Accepted singularity-container 3.1.1+ds-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 15 May 2019 02:04:21 -0400
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 3.1.1+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team 
Changed-By: Afif Elghraoui 
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (3.1.1+ds-1) unstable; urgency=medium
 .
   * Upstream version 3.1.1+ds
   * drop d/patches/ftbfs_mips
 (was ineffectual previously and no longer applies)
   * Incorporate upstream patch for CVE-2019-11328
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Accepted nvchecker 1.4.3-1 (source) into unstable

[Afif Elghraoui]

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Date: Sun, 31 Mar 2019 01:59:48 -0400
Source: nvchecker
Binary: nvchecker
Architecture: source
Version: 1.4.3-1
Distribution: unstable
Urgency: medium
Maintainer: Afif Elghraoui 
Changed-By: Afif Elghraoui 
Description:
 nvchecker  - new-version checker for software releases
Changes:
 nvchecker (1.4.3-1) unstable; urgency=medium
 .
   * New upstream release.
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Accepted nvchecker 1.3-2 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Fri, 08 Feb 2019 21:45:38 -0500
Source: nvchecker
Binary: nvchecker
Architecture: source
Version: 1.3-2
Distribution: unstable
Urgency: medium
Maintainer: Afif Elghraoui 
Changed-By: Afif Elghraoui 
Description:
 nvchecker  - new-version checker for software releases
Closes: 921800
Changes:
 nvchecker (1.3-2) unstable; urgency=medium
 .
   * Disable running the test suite during package build
 due to lack of network access (Closes: #921800)
   * Set up autopkgtest
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Accepted gridengine 8.1.9+dfsg-9 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 05 Feb 2019 01:09:19 -0500
Source: gridengine
Binary: gridengine-common gridengine-client gridengine-qmon gridengine-master 
gridengine-exec gridengine-dev gridengine-drmaa1.0 libdrmaa1.0-java 
libdrmaa1.0-java-doc gridengine-drmaa-dev libdrmaa1.0-ruby
Architecture: source
Version: 8.1.9+dfsg-9
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team 
Changed-By: Afif Elghraoui 
Description:
 gridengine-client - Utilities for Grid Engine queue management
 gridengine-common - Distributed resource management - common files
 gridengine-dev - Distributed resource management - development files
 gridengine-drmaa-dev - Distributed resource management Application API library 
- develop
 gridengine-drmaa1.0 - Distributed resource management Application API library
 gridengine-exec - Distributed resource management - Execution Server
 gridengine-master - Distributed resource management - Master Server
 gridengine-qmon - Graphical utilities for Grid Engine queue management
 libdrmaa1.0-java - Distributed resource management Application API library - 
Java bi
 libdrmaa1.0-java-doc - Distributed resource management Application API library 
- Java bi
 libdrmaa1.0-ruby - Distributed resource management Application API library - 
Ruby bi
Closes: 857659 903406
Changes:
 gridengine (8.1.9+dfsg-9) unstable; urgency=medium
 .
   [ Afif Elghraoui ]
   * Do not attempt building JGDI (Reduces severity of #875404)
   * d/watch: update to point to sourceforge
   * Fix FTBFS on armhf due to OpenJDK VM changes.
 Thanks to Adam Barratt for the patch (Closes: #903406)
 .
   [ Andreas Beckmann ]
   * Remove dangling /var/lib/gridengine/jobsbin symlink (Closes: #857659)
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Accepted singularity-container 3.0.3+ds-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Wed, 30 Jan 2019 22:14:04 -0500
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 3.0.3+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team 
Changed-By: Afif Elghraoui 
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (3.0.3+ds-1) unstable; urgency=medium
 .
   * New upstream version; code base rewritten in Go
   * New packaging to handle changes to the language and build system
 - Updated d/patches
 - Created a repack script to remove all but certain specific bundled
   dependencies when importing the source tarball.
   * Updated URLs and d/copyright for singularityware -> sylabs ownership
   * Standards-Version 4.3.0
   * Used canonical VCS URLs
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Accepted qperf 0.4.11-2 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sun, 27 Jan 2019 18:17:05 -0500
Source: qperf
Binary: qperf
Architecture: source
Version: 0.4.11-2
Distribution: unstable
Urgency: low
Maintainer: Debian HPC team 
Changed-By: Afif Elghraoui 
Description:
 qperf  - Measure socket and RDMA performance
Changes:
 qperf (0.4.11-2) unstable; urgency=low
 .
   * Correct the uploaders list
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Accepted swiglpk 4.65.0-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 26 Jan 2019 21:15:14 -0500
Source: swiglpk
Binary: python-swiglpk python3-swiglpk
Architecture: source
Version: 4.65.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Afif Elghraoui 
Description:
 python-swiglpk - Plain Python bindings for the GNU Linear Programming Kit 
(Python
 python3-swiglpk - Plain Python bindings for the GNU Linear Programming Kit 
(Python
Changes:
 swiglpk (4.65.0-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted optlang 1.4.4-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sat, 26 Jan 2019 21:19:47 -0500
Source: optlang
Binary: python-optlang python3-optlang
Architecture: source
Version: 1.4.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 

Changed-By: Afif Elghraoui 
Description:
 python-optlang - sympy based mathematical programming language (Python 2)
 python3-optlang - sympy based mathematical programming language (Python 3)
Changes:
 optlang (1.4.4-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted nvchecker 1.3-1 (source all) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 19 Jan 2019 01:37:25 -0500
Source: nvchecker
Binary: nvchecker
Architecture: source all
Version: 1.3-1
Distribution: unstable
Urgency: medium
Maintainer: Afif Elghraoui 
Changed-By: Afif Elghraoui 
Description:
 nvchecker  - new-version checker for software releases
Closes: 919748
Changes:
 nvchecker (1.3-1) unstable; urgency=medium
 .
   * Initial release. (Closes: #919748)
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Bug#919748: ITP: nvchecker -- new-version checker for software releases

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Afif Elghraoui 

* Package name: nvchecker
  Version : 1.3
  Upstream Author : lilydjwg 
* URL : https://github.com/lilydjwg/nvchecker
* License : MIT
  Programming Lang: Python
  Description : new-version checker for software releases

 nvchecker (short for new version checker) is for checking if a new
 version of some software has been released.


This is a nice vendor-neutral solution for release monitoring. I think it
can also be quite useful in research, for example, to watch for updates of all
tools used in an analysis. And it doesn't have to be limited to watching
software releases, either. It could be applied to watching updates in
reference databases.

I intend to maintain nvchecker in the Debian group on salsa.

Afif

Accepted singularity-container 2.6.1-2 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 14 Jan 2019 21:23:04 -0500
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.6.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team 
Changed-By: Afif Elghraoui 
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Closes: 919026
Changes:
 singularity-container (2.6.1-2) unstable; urgency=medium
 .
   * d/patches/reproducible_build: escape dollar signs in Makefile patch
 (Closes: #919026)
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Accepted singularity-container 2.6.1-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 13 Dec 2018 01:47:28 -0500
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.6.1-1
Distribution: unstable
Urgency: high
Maintainer: Debian HPC Team 
Changed-By: Afif Elghraoui 
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (2.6.1-1) unstable; urgency=high
 .
   [ Yaroslav Halchenko ]
   * d/rules
 + DEB_LDFLAGS_MAINT_STRIP=-Wl,-Bsymbolic-functions
   to prevent a weird side-effect on Ubuntu using those LDFLAGS
   and causing static variable to become having multiple "instances".
   Ref: https://github.com/singularityware/singularity/issues/1947
 .
   [ Afif Elghraoui ]
   * New upstream security release fixing CVE-2018-19295
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Accepted pyconfigure 0.2.3-2 (source) into unstable

[Afif Elghraoui]

