Re: Videoconference Saturday 2020-10-17 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020))

[Michael R. Crusoe]

On Fri, Oct 16, 2020 at 3:50 PM Andreas Tille  wrote:

> Hi,
>
> the video conferences of the Debian Med team have shifted to two
> meetings per month now.  Do enable different people joing we shift
> weekdays by simply meeting on every
>
>2th  and  17th
>
> of a month.  So the next meeting is tomorrow 18:00 UTC
>
> For those who would like to join our next videomeeting it will happen at
> Friday
>
>
> https://www.timeanddate.com/worldclock/fixedtime.html?msg=Debian+CoViD-19+Biohackathon+Video+Conference=20201017T20=37=1
>

Notes are at
https://storm.debian.net/shared/SlUYTQlMWDJUfhR7J2PIiDaMDa_e28was0bsjELz77k

Thanks to the attendees!


> The meeting is on the Debian Social channel
>
>  https://jitsi.debian.social/DebianMedCovid19
>
> These video meetings were started in the Debian Med Biohackathon[1].
> The topic is what contributors have done in the past week and to
> coordinate the work for next week.  Here are the reports of some past
> meetings:
>
>  https://wiki.debian.org/DebianMed/Meeting/WeeklyCovid19
>
> To repeat myself: Newcomers are always welcome.
>
> Most probably I will not be able to attend myself the meeting
> tomorrow - but I wish all attendees a lot of fun
>
>Andreas.
>
> [1] https://lists.debian.org/debian-devel-announce/2020/03/msg00010.html
>
> --
> http://fam-tille.de
>
>

Re: Videoconference today Friday 2020-06-12 18:00 UTC (Was: For those who want to keep on contributing (Was: Debian @ COVID-19 Biohackathon (April 5-11, 2020)))

[Michael R. Crusoe]

Thank you Andreas for announcing the meeting, and thanks to the attendees
for their participation. Our meeting notes are at
https://storm.debian.net/shared/6NfKT87njAmCg3tr_uhkE2Qp9SQhVxy8mwD1fQUzfMy

On Fri, Jun 12, 2020 at 1:07 PM Andreas Tille  wrote:

> Hi,
>
> for those who would like to join our next videomeeting it will happen at
>
>
> https://www.timeanddate.com/worldclock/fixedtime.html?msg=Debian+CoViD-19+Biohackathon+Video+Conference=20200612T20=37=1
>
> As last week we will use
>
>  https://jitsi.debian.social/DebianMedCovid19
>
> These weekly video meetings were started in the Debian Med
> Biohackathon[1].  The topic is what contributors have done in the past
> week and to coordinate the work for next week.  Despite the one week of
> hackathon is over Covid-19 is not and there is a lot of remaining work
> to do.  Newcomers are always welcome.
>
> See you
>
>Andreas.
>
> [1] https://lists.debian.org/debian-devel-announce/2020/03/msg00010.html
>
> --
> http://fam-tille.de
>
>

Accepted python-schema-salad 5.0.20200126033820-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Tue, 28 Jan 2020 14:05:51 +0100
Source: python-schema-salad
Architecture: source
Version: 5.0.20200126033820-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
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 .
   * New upstream version
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Accepted python-schema-salad 5.0.20200122085940-2 (source) into unstable

[Michael R. Crusoe]

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Source: python-schema-salad
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Version: 5.0.20200122085940-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-schema-salad (5.0.20200122085940-2) unstable; urgency=medium
 .
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   * debian/patches/better_is_fs_case_sensitive: allow test to work post-
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Accepted seqan3 3.0.1+ds-3 (source) into unstable

[Michael R. Crusoe]

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Date: Sun, 26 Jan 2020 23:36:12 +0100
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Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
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 .
   * Autopkgtests: correct {CXX,CPP,C}FLAGS exports
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Accepted python-schema-salad 5.0.20200122085940-1 (source) into unstable

[Michael R. Crusoe]

