PROTECTED]
 To: [EMAIL PROTECTED]
 Date: Thu, 29 May 2008 23:06:45 -0400
 Subject: Resolved
 Things seem to have (finally) resolved themselves... I wonder how?
 Anyway, the package is available for amd64 now.

 -jim

Thanks for the update, Jim. I'm glad to hear it. Sorry it took so long.

Cheers,
Shaun



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Bug#481011: azureus: required plugins are missing

2008-05-24 Thread Shaun Jackman
Hi Todd,

In bug #455351 and before that #405997, I was asked to remove
auto-update because it conflicts in purpose with Debian's package
management system. This change had the side effect of creating bugs
#452326, #452321, and now #481011. I'm unsure how to fix these bugs
without once again enabling azupdater.

Cheers,
Shaun

http://bugs.debian.org/azureus
#405997 azureus: should not prompt the user about updates
#455351 regression of azureus: should not prompt the user about
updates (bug #405997)
#452321: azureus: plugin installer fails to initiallize
#452326: azureus: restart doesn't work
#481011: azureus: required plugins are missing

On Mon, May 12, 2008 at 11:04 PM, Todd A. Jacobs
[EMAIL PROTECTED] wrote:
 Package: azureus
 Version: 3.0.5.0-1
 Severity: important

 Several functions, such as being able to restart azureus or download
 additional plugins, are broken because the azupdater plugin is missing.
 I get errors both when attempting to restart, as well as attempting to
 download any plugins at all.

 Debug output follows:
...



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Bug#482402: libswt-gtk-3.3-jni: where is libswt-awt-gtk-3346 ?

2008-05-24 Thread Shaun Jackman
tag 482402 +confirmed
thanks

Hi Sylvain,

It's not packaged. I'll add it to my wishlist for the next version.

Cheers,
Shaun

On Thu, May 22, 2008 at 5:44 AM, sferriol [EMAIL PROTECTED] wrote:
 Package: libswt-gtk-3.3-jni
 Version: 3.3.1-4
 Severity: normal

 hello
 instead of libswt3.2-gtk-jni, this package has not libswt-awt-gtk-3346.
 so where is it ?

 thanks
 sylvain



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Bug#360101: python-gtk2: want to view svg images

2008-05-12 Thread Shaun Jackman
Thanks!

Cheers,
Shaun

On Mon, May 12, 2008 at 2:56 AM, Loïc Minier [EMAIL PROTECTED] wrote:
 reassign 360101 python-gnome2-desktop 2.22.0-1
  stop

  On Thu, Mar 30, 2006, Matthias Wieser wrote:
   add a recommend for librsvg2-common as it makes it possible to view svg
   images. I had to search for a long time to figure things out.

   I added a Depends, but to python-gnome2-desktop; this will be fixed in
   next upload.

  --
  Loïc Minier



Bug#480741: [Debian-olpc-devel] python-gtk: ImportError: No module named cairo

2008-05-12 Thread Shaun Jackman
reassign 480741 python2.5
thanks

Thanks, Jonas. Reinstalling the package did fix the problem. I did,
however, have to reinstall *every* python package on my system. This
one-liner might come in handy to anyone else that gets bit by the same
bug.

sudo apt-get --reinstall install $(dpkg -l `apt p python` 2/dev/null
|awk '{if ($1 == ii) print $2}')

I'm reassigning this bug to python2.5. Although, I have no idea which
package and which version caused the bug.

Cheers,
Shaun

On Sun, May 11, 2008 at 2:14 PM, Jonas Smedegaard [EMAIL PROTECTED] wrote:
 -BEGIN PGP SIGNED MESSAGE-
  Hash: SHA1


  On Sun, May 11, 2008 at 01:27:39PM -0700, Shaun Jackman wrote:

  Both sugar-emulator and pychess fail with the same GTK+/Cairo related 
 message:
  $ pychess
  Traceback (most recent call last):
File /usr/games/pychess, line 9, in module
  import gtk, gtk.glade, gettext
File /var/lib/python-support/python2.5/gtk-2.0/gtk/__init__.py,
  line 48, in module
  from gtk import _gtk
  ImportError: No module named cairo
  
  I have both python-gtk and python-cairo installed. I recently upgraded
  to python2.5.

  Try reinstalling python-gtk and python-cairo - I experienced something
  similar with other Python libraries in the days right after the switch
  to Python-2.5 (I suspect it was an error in python-support and/or
  python-central which was fixed shortly after but might have caused
  broken installations).