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Date: Sat, 15 Sep 2018 16:27:14 -0400
Source: pyconfigure
Binary: pyconfigure
Architecture: source
Version: 0.2.3-2
Distribution: unstable
Urgency: low
Maintainer: Afif Elghraoui 
Changed-By: Afif Elghraoui 
Description:
 pyconfigure - automatic configure script builder for Python software
Changes:
 pyconfigure (0.2.3-2) unstable; urgency=low
 .
   * Bump Standards-Version to 4.2.1
   * Update VCS URLs to point to salsa.debian.org
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Accepted adduser 3.118 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 15 Sep 2018 15:12:39 -0400
Source: adduser
Binary: adduser
Architecture: source
Version: 3.118
Distribution: unstable
Urgency: low
Maintainer: Debian Adduser Developers 
Changed-By: Afif Elghraoui 
Description:
 adduser- add and remove users and groups
Closes: 898034 898769 901031
Changes:
 adduser (3.118) unstable; urgency=low
 .
   * Team upload
 .
   [ Afif Elghraoui ]
   * Remove myself from uploaders
 .
   [ Boyuan Yang ]
   * po: Refresh po files
   * po: Update Simplified Chinese (zh_CN) translation
   * debian/rules: Avoid invoking dpkg-parsechangelog directly
   * debian/control: Bump Standards-Version to 4.2.1.
 .
   [ Helge Kreutzmann ]
   * Update German debconf translation (Closes: #898034)
 .
   [ Frans Spiesschaert ]
   * Update Dutch debconf translation (Closes: #898769)
 .
   [ Julien Patriarca ]
   * Update French debconf translation (Closes: #901031)
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Accepted sniffles 1.0.8+ds-2 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 08 Jul 2018 00:49:22 -0400
Source: sniffles
Binary: sniffles
Architecture: source
Version: 1.0.8+ds-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 

Changed-By: Afif Elghraoui 
Description:
 sniffles   - structural variation caller using third-generation sequencing
Closes: 903192
Changes:
 sniffles (1.0.8+ds-2) unstable; urgency=low
 .
   * Use dh_installman rather than debian/manpages (Closes: #903192)
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Accepted singularity-container 2.5.2-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 04 Jul 2018 15:06:29 -0400
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.5.2-1
Distribution: unstable
Urgency: high
Maintainer: Debian HPC Team 
Changed-By: Afif Elghraoui 
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (2.5.2-1) unstable; urgency=high
 .
   * New upstream security and bug-fix release
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Accepted singularity-container 2.5.1-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 03 May 2018 22:12:31 -0400
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.5.1-1
Distribution: unstable
Urgency: high
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (2.5.1-1) unstable; urgency=high
 .
   [ Yaroslav Halchenko ]
   * debian/control
 - Homepage moved to www.sylabs.io
 .
   [ Afif Elghraoui ]
   * New upstream bug-fix release
   * Refresh patches
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Accepted singularity-container 2.5.0-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 30 Apr 2018 23:04:24 -0400
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.5.0-1
Distribution: unstable
Urgency: high
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (2.5.0-1) unstable; urgency=high
 .
   * New upstream version, including security updates
   * Add build-dependency on libarchive
   * Remove patch merged upstream
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Accepted optlang 1.4.1-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sun, 22 Apr 2018 18:17:41 -0400
Source: optlang
Binary: python-optlang python3-optlang
Architecture: source
Version: 1.4.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-optlang - sympy based mathematical programming language (Python 2)
 python3-optlang - sympy based mathematical programming language (Python 3)
Changes:
 optlang (1.4.1-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted python-easydev 0.9.35+dfsg-2 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sun, 22 Apr 2018 17:53:49 -0400
Source: python-easydev
Binary: python-easydev python3-easydev
Architecture: source
Version: 0.9.35+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-easydev - common utilities to ease the development of Python packages 
(Pyth
 python3-easydev - common utilities to ease the development of Python packages 
(Pyth
Closes: 896292 896402
Changes:
 python-easydev (0.9.35+dfsg-2) unstable; urgency=medium
 .
   * Correct ITP bug number in previous changelog entry
   * Add dependencies on python-pkg-resources (Closes: #896292, #896402)
   * Bump Standards-Version to 4.1.3
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Accepted singularity-container 2.4.5-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 24 Mar 2018 16:24:45 -0400
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.4.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Closes: 893133
Changes:
 singularity-container (2.4.5-1) unstable; urgency=medium
 .
   [ Yaroslav Halchenko ]
   * Revert 01fd7b1b0ab23b03b424e567342dec180b45e2d7 to bring back
 compatibility with debhelper 9 to ease backports (Closes: #893133)
 .
   [ Afif Elghraoui ]
   * New upstream version
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Accepted sniffles 1.0.8+ds-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sat, 24 Mar 2018 16:20:10 -0400
Source: sniffles
Binary: sniffles
Architecture: source
Version: 1.0.8+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 sniffles   - structural variation caller using third-generation sequencing
Changes:
 sniffles (1.0.8+ds-1) unstable; urgency=medium
 .
   * New upstream version
   * Run tests
   * Refresh patches
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Accepted optlang 1.4.0-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Sat, 24 Mar 2018 14:59:06 -0400
Source: optlang
Binary: python-optlang python3-optlang
Architecture: source
Version: 1.4.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-optlang - sympy based mathematical programming language (Python 2)
 python3-optlang - sympy based mathematical programming language (Python 3)
Changes:
 optlang (1.4.0-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted canu 1.7+dfsg-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 17 Mar 2018 18:09:13 -0400
Source: canu
Binary: canu
Architecture: source
Version: 1.7+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 canu   - single molecule sequence assembler for genomes
Changes:
 canu (1.7+dfsg-1) unstable; urgency=medium
 .
   * New upstream version
   * Update handling of mhap bundled copy
   * Refresh patches
   * Use a wrapper script for main program
   * move gnuplot to Depends from Recommends
   * Bump mhap minimum version
   * Bump Standards-Version to 4.1.3
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Accepted mhap 2.1.3+dfsg-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 16 Mar 2018 00:05:16 -0400
Source: mhap
Binary: mhap
Architecture: source
Version: 2.1.3+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 mhap   - locality-sensitive hashing to detect long-read overlaps
Changes:
 mhap (2.1.3+dfsg-1) unstable; urgency=medium
 .
   [ Afif Elghraoui ]
   * Bump minimum required libguava-java version
   * New upstream version 2.1.3+dfsg
   * Standards-Version 4.1.3
 .
   [ Steffen Moeller, Andreas Tille ]
   * Added ref to OMICtools
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Accepted gridengine 8.1.9+dfsg-8 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 11 Mar 2018 21:26:20 -0400
Source: gridengine
Binary: gridengine-common gridengine-client gridengine-qmon gridengine-master 
gridengine-exec gridengine-dev gridengine-drmaa1.0 libdrmaa1.0-java 
libdrmaa1.0-java-doc gridengine-drmaa-dev libdrmaa1.0-ruby
Architecture: source
Version: 8.1.9+dfsg-8
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 gridengine-client - Utilities for Grid Engine queue management
 gridengine-common - Distributed resource management - common files
 gridengine-dev - Distributed resource management - development files
 gridengine-drmaa-dev - Distributed resource management Application API library 
- develop
 gridengine-drmaa1.0 - Distributed resource management Application API library
 gridengine-exec - Distributed resource management - Execution Server
 gridengine-master - Distributed resource management - Master Server
 gridengine-qmon - Graphical utilities for Grid Engine queue management
 libdrmaa1.0-java - Distributed resource management Application API library - 
Java bi
 libdrmaa1.0-java-doc - Distributed resource management Application API library 
- Java bi
 libdrmaa1.0-ruby - Distributed resource management Application API library - 
Ruby bi
Closes: 891373 892296
Changes:
 gridengine (8.1.9+dfsg-8) unstable; urgency=medium
 .
   * Use correct paths to qmon pixmaps (Closes: #892296)
   * Update qmake for glibc 2.27.
 Thanks to Aurelien Jarno (Closes: #891373)
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Accepted smalr 1.1+dfsg-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 11 Mar 2018 19:19:43 -0400
Source: smalr
Binary: smalr
Architecture: source
Version: 1.1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 smalr  - interrogation of the methylation status of nucleotide sequencing
Changes:
 smalr (1.1+dfsg-1) unstable; urgency=medium
 .
   * New upstream version
   * Adjust packaging for changes in source organization
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Accepted singularity-container 2.4.4-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 10 Mar 2018 16:15:26 -0500
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.4.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (2.4.4-1) unstable; urgency=medium
 .
   * New upstream version
   * Refresh patches
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Accepted smalr 1.0.1-1 (source all) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 25 Feb 2018 20:38:09 -0500
Source: smalr
Binary: smalr
Architecture: source all
Version: 1.0.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 smalr  - interrogation of the methylation status of nucleotide sequencing
Closes: 891485
Changes:
 smalr (1.0.1-1) unstable; urgency=medium
 .
   * Initial release (Closes: #891485)
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Accepted trnascan-se 2.0.0-1 (source all amd64) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sat, 24 Feb 2018 22:18:01 -0500
Source: trnascan-se
Binary: trnascan-se trnascan-se-common
Architecture: source all amd64
Version: 2.0.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 trnascan-se - detection of transfer RNA genes in genomic sequence
 trnascan-se-common - detection of transfer RNA genes in genomic sequence 
(common files
Changes:
 trnascan-se (2.0.0-1) unstable; urgency=medium
 .
   [ Steffen Moeller ]
   * debian/upstream/metadata:
 - Added references to registries
 - yamllint cleanliness
   * upstream/metadata RRID->SciCrunch
 .
   [ Afif Elghraoui ]
   * debian/watch: update to new URL
   * New upstream version
   * Standards-Version 4.1.3
   * debhelper compat 11
   * d/rules: clean up and remove dh_installchangelogs
   * Overhaul packaging for new build system
   * d/copyright: license change (GPL 2+ -> 3+); updated copyright years
   * install examples
   * Add dependency on infernal
   * Update autopkgtest
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Accepted nanopolish 0.9.0-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sat, 17 Feb 2018 22:02:10 -0500
Source: nanopolish
Binary: nanopolish
Architecture: source
Version: 0.9.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 nanopolish - consensus caller for nanopore sequencing data
Changes:
 nanopolish (0.9.0-1) unstable; urgency=medium
 .
   * New upstream version
   * Refresh patches
   * Bump upstream copyright year
   * Bump minimum required fast5 version
   * Include upstream patch to fix HDF5 errors appearing in autopkgtest
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Accepted fast5 0.6.5-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sat, 17 Feb 2018 20:43:22 -0500
Source: fast5
Binary: fast5 libfast5-dev python-fast5 python3-fast5
Architecture: source
Version: 0.6.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 fast5  - utilities for manipulating Oxford Nanopore Fast5 files
 libfast5-dev - library for reading Oxford Nanopore Fast5 files -- headers
 python-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 2
 python3-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 3
Changes:
 fast5 (0.6.5-1) unstable; urgency=medium
 .
   * New upstream version
   * Standards-Version 4.1.3
   * Debhelper compat 11
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Accepted assemblytics 0~20170131+ds-2 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sat, 17 Feb 2018 17:58:15 -0500
Source: assemblytics
Binary: assemblytics
Architecture: source
Version: 0~20170131+ds-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 assemblytics - detect and analyze structural variants from a genome assembly
Changes:
 assemblytics (0~20170131+ds-2) unstable; urgency=low
 .
   * Add d/upstream/metadata
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Accepted singularity-container 2.4.2-4 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Sat, 17 Feb 2018 17:14:21 -0500
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.4.2-4
Distribution: unstable
Urgency: low
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Closes: 887192
Changes:
 singularity-container (2.4.2-4) unstable; urgency=low
 .
   * Standards-Version 4.1.3
   * debhelper compat 11
   * Change squashfs tools to Depends from Recommends
   * Recommend e2fsprogs (Closes: #887192)
   * d/rules: add comment explaining why test suite can't be run
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Accepted assemblytics 0~20170131+ds-1 (source all) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 12 Feb 2018 00:55:10 -0500
Source: assemblytics
Binary: assemblytics
Architecture: source all
Version: 0~20170131+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 assemblytics - detect and analyze structural variants from a genome assembly
Closes: 890220
Changes:
 assemblytics (0~20170131+ds-1) unstable; urgency=medium
 .
   * Initial release (Closes: #890220)
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Accepted mummer 3.23+dfsg-3 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 11 Feb 2018 18:02:05 -0500
Source: mummer
Binary: mummer mummer-doc
Architecture: source
Version: 3.23+dfsg-3
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 mummer - Efficient sequence alignment of full genomes
 mummer-doc - Documentation for MUMmer
Changes:
 mummer (3.23+dfsg-3) unstable; urgency=low
 .
   * Team upload
 .
   [ Fabian Klötzl ]
   * improve performance of delta2maf
 .
   [ Steffen Moeller ]
   * Corrected EDAM annotation file
 .
   [ Afif Elghraoui ]
   * d/watch: point to new upstream repository at GitHub
 .
   [ Andreas Tille ]
   * Update d/copyright
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Accepted swiglpk 1.4.4-2 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 06 Feb 2018 18:16:58 -0500
Source: swiglpk
Binary: python-swiglpk python3-swiglpk
Architecture: source
Version: 1.4.4-2
Distribution: unstable
Urgency: low
Maintainer: Debian Science Maintainers 
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-swiglpk - Plain Python bindings for the GNU Linear Programming Kit 
(Python
 python3-swiglpk - Plain Python bindings for the GNU Linear Programming Kit 
(Python
Changes:
 swiglpk (1.4.4-2) unstable; urgency=low
 .
   * Install examples
   * Add debian/watch
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Accepted optlang 1.3.0-1 (source all) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 04 Feb 2018 19:27:31 -0500
Source: optlang
Binary: python-optlang python3-optlang
Architecture: source all
Version: 1.3.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-optlang - sympy based mathematical programming language (Python 2)
 python3-optlang - sympy based mathematical programming language (Python 3)
Closes: 889611
Changes:
 optlang (1.3.0-1) unstable; urgency=medium
 .
   * Initial release (Closes: #889611)
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Accepted swiglpk 1.4.4-1 (source amd64) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 04 Feb 2018 18:47:18 -0500
Source: swiglpk
Binary: python-swiglpk python3-swiglpk
Architecture: source amd64
Version: 1.4.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-swiglpk - Plain Python bindings for the GNU Linear Programming Kit 
(Python
 python3-swiglpk - Plain Python bindings for the GNU Linear Programming Kit 
(Python
Closes: 889613
Changes:
 swiglpk (1.4.4-1) unstable; urgency=medium
 .
   * Initial release (Closes: #889613)
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Accepted singularity-container 2.4.2-3 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sun, 04 Feb 2018 20:04:43 -0500
Source: singularity-container
Binary: singularity-container
Architecture: source
Version: 2.4.2-3
Distribution: unstable
Urgency: low
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 singularity-container - container platform focused on supporting "Mobility of 
Compute"
Changes:
 singularity-container (2.4.2-3) unstable; urgency=low
 .
   * Add Recommends: squashfs-tools
   * lintian overrides: update suid binary locations
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Accepted nanopolish 0.8.5-2 (source) into unstable