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Date: Fri, 24 Jan 2020 16:52:41 +0100
Source: python-schema-salad
Architecture: source
Version: 5.0.20200122085940-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
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 .
   * New upstream version
   * Use secure URI in Homepage field.
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Accepted last-align 1047-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Fri, 24 Jan 2020 16:21:19 +0100
Source: last-align
Architecture: source
Version: 1047-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 last-align (1047-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
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Accepted seqan3 3.0.1+ds-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 24 Jan 2020 14:23:27 +0100
Source: seqan3
Architecture: source
Version: 3.0.1+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 seqan3 (3.0.1+ds-2) unstable; urgency=medium
 .
   * Autopkgtests: set the same flags as build time
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Accepted seqan3 3.0.1+ds-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Thu, 23 Jan 2020 18:38:07 +0100
Source: seqan3
Architecture: source
Version: 3.0.1+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 seqan3 (3.0.1+ds-1) unstable; urgency=medium
 .
   * New upstream version
   * Standards-Version: 4.4.1
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Accepted python-pysam 0.15.4+ds-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Thu, 23 Jan 2020 15:00:17 +0100
Source: python-pysam
Architecture: source
Version: 0.15.4+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-pysam (0.15.4+ds-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
   * python-pysam-tests: Multi-Arch: foreign
   * Try to keep example_no_seq_in_header_null_bytes.bam from being deleted
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Accepted seqan3 3.0.0.0.git.20200110.b42671eac39+ds-1 (source) into experimental

[Michael R. Crusoe]

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Hash: SHA512

Format: 1.8
Date: Mon, 20 Jan 2020 18:21:17 +0100
Source: seqan3
Architecture: source
Version: 3.0.0.0.git.20200110.b42671eac39+ds-1
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 seqan3 (3.0.0.0.git.20200110.b42671eac39+ds-1) experimental; urgency=medium
 .
   * New upstream snapshot. Very close to 3.0.1.
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Accepted libbio-procedural-perl 1.7.4-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 15 Jan 2020 18:55:49 +0100
Source: libbio-procedural-perl
Architecture: source
Version: 1.7.4-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-procedural-perl (1.7.4-2) unstable; urgency=medium
 .
   * No change source-only upload.
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Accepted seqan3 3.0.0.0.git.20200110.b42671eac39-3 (source) into experimental

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 14 Jan 2020 08:51:07 +0100
Source: seqan3
Architecture: source
Version: 3.0.0.0.git.20200110.b42671eac39-3
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 seqan3 (3.0.0.0.git.20200110.b42671eac39-3) experimental; urgency=medium
 .
   * Restrict the usage of the gold linker away from platforms where it isn't
 available.
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Accepted diamond-aligner 0.9.29+dfsg-5 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Tue, 14 Jan 2020 08:54:46 +0100
Source: diamond-aligner
Architecture: source
Version: 0.9.29+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 diamond-aligner (0.9.29+dfsg-5) unstable; urgency=medium
 .
   * Team upload.
   * Restrict the use of the gold linker on architectures where it is not
 available.
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Accepted seqan3 3.0.0.0.git.20200110.b42671eac39-2 (source) into experimental

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 13 Jan 2020 20:24:11 +0100
Source: seqan3
Architecture: source
Version: 3.0.0.0.git.20200110.b42671eac39-2
Distribution: experimental
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 seqan3 (3.0.0.0.git.20200110.b42671eac39-2) experimental; urgency=medium
 .
   * Only 64bit architectures are supported
   * Include patch from upstream for powerpc
   * Switch to ld.gold to work around the broken binutils.ld on arm64
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Accepted diamond-aligner 0.9.29+dfsg-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 13 Jan 2020 19:34:04 +0100
Source: diamond-aligner
Architecture: source
Version: 0.9.29+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 942850
Changes:
 diamond-aligner (0.9.29+dfsg-3) unstable; urgency=medium
 .
   * Team upload.
   * patch to enable non-x86 builds again (no -msse, etc..)
 Closes: #942850
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Accepted libbio-db-seqfeature-perl 1.7.4-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Mon, 13 Jan 2020 13:17:15 +0100
Source: libbio-db-seqfeature-perl
Architecture: source
Version: 1.7.4-1
Distribution: unstable
Urgency: medium
Maintainer: Michael R. Crusoe 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-seqfeature-perl (1.7.4-1) unstable; urgency=medium
 .
   * New upstream version
   * Standards-Version: 4.4.1
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Accepted libbio-db-gff-perl 1.7.4-1 (source) into unstable