  Please repost this email to the bugreport, and respond to both the
  bugreport and the OLPC mailinglist.


   - Jonas

  - --
  * Jonas Smedegaard - idealist og Internet-arkitekt
  * Tlf.: +45 40843136  Website: http://dr.jones.dk/

   - Enden er nær: http://www.shibumi.org/eoti.htm
  -BEGIN PGP SIGNATURE-
  Version: GnuPG v1.4.6 (GNU/Linux)

  iD8DBQFIJ2HIn7DbMsAkQLgRAvCBAJ9IOjokBa/i1HzefO/IbNDFHHgQxgCgjct2
  LcpzsSu0bvTZeaWY5S4+xVY=
  =Nnjo
  -END PGP SIGNATURE-



Bug#480741: python-gtk: ImportError: No module named cairo

2008-05-11 Thread Shaun Jackman
Package: python-gtk2
Version: 2.12.1-1
Severity: serious

Both sugar-emulator and pychess fail with the same GTK+/Cairo related message:
$ pychess
Traceback (most recent call last):
  File /usr/games/pychess, line 9, in module
import gtk, gtk.glade, gettext
  File /var/lib/python-support/python2.5/gtk-2.0/gtk/__init__.py,
line 48, in module
from gtk import _gtk
ImportError: No module named cairo

I have both python-gtk and python-cairo installed. I recently upgraded
to python2.5.

Cheers,
Shaun

-- System Information:
Debian Release: 4.0
  APT prefers stable
  APT policy: (500, 'stable'), (499, 'testing'), (498, 'unstable')
Architecture: i386 (i686)
Shell:  /bin/sh linked to /bin/bash
Kernel: Linux 2.6.23-rc3
Locale: LANG=en_CA.UTF-8, LC_CTYPE=en_CA.UTF-8 (charmap=UTF-8)

Versions of packages python-gtk2 depends on:
ii  libatk1.0-0   1.22.0-1   The ATK accessibility toolkit
ii  libc6 2.7-10 GNU C Library: Shared libraries
ii  libcairo2 1.4.14-1   The Cairo 2D vector graphics libra
ii  libglib2.0-0  2.16.1-2   The GLib library of C routines
ii  libgtk2.0-0   2.12.9-2   The GTK+ graphical user interface
ii  libpango1.0-0 1.20.2-2   Layout and rendering of internatio
ii  python2.5.2-1An interactive high-level object-o
ii  python-cairo [python2.5-cairo 1.4.12-1   Python bindings for the Cairo vect
ii  python-gobject [python2.5-gob 2.14.1-4   Python bindings for the GObject li
ii  python-numeric [python2.5-num 24.2-8.2   Numerical (matrix-oriented) Mathem
ii  python-support0.7.7  automated rebuilding support for P
pn  python2.4-cairo   none (no description available)
pn  python2.4-gobject none (no description available)
pn  python2.4-numeric none (no description available)

python-gtk2 recommends no packages.

-- no debconf information



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Bug#360101: python-gtk2: want to view svg images

2008-05-11 Thread Shaun Jackman
+1 vote for this bug, which fixing would have prevented bug #476789. Please fix.

Cheers,
Shaun



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Bug#479751: azureus: Requires Sun Java

2008-05-08 Thread Shaun Jackman
It's only a temporary situation that Azureus does not currently work
with a free Java VM. It very nearly works with GIJ -- and has worked
with GIJ in the past -- and there's the possibility of running it with
openjdk, as Peter mentioned.

Cheers,
Shaun

On Tue, May 6, 2008 at 3:18 PM, peter green [EMAIL PROTECTED] wrote:
 The package seems to require Sun Java as it stated in README.txt. I gave
 up with trying to run it on free VM's available in Debian etch.

 It would appear that way

 In addition, the azureus wrapper expects java in the path, which is
 available only with Sun Java package installed.

 Afaict this is not correct, many of the free vms have compatibility wrappers
 which are placed in the path through the alternatives system (though in my
 experiance alternatives is rather fragile so they may be broken on your
 system).

 I believe, the package should be moved out from main with dependencies
 corrected unless it works with free VM's in lenny witch is unlikely.

 Openjdk is currently sitting in new. Hopefully it will get into lenny before
 release making such a move unnessacery. As such moving azureus to contrib
 right now seems like a waste of time to me.







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Bug#475669: Suggest informing the user

2008-05-01 Thread Shaun Jackman
Hi Adam,

My preference would be to fix the bug, of course! But with the bug
being 180 days old now, it might be time to look at a workaround like
this. Do you know, does Azureus work with any other versions of GIJ? I
know that it works with Sun's VM.