[Afif Elghraoui]

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Date: Sun, 04 Feb 2018 19:38:40 -0500
Source: nanopolish
Binary: nanopolish
Architecture: source
Version: 0.8.5-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 nanopolish - consensus caller for nanopore sequencing data
Changes:
 nanopolish (0.8.5-2) unstable; urgency=low
 .
   * Remove dependency on nonexistent package sse-support [i386]
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Accepted nanopolish 0.8.5-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

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Date: Sun, 04 Feb 2018 16:17:01 -0500
Source: nanopolish
Binary: nanopolish
Architecture: source
Version: 0.8.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 nanopolish - consensus caller for nanopore sequencing data
Changes:
 nanopolish (0.8.5-1) unstable; urgency=medium
 .
   * New upstream version
   * d/control:
 + Add sse-support to Build-Depends for i386
 + Remove explicit declaration of x32
   * Bump Standards-Version to 4.1.3
   * Drop patches applied upstream
   * Drop useless patch
   * Bump copyright years
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Accepted hinge 0.5.0-3 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Sun, 04 Feb 2018 14:07:59 -0500
Source: hinge
Binary: hinge
Architecture: source
Version: 0.5.0-3
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 hinge  - long read genome assembler based on hinging
Changes:
 hinge (0.5.0-3) unstable; urgency=low
 .
   * Mark spdlog patch as forwarded upstream
   * d/control: copy Depends into Build-Depends
 to allow migration to Testing
   * Bump Standards-Version to 4.1.3
   * Bump copyright year
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Accepted dascrubber 0~20180108-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sun, 04 Feb 2018 13:54:09 -0500
Source: dascrubber
Binary: dascrubber
Architecture: source
Version: 0~20180108-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
Changes:
 dascrubber (0~20180108-1) unstable; urgency=medium
 .
   * New upstream snapshot (git 3491b14)
   * Bump copyright years
   * Bump Standards-Version to 4.1.3
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Accepted dazzdb 1.0+20180115-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sun, 04 Feb 2018 13:43:31 -0500
Source: dazzdb
Binary: dazzdb
Architecture: source
Version: 1.0+20180115-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 dazzdb - manage nucleotide sequencing read data
Changes:
 dazzdb (1.0+20180115-1) unstable; urgency=medium
 .
   * New upstream snapshot (git 7104852)
   * Bump copyright years
   * Bump Standards-Version to 4.1.3
   * Update and refresh patches
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Accepted daligner 1.0+20180108-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 04 Feb 2018 05:26:26 -0500
Source: daligner
Binary: daligner
Architecture: source
Version: 1.0+20180108-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 daligner   - local alignment discovery between long nucleotide sequencing read
Changes:
 daligner (1.0+20180108-1) unstable; urgency=medium
 .
   * New upstream snapshot (git 233274a)
   * Bump Standards-Version to 4.1.3
   * Bump copyright years
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daligner_1.0+20180108-1.debian.tar.xz
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Accepted sprai 0.9.9.23+dfsg-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 04 Feb 2018 05:10:53 -0500
Source: sprai
Binary: sprai
Architecture: source
Version: 0.9.9.23+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 sprai  - single-pass sequencing read accuracy improver
Changes:
 sprai (0.9.9.23+dfsg-1) unstable; urgency=medium
 .
   * New upstream version
   * Bump Standards-Version to 4.1.3
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Re: salsa.debian.org (git.debian.org replacement) going into beta