[Michael R. Crusoe]

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Date: Mon, 13 Jan 2020 13:16:18 +0100
Source: libbio-db-gff-perl
Architecture: source
Version: 1.7.4-1
Distribution: unstable
Urgency: medium
Maintainer: Michael R. Crusoe 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-gff-perl (1.7.4-1) unstable; urgency=medium
 .
   * New upstream version
   * Standards-Version: 4.4.1
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Accepted libbio-db-biofetch-perl 1.7.3-3 (source) into unstable

[Michael R. Crusoe]

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Date: Mon, 13 Jan 2020 16:35:41 +0100
Source: libbio-db-biofetch-perl
Architecture: source
Version: 1.7.3-3
Distribution: unstable
Urgency: medium
Maintainer: Michael R. Crusoe 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-biofetch-perl (1.7.3-3) unstable; urgency=medium
 .
   * debian/control: fix broken Vcs-Git field
   * Standards-Version: 4.4.1
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Accepted seqan3 3.0.0.0.git.20200110.b42671eac39-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Mon, 13 Jan 2020 15:41:25 +0100
Source: seqan3
Architecture: source
Version: 3.0.0.0.git.20200110.b42671eac39-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 seqan3 (3.0.0.0.git.20200110.b42671eac39-1) unstable; urgency=medium
 .
   * Experimental snapshot from upstream
   * Try using the Debian package for range-v3
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Accepted proteinortho 6.0.12+dfsg-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Mon, 13 Jan 2020 13:12:59 +0100
Source: proteinortho
Architecture: source
Version: 6.0.12+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 proteinortho (6.0.12+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * patch: Use #!/usr/bin/python3 (fixes autopkgtests)
   * patch: Find the packaged version of the Diamond aligner in
 /usr/lib/debian-med/bin, which will help with backports
   * patch: Improve build hardening via CPPFLAGS & CFLAGS
   * Expanded autopkgtests, following `make test`
   * patch: fix a spelling typo
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Accepted bioperl-run 1.7.3-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 07 Jan 2020 12:07:09 +0100
Source: bioperl-run
Architecture: source
Version: 1.7.3-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 948323
Changes:
 bioperl-run (1.7.3-3) unstable; urgency=medium
 .
   * Team upload.
   * Depends: libbio-tools-run-alignment-clustalw-perl (Closes: #948323)
   * Depends: libbio-featureio-perl
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Accepted libbio-featureio-perl 1.6.905-1 (source all) into unstable, unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 7 Jan 2020 11:25:43 +
Source: libbio-featureio-perl
Binary: libbio-featureio-perl
Architecture: source all
Version: 1.6.905-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 libbio-featureio-perl - Modules for reading, writing, and manipulating 
sequence features
Closes: 948325
Changes:
 libbio-featureio-perl (1.6.905-1) unstable; urgency=low
 .
   * Initial release. (Closes: #948325)
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Accepted minimap2 2.17+dfsg-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Sun, 12 Jan 2020 18:22:11 +0100
Source: minimap2
Architecture: source
Version: 2.17+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 922620
Changes:
 minimap2 (2.17+dfsg-2) unstable; urgency=medium
 .
   [ Michael R. Crusoe ]
   * Team upload.
   * Add support for more architectures using the SIMD Everyhere library
 Closes: #922620
   * Standards-Version: 4.4.1
 .
   [ Andreas Tille ]
   * Set upstream metadata fields: Bug-Database, Bug-Submit.
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Accepted bio-tradis 1.4.5+dfsg2-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 11 Jan 2020 16:41:24 +0100
Source: bio-tradis
Architecture: source
Version: 1.4.5+dfsg2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 947463
Changes:
 bio-tradis (1.4.5+dfsg2-1) unstable; urgency=medium
 .
   * Team upload.
   * debian/patches/samtools1.10: remove version parsing code that can't handle
 samtools version 1.10 (Closes: #947463)
   * Switch to cpan for the source
   * autopkgtests: ignore the tests that are not yet updated for
 samtools 1.10.x
   * Set fields Upstream-Contact in debian/copyright.
   * Remove obsolete fields Contact from debian/upstream/metadata.
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Accepted bowtie 1.2.3+dfsg-4 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 11 Jan 2020 12:14:53 +0100