Cheers,
Shaun

On Thu, May 1, 2008 at 1:45 PM, Adam Rice [EMAIL PROTECTED] wrote:
 The problem is that it comes so close to working with gij-4.3 that it's hard
  to notice that anything is actually wrong. How about putting a temporary hack
  in the /usr/bin/azureus script to check if /usr/bin/java is gij-4.3 and popup
  an xmessage saying something like

  
  You are running azureus with gij-4.3. There are known problems with this
  combination. See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=475669 for
  details. If your torrents fail to download, please consider selecting a
  different java interpreter using the update-alternatives program.
  

  ?

  I guess that would add a dependency on the xll-utils package, which is not so
  nice. But printing a message to the console is not much use for people who
  start azureus from iceweasel like I usually do.






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Bug#477905: swt-gtk: adjust build-dependency (gcj not built on alpha, arm, hppa and hurd-i386)

2008-04-27 Thread Shaun Jackman
Hi Matthias,

Is there a document describing how best to use dh_nativejava?

In other packages, I've seen calls to dh_nativejava wrapped in
ifneq (,$(filter $(DEB_HOST_ARCH), $(gcj_native_archs)))
Is this necessary, and would the build fail on architectures without
gcj if this protection were omitted? Could this test be moved into
dh_nativejava?

Should the Architecture of a libxxx-java-gcj package be `any' or
!alpha !arm !hppa !hurd-i386?

Cheers,
Shaun



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Bug#476789: [Debian-olpc-devel] Bug#476789: sugar: fails to find icon system-search

2008-04-21 Thread Shaun Jackman
On Mon, Apr 21, 2008 at 1:51 AM, Jonas Smedegaard [EMAIL PROTECTED]
...
  Could you perhaps share some insight about how you went about?  Any
  tools or tricks I could use in future cases like this?

Unfortunately, it was just dumb look. I had the idea that perhaps GTK
needed a plugin to provide SVG support. So, I used apt-cache pkgnames
and grepped for gtk.*svg|svg.*gtk but came up with nothing. Later that
day, I installeed pychess -- for which I'm thinking about creating a
sugar activity -- and noticed it depended on librsvg2-common:

This package includes the gdk-pixbuf loader and a GTK+ engine,
allowing to load SVG images transparently inside GTK+ applications.

Like I said, dumb luck.

Cheers,
Shaun



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Bug#474738: azureus: Fails to reappear after minimising

2008-04-20 Thread Shaun Jackman
Hi Ben,

I haven't seen that problem myself.
When you minimize Azures, does it appear on your task bar?
What exactly happens when you click on the minimized item on your task bar?
Does it appear in your system tray icons?
What exactly happens when you click on the icon in your system tray?

Cheers,
Shaun

On Mon, Apr 7, 2008 at 6:55 AM, Ben Whyte [EMAIL PROTECTED] wrote:
 Package: azureus
  Version: 3.0.4.2-1
  Severity: important


  When I minimise Azureus and then attempt to reshow it, it fails to
  reappear.

  The application continues running but I cant bring up the interface.

  Ben



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Bug#476789: [Debian-olpc-devel] Bug#476789: sugar: fails to find icon system-search

2008-04-20 Thread Shaun Jackman
Success! Sugar depends on librsvg2-common for its `gdk-pixbuf loader
and a GTK+ engine, allowing to load SVG images transparently inside
GTK+ applications'.

Why does sugar only recommend sugar-artwork? It seems to be rather
dependent on it.

Cheers,
Shaun

On Sat, Apr 19, 2008 at 1:21 PM, Jonas Smedegaard [EMAIL PROTECTED] wrote:
 On Sat, Apr 19, 2008 at 12:12:02PM -0700, Shaun Jackman wrote:
  I do have sugar-artwork 0.79.2-1 installed. If you scroll down to the
  bottom of the bug report, you can see the versions of all the
  dependencies that I have installed: http://bugs.debian.org/476789

  Ah, yes. Sorry - I was responding too fast.

  Afterwards I even tried removing sugar-artwork in an attempt at
  provoking that same error, but couldn't.

  I will try harder...



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Bug#476789: sugar: fails to find icon system-search

2008-04-19 Thread Shaun Jackman
Package: sugar
Version: 0.79.3-2
Severity: serious

Both sugar and sugar-emulator fail:
AttributeError: 'NoneType' object has no attribute 'get_filename'

The full log follows.