[Afif Elghraoui]

على الأربعاء 27 كانون الأول 2017 ‫02:46، كتب Mattia Rizzolo:
> On Wed, Dec 27, 2017 at 01:35:50AM +0100, Philip Rinn wrote:
>> Is it true (and intended) that -guest users can't create projects within
>> teams/groups they are member of? Or am I missing something? [I was not able 
>> to
>> create a project within the Debian Science Team]
> As Anton noted, you need to be a "master" in that group.  The difference
> between "master" and "developer" in groups is only that masters can
> create projects.
> 

here is the breakdown: https://docs.gitlab.com/ce/user/permissions.html

Masters can create projects, but not delete them. Only Owners can do that.

Developers also can't push to protected branches (and I believe master
is by default a protected branch).

regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Accepted gridengine 8.1.9+dfsg-7 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 27 Dec 2017 01:58:20 -0500
Source: gridengine
Binary: gridengine-common gridengine-client gridengine-qmon gridengine-master 
gridengine-exec gridengine-dev gridengine-drmaa1.0 libdrmaa1.0-java 
libdrmaa1.0-java-doc gridengine-drmaa-dev libdrmaa1.0-ruby
Architecture: source
Version: 8.1.9+dfsg-7
Distribution: unstable
Urgency: low
Maintainer: Debian HPC Team <debian-...@lists.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 gridengine-client - Utilities for Grid Engine queue management
 gridengine-common - Distributed resource management - common files
 gridengine-dev - Distributed resource management - development files
 gridengine-drmaa-dev - Distributed resource management Application API library 
- develop
 gridengine-drmaa1.0 - Distributed resource management Application API library
 gridengine-exec - Distributed resource management - Execution Server
 gridengine-master - Distributed resource management - Master Server
 gridengine-qmon - Graphical utilities for Grid Engine queue management
 libdrmaa1.0-java - Distributed resource management Application API library - 
Java bi
 libdrmaa1.0-java-doc - Distributed resource management Application API library 
- Java bi
 libdrmaa1.0-ruby - Distributed resource management Application API library - 
Ruby bi
Changes:
 gridengine (8.1.9+dfsg-7) unstable; urgency=low
 .
   * Maintain under the Debian HPC team
   * Move VCS repository to salsa.debian.org.
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Accepted falcon 1.8.8-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 16 Dec 2017 02:57:27 -0500
Source: falcon
Binary: falcon
Architecture: source
Version: 1.8.8-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 falcon - diploid-aware genome assembly of single-molecule sequencing reads
Closes: 864376 864378
Changes:
 falcon (1.8.8-1) unstable; urgency=medium
 .
   [ Afif Elghraoui ]
   * New upstream version
   * Update and refresh patches
   * Update unit test invocation
   * d/get-orig-source: clean-ups and corrections
   * d/control: Exclude x32 architecture (Closes: #864378)
   * d/tests/control: s/ADTTMP/AUTOPKGTEST_TMP/
   * Re-enable integration tests (Closes: #864376)
   * Update copyright years
   * Bump Standards-Version to 4.1.2
 .
   [ Steffen Moeller ]
   * debian/upstream/metadata:
 - yamllint cleanliness
 - Added references to registries.
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Accepted fast5 0.6.4-2 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sat, 16 Dec 2017 00:13:32 -0500
Source: fast5
Binary: fast5 libfast5-dev python-fast5 python3-fast5
Architecture: source
Version: 0.6.4-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 fast5  - utilities for manipulating Oxford Nanopore Fast5 files
 libfast5-dev - library for reading Oxford Nanopore Fast5 files -- headers
 python-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 2
 python3-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 3
Changes:
 fast5 (0.6.4-2) unstable; urgency=low
 .
   * Allow stderr output in autpkgtests to ignore notes
 emitted by GCC7 on armhf.
 Thanks to Graham Inggs
   * Bump Standards-Version to 4.1.2
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Accepted hinge 0.5.0-1 (source amd64) into unstable, unstable

[Afif Elghraoui]

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Date: Fri, 20 Oct 2017 00:27:38 -0400
Source: hinge
Binary: hinge
Architecture: source amd64
Version: 0.5.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 hinge  - long read genome assembler based on hinging
Closes: 878962
Changes:
 hinge (0.5.0-1) unstable; urgency=medium
 .
   * Initial release (Closes: #878962)
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Accepted sniffles 1.0.7+ds-1 (source) into unstable

[Afif Elghraoui]

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Date: Thu, 23 Nov 2017 01:36:25 -0500
Source: sniffles
Binary: sniffles
Architecture: source
Version: 1.0.7+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 sniffles   - structural variation caller using third-generation sequencing
Changes:
 sniffles (1.0.7+ds-1) unstable; urgency=medium
 .
   * New upstream version
   * Update/refresh patches
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Accepted gridengine 8.1.9+dfsg-6 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sun, 19 Nov 2017 00:18:39 -0500
Source: gridengine
Binary: gridengine-common gridengine-client gridengine-qmon gridengine-master 
gridengine-exec gridengine-dev gridengine-drmaa1.0 libdrmaa1.0-java 
libdrmaa1.0-java-doc gridengine-drmaa-dev libdrmaa1.0-ruby
Architecture: source
Version: 8.1.9+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Grid Engine Maintainers 
<pkg-gridengine-de...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 gridengine-client - Utilities for Grid Engine queue management
 gridengine-common - Distributed resource management - common files
 gridengine-dev - Distributed resource management - development files
 gridengine-drmaa-dev - Distributed resource management Application API library 
- develop
 gridengine-drmaa1.0 - Distributed resource management Application API library
 gridengine-exec - Distributed resource management - Execution Server
 gridengine-master - Distributed resource management - Master Server
 gridengine-qmon - Graphical utilities for Grid Engine queue management
 libdrmaa1.0-java - Distributed resource management Application API library - 
Java bi
 libdrmaa1.0-java-doc - Distributed resource management Application API library 
- Java bi
 libdrmaa1.0-ruby - Distributed resource management Application API library - 
Ruby bi
Closes: 827076
Changes:
 gridengine (8.1.9+dfsg-6) unstable; urgency=medium
 .
   * Fix FTBFS with openssl 1.1
 Thanks to Mark Hymers for the patches (Closes: #827076)
   * Bump Standards-Version to 4.1.1
   * Drop explicit build-dependency on autotools-dev
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Accepted nanopolish 0.8.4-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sat, 11 Nov 2017 00:45:23 -0500
Source: nanopolish
Binary: nanopolish
Architecture: source
Version: 0.8.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 nanopolish - consensus caller for nanopore sequencing data
Changes:
 nanopolish (0.8.4-1) unstable; urgency=medium
 .
   [ Steffen Moeller ]
   * upstream/metadata RRID->SciCrunch
 .
   [ Afif Elghraoui ]
   * New upstream version
   * Bump fast5 minimum version
   * Update and refine patch stack
   * Improve handling of external dependencies and build flags
   * d/rules
 + Remove redundant LDFLAGS setting
 + Don't override upstream optimization flags with default -O2
   * Bump Standards-Version to 4.1.1
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Accepted fast5 0.6.4-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 10 Nov 2017 15:56:45 -0500
Source: fast5
Binary: fast5 libfast5-dev python-fast5 python3-fast5
Architecture: source
Version: 0.6.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 fast5  - utilities for manipulating Oxford Nanopore Fast5 files
 libfast5-dev - library for reading Oxford Nanopore Fast5 files -- headers
 python-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 2
 python3-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 3
Changes:
 fast5 (0.6.4-1) unstable; urgency=medium
 .
   * New upstream version
   * Bump Standards-Version to 4.1.1
   * Bump copyright years
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Accepted sniffles 1.0.6+ds-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 10 Nov 2017 01:34:05 -0500
Source: sniffles
Binary: sniffles
Architecture: source
Version: 1.0.6+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 sniffles   - structural variation caller using third-generation sequencing
Changes:
 sniffles (1.0.6+ds-1) unstable; urgency=medium
 .
   * New upstream version
   * Install upstream README
   * d/watch: remove unnecessary script invocations
   * Add d/upstream/metadata with preprint reference
   * Bump Standards-Version to 4.1.1
   * Add support for the nodoc build profile
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Accepted pbseqlib 0~20161219-2 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 09 Nov 2017 22:48:55 -0500
Source: pbseqlib
Binary: libpbseq libpbseq-dev libpbdata-dev libpbdata libpbihdf-dev libpbihdf 
libblasr-dev libblasr
Architecture: source
Version: 0~20161219-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 libblasr   - tools for aligning PacBio reads to target sequences
 libblasr-dev - tools for aligning PacBio reads to target sequences (development
 libpbdata  - tools for handling PacBio sequences
 libpbdata-dev - tools for handling PacBio sequences (development files)
 libpbihdf  - tools for handling PacBio hdf5 files
 libpbihdf-dev - tools for handling PacBio hdf5 files (development files)
 libpbseq   - library for analyzing PacBio sequencing data
 libpbseq-dev - library for analyzing PacBio sequencing data (development files)
Closes: 880805
Changes:
 pbseqlib (0~20161219-2) unstable; urgency=medium
 .
   * Add support for HDF5 1.10.1
 Thanks to Gilles Filippini for the patches (Closes: #880805)
   * Bump Standards-Version to 4.1.1
   * Update copyright year
   * Handle nocheck build profile
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Re: question about build profile nocheck