Source: bowtie
Architecture: source
Version: 1.2.3+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 bowtie (1.2.3+dfsg-4) unstable; urgency=medium
 .
   * Team upload.
   * Switch to single threaded testing, add riscv64
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Accepted libfastahack 1.0.0+dfsg-5 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 10 Jan 2020 19:40:17 +0100
Source: libfastahack
Architecture: source
Version: 1.0.0+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libfastahack (1.0.0+dfsg-5) unstable; urgency=medium
 .
   * Team upload.
   * Breaks+Replaces: libfastahack0 (<< 1.0.0+dfsg-4)
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Accepted ngs-sdk 2.10.1-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 10 Jan 2020 16:45:29 +0100
Source: ngs-sdk
Architecture: source
Version: 2.10.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 ngs-sdk (2.10.1-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream release.
   * Standards-Version: 4.4.1
   * Fixed more-archs patch, was missing a semicolon
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Accepted ngs-sdk 2.10.0-4 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 10 Jan 2020 14:19:11 +0100
Source: ngs-sdk
Architecture: source
Version: 2.10.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 ngs-sdk (2.10.0-4) unstable; urgency=medium
 .
   * Team upload.
   * debian/patches/more_archs: don't hardcode 32 vs 64 bits, use
 dpkg-architecture -qDEB_TARGET_ARCH_BITS
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Accepted ngs-sdk 2.10.0-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 10 Jan 2020 11:20:47 +0100
Source: ngs-sdk
Architecture: source
Version: 2.10.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 813559
Changes:
 ngs-sdk (2.10.0-3) unstable; urgency=medium
 .
   * Team upload.
 .
   [Frédéric Bonnard]
   * Add support for other architectures based on gcc atomic built-ins
(Closes: #813559)
 .
   [Michael R. Crusoe]
   * debian/patches/more_archs: enable arm64, mips64el, ppc64el, s390x, riscv64
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Accepted examl 3.0.21-3 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Fri, 10 Jan 2020 09:07:09 +0100
Source: examl
Architecture: source
Version: 3.0.21-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 examl (3.0.21-3) unstable; urgency=medium
 .
   * Team upload.
   * Use the SIMD Everywhere library for greater portability.
   * debhelper-compat 12
   * Standards-Version: 4.4.1
   * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
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Accepted hopscotch-map 2.2.1-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Thu, 09 Jan 2020 20:01:37 +0100
Source: hopscotch-map
Architecture: source
Version: 2.2.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 hopscotch-map (2.2.1-2) unstable; urgency=medium
 .
   * Add g++ to the autopkgtest dependencies
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Accepted bowtie 1.2.3+dfsg-3 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 08 Jan 2020 12:39:33 +0100
Source: bowtie
Architecture: source
Version: 1.2.3+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 bowtie (1.2.3+dfsg-3) unstable; urgency=medium
 .
   * Team upload.
   * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
   * `make simple-test` in addition to our own tests
   * Remove obsolete fields Contact from debian/upstream/metadata.
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Accepted libfastahack 1.0.0+dfsg-4 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 08 Jan 2020 10:55:37 +0100
Source: libfastahack
Architecture: source
Version: 1.0.0+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libfastahack (1.0.0+dfsg-4) unstable; urgency=medium
 .
   * Team upload.
   * Generate a manual page with help2man
   * Run some basic tests
   * Use those tests as an autopkgtest
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Accepted libbio-cluster-perl 1.7.3-4 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Tue, 07 Jan 2020 14:34:20 +0100
Source: libbio-cluster-perl
Architecture: source
Version: 1.7.3-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libbio-cluster-perl (1.7.3-4) unstable; urgency=medium
 .
   * libbio-variation-perl is in the archive, so remove our patch that avoided
 it.
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Accepted libbio-variation-perl 1.7.5-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Tue, 07 Jan 2020 14:27:05 +0100
Source: libbio-variation-perl