Cheers,
Shaun

$ sugar-emulator
INFO:sugar-emulator:Attempting to find free port for X11 (Xephyr)
INFO:sugar-emulator:  Found free port: #5 (6005)
INFO:sugar-emulator:Starting the Xephyr nested X display on display 5
DEBUG:sugar-emulator:Xephyr command: Xephyr :5 -ac -screen 1200x900 -dpi 98
INFO:sugar-emulator:Attempting to launch sugar to replace this
process: dbus-launch dbus-launch --exit-with-session sugar-shell
Extended Input Devices not yet supported. Impelement it at line 625 in
../../../../hw/kdrive/src/kinput.c
xkb_keycodes { include xfree86+aliases(qwerty) };
xkb_types{ include complete };
xkb_compatibility{ include complete };
xkb_symbols  { include pc(pc105)+us };
xkb_geometry { include pc(pc101) };
Could not init font path element /usr/share/fonts/X11/cyrillic,
removing from list!
---
exceptions.AttributeErrorTraceback (most
recent call last)

/usr/bin/sugar-shell
 30 from main import main
 31
--- 32 main()
main = function main at 0xb564de64
 33
 34

/usr/share/sugar/shell/main.py in main()
140
141 # TODO: move initializations from the Shell constructor to
a start() method
-- 142 shell = view.Shell.get_instance()
shell = undefined
global view.Shell.get_instance = function get_instance at 0xb56a3a04
143 service = ShellService()
144

/usr/share/sugar/shell/view/Shell.py in get_instance()
274 global _instance
275 if not _instance:
-- 276 _instance = Shell()
global _instance = None
global Shell = class 'view.Shell.Shell'
277 return _instance
278

/usr/share/sugar/shell/view/Shell.py in __init__(self=Shell object at
0xb56509b4 (GObject at 0x86eed20))
 64 self._frame = frame.get_instance()
 65
--- 66 self._home_window = HomeWindow()
self._home_window = undefined
global HomeWindow = class 'view.home.HomeWindow.HomeWindow'
 67 self._home_window.show()
 68

/usr/share/sugar/shell/view/home/HomeWindow.py in
__init__(self=HomeWindow object at 0xb566257c (GtkWindow at
0x871cc60))
 62 self._motion_notify_event_cb)
 63
--- 64 self._home_box = HomeBox()
self._home_box = undefined
global HomeBox = class 'view.home.HomeBox.HomeBox'
 65 self._friends_box = FriendsBox()
 66 self._mesh_box = MeshBox()

/usr/share/sugar/shell/view/home/HomeBox.py in __init__(self=HomeBox
object at 0xb5662694 (SugarHomeBox at 0x8720260))
 41 self._enable_xo_palette = False
 42
--- 43 self._toolbar = HomeToolbar()
self._toolbar = undefined
global HomeToolbar = class 'view.home.HomeBox.HomeToolbar'
 44 #self._toolbar.connect('query-changed',
self.__toolbar_query_changed_cb)
 45 self._toolbar.connect('view-changed',
self.__toolbar_view_changed_cb)

/usr/share/sugar/shell/view/home/HomeBox.py in
__init__(self=HomeToolbar object at 0xb56626e4 (SugarHomeToolbar at
0x870bb48))
129 self._search_entry = iconentry.IconEntry()
130
self._search_entry.set_icon_from_name(iconentry.ICON_ENTRY_PRIMARY,
-- 131   'system-search')
132 self._search_entry.add_clear_button()
133 self._search_entry.set_width_chars(25)

/usr/lib/python2.4/site-packages/sugar/graphics/iconentry.py in
set_icon_from_name(self=IconEntry object at 0xb5662784 (SexyIconEntry
at 0x85fc800), position=enum SEXY_ICON_ENTRY_PRIMARY of type
SexyIconEntryPosition, name='system-search')
 430)
 44
--- 45 if icon_info.get_filename().endswith('.svg'):
icon_info.get_filename.endswith = undefined
 46 loader = _SVGLoader()
 47 color = sugar.profile.get_color()

AttributeError: 'NoneType' object has no attribute 'get_filename'

(sugar-shell:5558): GStreamer-CRITICAL **:
Trying to dispose element alsamixerelement0, but it is not in the NULL state.
You need to explicitly set elements to the NULL state before
dropping the final reference, to allow them to clean up.