[Afif Elghraoui]

Hi, Wookey and Chris,

Many thanks for the detailed answer and the links!

على الأربعاء  1 تشرين الثاني 2017 ‫23:19، كتب Wookey:
> On 2017-11-01 21:46 -0400, Afif Elghraoui wrote:
[...]
>>  Am I mistaken? 
> 
> Yes. Somewhat discussed in 
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=568897
> and marked willnotfix.
> 
> Debhelper doesn't automagically do anything due to profiles SFAIK.
> 
> Hmm. actually it recently learned how to do nodoc automatically:
> https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=865869
> 
> so having started down that slippery slope maybe it's time to ponder
> 568897 again as its under new management :-) 

I agree--I think I'll follow up on 568897. I found it surprising that
debhelper doesn't do anything about this. That then requires adding
boilerplate code to d/rules in every package trying to support this profile.

> 
[...]
> 
> Right, I generally expect the packaging to have to deal with
> DEB_BUILD_OPTIONS, which deals with actions. DEB_BUILD_PROFILES deals
> with dependencies (so dpkg and apt do some things automagically for
> you).
> 
> Helmut and Josch have a lot more to with this recently than me and
> will no doubt be along soon with chapter and verse.
> 

Thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

question about build profile nocheck

[Afif Elghraoui]

Hello,

The BuildProfileSpec on the wiki [1] defines the `nocheck` profile as:


> No test suite should be run, and build dependencies used only for that
purpose should be ignored. Builds that set this profile must also add
`nocheck` to `DEB_BUILD_OPTIONS`
```

I understand this as saying that the debhelper step for dh_auto_test or
override_dh_auto_test would be automatically skipped if this profile is
defined. Am I mistaken? I'm asking because I've seen the following
pattern in a couple of packages already:

```
ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))
override_dh_auto_test:
commands...
commands...
else
override_dh_auto_test:
endif
```
Thanks and regards
Afif


1. https://wiki.debian.org/BuildProfileSpec

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Accepted python-colormap 1.0.1-1 (source all) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 18 Oct 2017 21:12:38 -0400
Source: python-colormap
Binary: python-colormap python3-colormap
Architecture: source all
Version: 1.0.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-colormap - ease manipulation of matplotlib colormaps and color codecs 
(Pytho
 python3-colormap - ease manipulation of matplotlib colormaps and color codecs 
(Pytho
Closes: 878963
Changes:
 python-colormap (1.0.1-1) unstable; urgency=medium
 .
   * Initial release (Closes: #878963)
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Accepted dazzdb 1.0+20171014-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 20 Oct 2017 00:00:08 -0400
Source: dazzdb
Binary: dazzdb
Architecture: source
Version: 1.0+20171014-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 dazzdb - manage nucleotide sequencing read data
Changes:
 dazzdb (1.0+20171014-1) unstable; urgency=medium
 .
   * New upstream snapshot (git 8ab7daf)
   * Update and refresh patches
   * Bump Standards-Version to 4.1.1
   * Bump copyright years
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Accepted dascrubber 0~20171015-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 20 Oct 2017 00:06:04 -0400
Source: dascrubber
Binary: dascrubber
Architecture: source
Version: 0~20171015-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
Changes:
 dascrubber (0~20171015-1) unstable; urgency=medium
 .
   [ Steffen Moeller ]
   * Created debian/upstream/metadata with refs to
 registries
 .
   [ Afif Elghraoui ]
   * New upstream snapshot (git 2896d22)
   * Update name of README file
   * Update and refresh patches
   * Use default hardening
   * Bump Standards-Version to 4.1.1
   * Bump copyright years
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dascrubber_0~20171015-1.debian.tar.xz
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Accepted daligner 1.0+20171010-2 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Thu, 19 Oct 2017 23:42:51 -0400
Source: daligner
Binary: daligner
Architecture: source
Version: 1.0+20171010-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 daligner   - local alignment discovery between long nucleotide sequencing read
Changes:
 daligner (1.0+20171010-2) unstable; urgency=low
 .
   [ Steffen Moeller ]
   * [debian/upstream/metadata] Reference to OMICtools added.
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Accepted daligner 1.0+20171010-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 19 Oct 2017 23:18:52 -0400
Source: daligner
Binary: daligner
Architecture: source
Version: 1.0+20171010-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 daligner   - local alignment discovery between long nucleotide sequencing read
Changes:
 daligner (1.0+20171010-1) unstable; urgency=medium
 .
   * New upstream snapshot (git b966696)
   * Bump Standards Version to 4.1.1
   * Bump copyright years
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Accepted python-easydev 0.9.35+dfsg-1 (source all) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 18 Oct 2017 01:56:51 -0400
Source: python-easydev
Binary: python-easydev python3-easydev
Architecture: source all
Version: 0.9.35+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-easydev - common utilities to ease the development of Python packages 
(Pyth
 python3-easydev - common utilities to ease the development of Python packages 
(Pyth
Closes: 878963
Changes:
 python-easydev (0.9.35+dfsg-1) unstable; urgency=medium
 .
   * Initial release (Closes: #878963)
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Bug#878964: ITP: python-easydev -- common utilities to ease the development of Python packages

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Team 
Control: block 878962 by -1
Control: block 878963 by -1

* Package name: python-easydev
  Version : 0.9.35
  Upstream Author : Thomas Cokelaer
* URL : https://easydev-python.readthedocs.io/en/latest/
* License : BSD
  Programming Lang: Python
  Description : common utilities to ease the development of Python packages

 The package easydev provides miscellaneous functions that are often used in
 other Python packages. easydev should help developers in speeding up their
 own developments.

This is a dependency of hinge and python-colormap. It will be maintained by the 
Debian Med team.

Bug#878963: ITP: python-colormap -- ease manipulation of matplotlib colormaps and color codecs

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Team 
Control: block 878962 by -1

* Package name: python-colormap
  Version : 1.0.1
  Upstream Author : Thomas Cokelaer
* URL : https://colormap.readthedocs.io/
* License : BSD
  Programming Lang: Python
  Description : ease manipulation of matplotlib colormaps and color codecs

 The colormap package provides simple utilities to convert colors between RGB,
 HEX, HLS, HUV and a class to easily build colormaps for matplotlib. All
 matplotlib colormaps and some R colormaps are available altogether. The
 plot_colormap method (see below) is handy to quickly pick up a colormaps and
 the test_colormap is useful to see test a new colormap.

This is a dependency for hinge and so will be maintained by Debian Med as well.

Bug#878962: ITP: hinge -- long read genome assembler based on hinging

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Team 

* Package name: hinge
  Version : 0.5
  Upstream Author : Govinda Kamath,
Fei Xia,
Ilan Shomorony,
Thomas Courtade, and
David Tse
* URL : https://github.com/HingeAssembler/HINGE
* License : BSD
  Programming Lang: C++, Python
  Description : long read genome assembler based on hinging

 HINGE is a genome assembler that seeks to achieve optimal repeat resolution
 by distinguishing repeats that can be resolved given the data from those that
 cannot. This is accomplished by adding “hinges” to reads for constructing an
 overlap graph where only unresolvable repeats are merged. As a result, HINGE
 combines the error resilience of overlap-based assemblers with
 repeat-resolution capabilities of de Bruijn graph assemblers.


This will be maintained by the Debian Med team.

Accepted fast5 0.6.3-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 17 Oct 2017 20:03:31 -0400
Source: fast5
Binary: fast5 libfast5-dev python-fast5 python3-fast5
Architecture: source
Version: 0.6.3-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 fast5  - utilities for manipulating Oxford Nanopore Fast5 files
 libfast5-dev - library for reading Oxford Nanopore Fast5 files -- headers
 python-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 2
 python3-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 3
Closes: 876283
Changes:
 fast5 (0.6.3-1) unstable; urgency=medium
 .
   * New upstream version
   * Vastly simplified packaging after upstream patches accepted
   * Don't hard-code hdf5-serial
   * Fix source build in autopkgtest (Closes: #876283)
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Accepted fast5 0.6.2-7 (source all amd64) into unstable, unstable

[Afif Elghraoui]

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Format: 1.8
Date: Sun, 01 Oct 2017 11:55:15 -0400
Source: fast5
Binary: fast5 libfast5-dev python-fast5 python3-fast5
Architecture: source all amd64
Version: 0.6.2-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 fast5  - utilities for manipulating Oxford Nanopore Fast5 files
 libfast5-dev - library for reading Oxford Nanopore Fast5 files -- headers
 python-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 2
 python3-fast5 - library for reading Oxford Nanopore Fast5 files -- Python 3
Changes:
 fast5 (0.6.2-7) unstable; urgency=medium
 .
   * Reorganize executables package
 - replace python{,3}-fast5-bin with fast5
 - require executables package version to match
   library version
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Accepted bcftools 1.5-2 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Thu, 12 Oct 2017 00:14:38 -0400
Source: bcftools
Binary: bcftools
Architecture: source
Version: 1.5-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 bcftools   - genomic variant calling and manipulation of VCF/BCF files
Closes: 868958
Changes:
 bcftools (1.5-2) unstable; urgency=low
 .
   * Incorporate lost changes from 1.4.1-3 (Closes: #868958)
   * Update Standards-Version to 4.1.1
   * d/control: use build profiles to mark build-dependencies
 needed only for running tests
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Accepted python-pysam 0.12.0.1+ds-2 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Fri, 06 Oct 2017 23:38:45 -0400
Source: python-pysam
Binary: python-pysam python3-pysam python-pysam-tests
Architecture: source
Version: 0.12.0.1+ds-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-pysam - interface for the SAM/BAM sequence alignment and mapping format 
(
 python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping 
format (
 python3-pysam - interface for the SAM/BAM sequence alignment and mapping 
format (
Changes:
 python-pysam (0.12.0.1+ds-2) unstable; urgency=low
 .
   * Update autopkgtest for new test suite driver
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Accepted bcftools 1.5-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 01 Oct 2017 12:39:31 -0400
Source: bcftools
Binary: bcftools
Architecture: source
Version: 1.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 bcftools   - genomic variant calling and manipulation of VCF/BCF files
Changes:
 bcftools (1.5-1) unstable; urgency=medium
 .
   * migrate to Unstable
 .
 bcftools (1.5-1~exp1) experimental; urgency=medium
 .
   [ Afif Elghraoui ]
   * Update packaging for new build system
 .
   [ Andreas Tille ]
   * New upstream version
   * Bump version in Build-Depends libhts-dev from 1.3.1 to 1.5
   * Standards-Version: 4.0.0 (no changes needed)
 .
   [Steffen Moeller ]
   * [debian/upstream/metadata] Added registry references for
 OMICtools, RRID, bio.tools
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Accepted python-pysam 0.12.0.1+ds-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 01 Oct 2017 12:30:30 -0400
Source: python-pysam
Binary: python-pysam python3-pysam python-pysam-tests
Architecture: source
Version: 0.12.0.1+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-pysam - interface for the SAM/BAM sequence alignment and mapping format 
(
 python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping 
format (
 python3-pysam - interface for the SAM/BAM sequence alignment and mapping 
format (
Closes: 834856 871083
Changes:
 python-pysam (0.12.0.1+ds-1) unstable; urgency=medium
 .
   [ Andreas Tille ]
   * Drop patch applied upstream
   * Standards-Version: 4.1.0 (no changes needed)
   * Apply upstream patch to fix test suite
   * Use pytest instead of nosetest
 .
   [ Afif Elghraoui ]