-- System Information:
Debian Release: 4.0
  APT prefers stable
  APT policy: (500, 'stable'), (499, 'testing'), (498, 'unstable')
Architecture: i386 (i686)
Shell:  /bin/sh linked to /bin/bash
Kernel: Linux 2.6.23-rc3
Locale: LANG=en_CA.UTF-8, LC_CTYPE=en_CA.UTF-8 (charmap=UTF-8)

Versions of packages sugar depends on:
ii  dbus-x11  1.1.20-1   simple interprocess messaging syst
ii  matchbox-window-manager   1.1-1  window manager for 

Bug#476789: [Debian-olpc-devel] Bug#476789: sugar: fails to find icon system-search

2008-04-19 Thread Shaun Jackman
Hi Jonas,

I do have sugar-artwork 0.79.2-1 installed. If you scroll down to the
bottom of the bug report, you can see the versions of all the
dependencies that I have installed:
http://bugs.debian.org/476789

Cheers,
Shaun

On Sat, Apr 19, 2008 at 2:12 AM, Jonas Smedegaard [EMAIL PROTECTED] wrote:
  Hi shaun,

  On Sat, Apr 19, 2008 at 12:09:57AM -0700, Shaun Jackman wrote:

  Both sugar and sugar-emulator fail:
  AttributeError: 'NoneType' object has no attribute 'get_filename'

  Thanks for the bugreport!

  I suspect the cause of this is sugar-artwork missing.  Could you please
  check if you have sugar-artwork installed, and if not see if doing so
  makes the error go away.


   - Jonas



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Bug#475669: azureus: downloads never start with gij-4.3

2008-04-12 Thread Shaun Jackman
package azureus
severity 475669 serious
tag 475669 confirmed
merge 449176 475669
thanks

On Sat, Apr 12, 2008 at 1:40 AM, Hamish Moffatt [EMAIL PROTECTED] wrote:
 Package: azureus
  Version: 3.0.4.2-1
  Severity: normal

  Somehow I ended up with gij-4.3 as my /usr/bin/java, from the
  java-gcj-compat-headless package. Azureus runs but downloads never
  start.. it says NAT OK and Scrape OK but no torrent data
  is transferred. I changed my jvm to sun-java5 and restarted and
  instantly the downloads of the same torrents start.


  [ 6:33PM] [EMAIL PROTECTED]:~ $ sudo update-alternatives --config java

  There are 4 alternatives which provide `java'.

   SelectionAlternative
  ---
   1/usr/bin/gij-4.3
   2/usr/bin/gij-4.2
  *+3/usr/lib/jvm/java-gcj/jre/bin/java
   4/usr/lib/jvm/java-1.5.0-sun/jre/bin/java

  Press enter to keep the default[*], or type selection number: 4
  Using '/usr/lib/jvm/java-1.5.0-sun/jre/bin/java' to provide 'java'.


  Hamish

  -- System Information:
  Debian Release: lenny/sid
   APT prefers unstable
   APT policy: (500, 'unstable'), (1, 'experimental')
  Architecture: amd64 (x86_64)

  Kernel: Linux 2.6.22-2-amd64 (SMP w/2 CPU cores)
  Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
  Shell: /bin/sh linked to /bin/bash

  Versions of packages azureus depends on:
  ii  gij-4.2 [java-virtual-machine 4.2.3-3The GNU Java bytecode 
 interpreter
  ii  gij-4.3 [java-virtual-machine 4.3.0-2The GNU Java bytecode 
 interpreter
  ii  java-gcj-compat [java2-runtim 1.0.77-5   Java runtime environment using 
 GIJ
  ii  java-gcj-compat-headless [jav 1.0.77-5   Java runtime environment using 
 GIJ
  ii  libcommons-cli-java   1.1-2  API for working with the 
 command l
  ii  liblog4j1.2-java  1.2.15-2   Logging library for java
  ii  libseda-java  3.0-3  the Staged Event-Driven 
 Architectu
  ii  libswt-gtk-3.3-java   3.3.1-3Standard Widget Toolkit for GTK 
 Ja
  ii  sun-java5-jre [java2-runtime] 1.5.0-15-1 Sun Java(TM) Runtime 
 Environment (

  azureus recommends no packages.

  -- no debconf information






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Bug#475787: sugar: Requires recent python-gst0.10

2008-04-12 Thread Shaun Jackman
Package: sugar
Version: 0.79.2-1 0
Severity: important

sugar does not work with the version of python-gst0.10 that is in
etch: 0.10.5-5. It gives the following error message
GstAlsaMixerElement object has no attribute 'set_volume'

It works fine with python-gst0.10 0.10.11-1 in testing.

Cheers,
Shaun



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