   * New upstream version
 Closes: #871083, #834856
   * Bump htslib suite minimum versions
   * Use Build Profiles to mark build-dependencies needed only for tests
   * Temporarily skip a failing test (reported upstream)
 .
   [ Steffen Moeller ]
   * created debian/upstream/metadata: references to registries
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Accepted adduser 3.116 (source) into unstable

[Afif Elghraoui]

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Date: Sat, 12 Aug 2017 16:05:34 -0400
Source: adduser
Binary: adduser
Architecture: source
Version: 3.116
Distribution: unstable
Urgency: medium
Maintainer: Debian Adduser Developers <adduser-de...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 adduser- add and remove users and groups
Closes: 708073 759740 763055 840982 845791
Changes:
 adduser (3.116) unstable; urgency=medium
 .
   * Advise installation of 'perl' rather than 'perl-modules'
 (Closes: #840982)
   * Improve distinction between informational and essential messages
 (Closes: #763055)
   * Improve message accompanying error code for creating system user
 (Closes: #708073, #759740)
   * testsuite: add current directory to Perl module search path
   * Use /usr/sbin/nologin instead of /bin/false for default system shell
 (Closes: #845791)
   * Bump Standards-Version to 4.0.1
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Accepted python-avro 1.8.2+dfsg-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Fri, 11 Aug 2017 14:50:50 -0400
Source: python-avro
Binary: python-avro python3-avro
Architecture: source
Version: 1.8.2+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-avro - Apache Avro serialization system — Python 2 library
 python3-avro - Apache Avro serialization system — Python 3 library
Changes:
 python-avro (1.8.2+dfsg-1) unstable; urgency=medium
 .
   * New upstream release.
   * Bump Standards-Version.
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Accepted gridengine 8.1.9+dfsg-5 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 11 Aug 2017 15:29:37 -0400
Source: gridengine
Binary: gridengine-common gridengine-client gridengine-qmon gridengine-master 
gridengine-exec gridengine-dev gridengine-drmaa1.0 libdrmaa1.0-java 
libdrmaa1.0-java-doc gridengine-drmaa-dev libdrmaa1.0-ruby
Architecture: source
Version: 8.1.9+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Grid Engine Maintainers 
<pkg-gridengine-de...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 gridengine-client - Utilities for Grid Engine queue management
 gridengine-common - Distributed resource management - common files
 gridengine-dev - Distributed resource management - development files
 gridengine-drmaa-dev - Distributed resource management Application API library 
- develop
 gridengine-drmaa1.0 - Distributed resource management Application API library
 gridengine-exec - Distributed resource management - Execution Server
 gridengine-master - Distributed resource management - Master Server
 gridengine-qmon - Graphical utilities for Grid Engine queue management
 libdrmaa1.0-java - Distributed resource management Application API library - 
Java bi
 libdrmaa1.0-java-doc - Distributed resource management Application API library 
- Java bi
 libdrmaa1.0-ruby - Distributed resource management Application API library - 
Ruby bi
Closes: 554036 856671 870637
Changes:
 gridengine (8.1.9+dfsg-5) unstable; urgency=medium
 .
   * Wrap qstatus and qsched commands (Closes: #870637)
   * Remove unused config files from /etc/gridengine (Closes: #554036)
   * d/rules: minor simplification
   * Set SGE_ARCH variable (Closes: #856671)
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Accepted bcftools 1.5-1~exp1 (source) into experimental

[Afif Elghraoui]

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Format: 1.8
Date: Tue, 08 Aug 2017 12:35:44 -0400
Source: bcftools
Binary: bcftools
Architecture: source
Version: 1.5-1~exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 bcftools   - genomic variant calling and manipulation of VCF/BCF files
Changes:
 bcftools (1.5-1~exp1) experimental; urgency=medium
 .
   [ Afif Elghraoui ]
   * Update packaging for new build system
 .
   [ Andreas Tille ]
   * New upstream version
   * Bump version in Build-Depends libhts-dev from 1.3.1 to 1.5
   * Standards-Version: 4.0.0 (no changes needed)
 .
   [Steffen Moeller ]
   * [debian/upstream/metadata] Added registry references for
 OMICtools, RRID, bio.tools
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Re: Too many Recommends (in particular on mail-transport-agent)

[Afif Elghraoui]

على الثلاثاء  6 حزيران 2017 ‫04:42، كتب Jonas Smedegaard:
> Quoting Ghislain Vaillant (2017-06-06 10:13:55)
>>
>> Given this is a Python package, we should not even have to argue about 
>> package relationships. Setuptools metadata provides install_requires 
>> and extras_require, the former mapping to Depends, the latter to 
>> Suggests. Period.
>>
>> Your typical Python project README would instruct users to install the 
>> Python package via `pip install`. If one runs `pip install networkx`, 
>> the graphics dependencies do not get pulled. That alone is enough to 
>> justify that these dependencies should not go to Recommends.
>>
>> FYI, I have a similar problem with sympy (#861741), which pulls an 
>> insane amount of packages via chained Recommends.
> 
> We should certainly continue to align package relations with Debian 
> Policy - and therefore by extension continue to argue about that as 
> necessary to evolve Debian Policy:
> 
> Upstream (or other) package relation hints can be a valuable _aid_ in 
> resolving Debian package relations, but only that: An aid!
> 
> Debian packaging follows Debian Policy - other hints do not.
> 

Both good points, but upstream is in the best position to decide whether
something is a strong-yet-not-absolute-dependency (Recommends) of their
software. What Ghislain is saying about Python packages here makes a lot
of sense to me.

regards
Afif
-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: Too many Recommends (in particular on mail-transport-agent)

[Afif Elghraoui]

على الإثنين  5 حزيران 2017 ‫09:52، كتب Scott Kitterman:
>> The answer to that is not clear from the maintainer's response; nor is
>> it clear from what the submitter has written whether they know the
>> answer.
> Why is that question relevant?  The policy definition of Recommends (versus 
> Suggests) has nothing to with if there will be a failure or not:
> 
>> The Recommends field should list packages that would be found together with
>> this one in all but unusual installations

That's not the complete definition of Recommends. The part you left out
states that there should be a strong, but not absolute dependency.
Presumably their being almost always found together on all but unusual
installations is a consequence of that.

> Personally, I think the maintainer articulated what he views as the usual 
> situation and declines to remove Recommends that are, in the maintainer's 
> view, appropriate.  His rationale makes complete sense to me.
>  I'm not saying 
> there aren't other, reasonable choices that could be made, but it make sense. 
>  
> I don't think this is the kind of thing the TC should even entertain 
> overruling a maintainer on.

It's not about targeting the maintainer. It's about clarifying what
should be done. I'd be happy to know whether I should have turned the
pbhoney Recommends into a Depends to avoid unwarranted fallback behavior
when people disable Recommends to avoid numerous unneeded packages.

regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: Too many Recommends (in particular on mail-transport-agent)

[Afif Elghraoui]

 86.6 MB of additional disk space will be used.


But with the latter, you won't get pbdagcon (Recommends of pbhoney) and
will end up using pbhoney's inferior fallback implementation.

regards
Afif


1.
https://networkx.github.io/documentation/networkx-1.10/reference/drawing.html

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Re: Too many Recommends (in particular on mail-transport-agent)

[Afif Elghraoui]

على الثلاثاء 30 أيار 2017 ‫07:57، كتب Ansgar Burchardt:
> my impression is that too many packages use Recommends that should
> really be Suggests.  As a random example: installing dracut as a
> initramfs provider will pull in exim4... (dracut-core Recommends: mdadm
> which Recommends: default-mta | mail-transport-agent).  This seems
> really not ideal.
> 
> As a result many people seem to disable installing recommended packages
> by default.  I believe we should be much more agressive in downgrading
> dependencies to Suggests.

I completely agree. I've teken issue with packages recommending packages
in the spirit of "if you want this, you might also want X", which is the
literal sense of the word "recommends", but fits the definition in
policy for Suggests ("package may be more useful with one or more
others"). I've been unsuccessful in arguing this case before (#849619),
so I don't think the bug-filing method previously suggested [1] will
work. I think there needs to be a clarification to everyone of what
Recommends is for, since there seem to be different interpretations
(although the policy looks quite clear to me).

I see this as a real problem for cases where a Recommends is actually
important. As an example, I have a package pbhoney that Recommends
pbdagcon. If pbdagcon is not installed, pbhoney has a fallback
implementation that is not as good. So it is highly preferable to have
pbdagcon installed if it is available, but you can still use pbhoney
without it--although it will not run as well. I see that this perfectly
fits the definition of Recoomends ("a strong, but not absolute,
dependency"). but if people go on and globally use
--no-install-recommends, there may be an unnecessarily negative
consequence here.


regards
Afif

1. https://lists.debian.org/debian-devel/2016/04/msg00159.html

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Accepted canu 1.5+dfsg-1 (source) into unstable

[Afif Elghraoui]

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Date: Thu, 18 May 2017 01:59:14 -0400
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Binary: canu
Architecture: source
Version: 1.5+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 canu   - single molecule sequence assembler for genomes
Changes:
 canu (1.5+dfsg-1) unstable; urgency=medium
 .
   * New upstream release
   * d/copyright: Drop Files-Excluded entries for files removed upstream
   * Refresh and update patches
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Accepted trnascan-se 1.3.1-1 (source all amd64) into unstable, unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 13 Dec 2016 23:35:18 -0800
Source: trnascan-se
Binary: trnascan-se trnascan-se-common
Architecture: source all amd64
Version: 1.3.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 trnascan-se - detection of transfer RNA genes in genomic sequence
 trnascan-se-common - detection of transfer RNA genes in genomic sequence 
(common files
Closes: 803542
Changes:
 trnascan-se (1.3.1-1) unstable; urgency=medium
 .
   * Initial release (Closes: #803542)
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Accepted canu 1.3+dfsg-1 (source amd64) into unstable, unstable

[Afif Elghraoui]

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Date: Sun, 09 Oct 2016 21:53:18 -0700
Source: canu
Binary: canu
Architecture: source amd64
Version: 1.3+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 canu   - single molecule sequence assembler for genomes
Closes: 395843
Changes:
 canu (1.3+dfsg-1) unstable; urgency=medium
 .
   * Initial release (Closes: #395843)
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Re: Bug#855597: ITP: phyx -- phylogenetic analyses on trees and sequences for UNIX

[Afif Elghraoui]

Hi, Andreas,

على الإثنين 20 شباط 2017 ‫08:26، كتب Andreas Tille:
> Hi Afif
> 
> On Mon, Feb 20, 2017 at 08:14:30AM -0800, Afif Elghraoui wrote:
>>   Description : phylogenetic analyses on trees and sequences for UNIX
> 
> Please drop " for UNIX" here - since this is redundant on a Debian system.
> May be
> 
>s/ for UNIX/ at command line enabling pipes/
> 
> or something like this makes the specific features of the tools more clear.
>  

Thanks for your comment; I was myself unsure about the wording. However,
this was meant to emphasize the nature of the tools in following the
UNIX style, but your suggestion is a bit wordy.

How about "UNIX-style phylogenetic analyses on trees and sequences"?

Thanks and regards
Afif

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name

Bug#855597: ITP: phyx -- phylogenetic analyses on trees and sequences for UNIX

[Afif Elghraoui]

Package: wnpp
Severity: wishlist
Owner: Debian Med Packaging Team 

* Package name: phyx
  Version : 0.99
  Upstream Author : Joseph W. Brown, Joseph F. Walker, and Stephen A. Smith
* URL : https://github.com/FePhyFoFum/phyx
* License : GPL
  Programming Lang: C++
  Description : phylogenetic analyses on trees and sequences for UNIX

 phyx provides a convenient, lightweight and inclusive toolkit consisting of
 programs spanning the wide breadth of programs utilized by researchers
 performing phylogenomic analyses. Modeled after Unix/GNU/Linux command
 line tools, individual programs perform a single task and operate on
 standard I/O streams. A result of this stream-centric approach is that, for
 most programs, only a single sequence or tree is in memory at any moment.
 Thus, large datasets can be processed with minimal memory requirements.
 phyx’s ever-growing complement of programs consists of over 35 programs
 focused on exploring, manipulating, analyzing and simulating phylogenetic
 objects (alignments, trees and MCMC logs). As with standard Unix command
 line tools, these programs can be piped (together with non-phyx tools),
 allowing the easy construction of efficient analytical pipelines.


This package will be maintained by the Debian Med team.

Accepted python-pysam 0.10.0+ds-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Thu, 26 Jan 2017 04:36:11 -0800
Source: python-pysam
Binary: python-pysam python3-pysam python-pysam-tests
Architecture: source
Version: 0.10.0+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-pysam - interface for the SAM/BAM sequence alignment and mapping format 
(
 python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping 
format (
 python3-pysam - interface for the SAM/BAM sequence alignment and mapping 
format (
Changes:
 python-pysam (0.10.0+ds-1) unstable; urgency=medium
 .
   [ Afif Elghraoui ]
   * New upstream release
   * Update patches
 .
   [ Andreas Tille ]
   * d/rules: Remove redundant get-orig-source target
   * hardening=+all
   * Fix lintian overrides
 .
   [ Afif Elghraoui ]
   * Do not use internal htslib
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Accepted python-pbcore 1.2.11+dfsg-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Thu, 26 Jan 2017 00:23:02 -0800
Source: python-pbcore
Binary: python-pbcore python-pbcore-doc
Architecture: source
Version: 1.2.11+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-pbcore - Python library for processing PacBio data files
 python-pbcore-doc - Python library for processing PacBio data files 
(documentation)
Changes:
 python-pbcore (1.2.11+dfsg-1) unstable; urgency=medium
 .
   * New upstream release (git 32b6883 from 2016-09-19)
   * Update patches
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Accepted python-cobra 0.5.9-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Wed, 25 Jan 2017 01:22:48 -0800
Source: python-cobra
Binary: python-cobra python3-cobra python-cobra-data
Architecture: source
Version: 0.5.9-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-cobra - constraint-based modeling of biological networks (Python 2)
 python-cobra-data - constraint-based modeling of biological networks (data)
 python3-cobra - constraint-based modeling of biological networks (Python 3)
Changes:
 python-cobra (0.5.9-1) unstable; urgency=medium
 .
   * New upstream release
   * Refresh patch
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Accepted falcon 1.8.6-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Mon, 23 Jan 2017 22:56:36 -0800
Source: falcon
Binary: falcon
Architecture: source
Version: 1.8.6-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 falcon - diploid-aware genome assembly of single-molecule sequencing reads
Changes:
 falcon (1.8.6-1) unstable; urgency=medium
 .
   * New upstream release
   * Remove Files-Excluded line
   * New dependencies: rsync, time
   * Update patches
   * Remove copyright statements for removed sources
   * autopkgtest:
 - work around failure caused by trying to use /tmp while
   running in /tmp
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Accepted python-avro 1.8.2~rc1+dfsg-1 (source) into experimental

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 23 Jan 2017 02:55:15 -0800
Source: python-avro
Binary: python-avro python3-avro
Architecture: source
Version: 1.8.2~rc1+dfsg-1
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 python-avro - Apache Avro serialization system — Python 2 library
 python3-avro - Apache Avro serialization system — Python 3 library
Changes:
 python-avro (1.8.2~rc1+dfsg-1) experimental; urgency=medium
 .
   * New upstream release candidate
   * Refresh patch
   * Bump copyright years
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Accepted pbbam 0.7.4+ds-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Sat, 21 Jan 2017 23:48:21 -0800
Source: pbbam
Binary: pbbamtools libpbbam libpbbam-dev
Architecture: source
Version: 0.7.4+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 libpbbam   - Pacific Biosciences binary alignment/map (BAM) library
 libpbbam-dev - Pacific Biosciences binary alignment/map (BAM) library (headers)
 pbbamtools - processing Pacific Biosciences binary alignment/map files
Changes:
 pbbam (0.7.4+ds-1) unstable; urgency=medium
 .
   * New upstream release snapshot
 - Exclude dependency convenience copy
 - Update patches
 - Update running of tests at build-time
 - Update .install files
 - Update autopkgtest commands
   * Use debhelper compat 10
   * libpbbam-dev: depend on libssl-dev
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Accepted pbgenomicconsensus 2.1.0-1 (source) into unstable

[Afif Elghraoui]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 21 Jan 2017 16:15:53 -0800
Source: pbgenomicconsensus
Binary: pbgenomicconsensus python-pbgenomicconsensus
Architecture: source
Version: 2.1.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 pbgenomicconsensus - Pacific Biosciences variant and consensus caller
 python-pbgenomicconsensus - Pacific Biosciences variant and consensus caller 
(Python 2)
Changes:
 pbgenomicconsensus (2.1.0-1) unstable; urgency=medium
 .
   * New upstream release snapshot
 (git 5893b16, 2016-07-19)
   * Update manpage for new release
   * Adapt test suite for missing pbtestdata
   * autopkgtest: make sure to test installed version of the package
   * Add python-consensuscore2 to Recommends
   * Add lintian override for autopkgtest dependency list
   * Install FAQ into docs rather than as a manpage
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Accepted sprai 0.9.9.22+dfsg-1 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Fri, 20 Jan 2017 00:44:23 -0800
Source: sprai
Binary: sprai
Architecture: source
Version: 0.9.9.22+dfsg-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 sprai  - single-pass sequencing read accuracy improver
Changes:
 sprai (0.9.9.22+dfsg-1) unstable; urgency=low
 .
   * Add example data
   * Bump copyright year
   * New upstream release
   * Update upstream contact email address
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Accepted ori 0.8.1+ds1-3 (source) into unstable

[Afif Elghraoui]

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Date: Thu, 19 Jan 2017 03:19:48 -0800
Source: ori
Binary: ori
Architecture: source
Version: 0.8.1+ds1-3
Distribution: unstable
Urgency: low
Maintainer: Afif Elghraoui <a...@debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 ori- peer-to-peer distributed file system
Closes: 851004
Changes:
 ori (0.8.1+ds1-3) unstable; urgency=low
 .
   * d/control, d/rules: clean-ups and readability improvements
   * Use debhelper compat 10
   * Build-depend on zlib (Closes: #851004)
   * Bump copyright year
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Accepted dazzdb 1.0+20161112-2 (source) into unstable

[Afif Elghraoui]

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Format: 1.8
Date: Wed, 18 Jan 2017 23:45:14 -0800
Source: dazzdb
Binary: dazzdb
Architecture: source
Version: 1.0+20161112-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 dazzdb - manage nucleotide sequencing read data
Changes:
 dazzdb (1.0+20161112-2) unstable; urgency=medium
 .
   * compiler-flags.patch: slight corrections for DBwipe
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Accepted dazzdb 1.0+20161112-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Wed, 18 Jan 2017 22:57:17 -0800
Source: dazzdb
Binary: dazzdb
Architecture: source
Version: 1.0+20161112-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 dazzdb - manage nucleotide sequencing read data
Changes:
 dazzdb (1.0+20161112-1) unstable; urgency=medium
 .
   * New upstream snapshot (git e31d451)
   * Refresh and update patches
   * New build-dependency: zlib
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Accepted daligner 1.0+20161119-1 (source) into unstable

[Afif Elghraoui]

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Hash: SHA256

Format: 1.8
Date: Wed, 18 Jan 2017 22:16:19 -0800
Source: daligner
Binary: daligner
Architecture: source
Version: 1.0+20161119-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Afif Elghraoui <a...@debian.org>
Description:
 daligner   - local alignment discovery between long nucleotide sequencing read
Changes:
 daligner (1.0+20161119-1) unstable; urgency=medium
 .
   * New upstream snapshot (git a9458dc)
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