Architecture: source
Version: 1.7.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Team 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-variation-perl (1.7.5-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted cnvkit 0.9.6-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Tue, 07 Jan 2020 11:48:23 +0100
Source: cnvkit
Architecture: source
Version: 0.9.6-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 cnvkit (0.9.6-3) unstable; urgency=medium
 .
   * Don't run the autopkgtests in parallel.
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Accepted gatb-core 1.4.1+git20191209.9398f28+dfsg-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 05 Jan 2020 22:40:32 +0100
Source: gatb-core
Architecture: source
Version: 1.4.1+git20191209.9398f28+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 947964
Changes:
 gatb-core (1.4.1+git20191209.9398f28+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Add -latomic where needed to fix the build on armel, mipsel & powerpc.
   * new patch to avoid "-msse2" on build hosts that use qemu
   * Simplify library dependencies. Closes: #947964.
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Accepted python-pysam 0.15.3+ds-4 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sun, 05 Jan 2020 21:23:11 +0100
Source: python-pysam
Architecture: source
Version: 0.15.3+ds-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-pysam (0.15.3+ds-4) unstable; urgency=medium
 .
   * Team upload.
   * Replace missing hts_seek and hts_tell equivalents
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Accepted python-pysam 0.15.3+ds-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 05 Jan 2020 08:01:33 +0100
Source: python-pysam
Architecture: source
Version: 0.15.3+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-pysam (0.15.3+ds-3) unstable; urgency=medium
 .
   * Team upload.
   * -docs: oops, don't try to ship nonexistent debian/tests/run-nose{3,}-tests
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Accepted libbio-db-ncbihelper-perl 1.7.6-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sun, 05 Jan 2020 07:56:13 +0100
Source: libbio-db-ncbihelper-perl
Architecture: source
Version: 1.7.6-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-ncbihelper-perl (1.7.6-2) unstable; urgency=medium
 .
   * Be more strict about the libbio-asn1-entrezgene-perl dependency
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Accepted python-pysam 0.15.3+ds-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 04 Jan 2020 23:19:04 +0100
Source: python-pysam
Architecture: source
Version: 0.15.3+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-pysam (0.15.3+ds-2) unstable; urgency=medium
 .
   * Team upload.
   * new patch: Update deprecated samtools import test commands to samtools view
   * new patch: Update samtools + bcftools to v1.10
   * disable tests for now
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Accepted hisat2 2.1.0-2nopython3hisat3 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sat, 04 Jan 2020 22:52:02 +0100
Source: hisat2
Architecture: source
Version: 2.1.0-2nopython3hisat3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 hisat2 (2.1.0-2nopython3hisat3) unstable; urgency=medium
 .
   * armhf armel ppc64el s390x: add -Wno-narrowing
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Accepted python-gffutils 0.10.1-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 01 Jan 2020 12:49:11 +0100
Source: python-gffutils
Architecture: source
Version: 0.10.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-gffutils (0.10.1-1) unstable; urgency=medium
 .
   * New upstream version
   * Freshen patches, removing two applied upstream
   * Remove obsolete fields Name from debian/upstream/metadata.
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Accepted iva 1.0.9+ds-8 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sat, 04 Jan 2020 18:21:02 +0100
Source: iva
Architecture: source
Version: 1.0.9+ds-8
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 iva (1.0.9+ds-8) unstable; urgency=medium
 .
   * Team upload.
   * Add missing python3-packaging dependency for the autopkgtests
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Accepted hisat2 2.1.0-2nopython3hisat2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 30 Dec 2019 20:08:00 +0100
Source: hisat2
Architecture: source
Version: 2.1.0-2nopython3hisat2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 943125
Changes:
 hisat2 (2.1.0-2nopython3hisat2) unstable; urgency=medium
 .
   [ Saira Hussain ]
   * Add autopkgtest
 .
   [ Andreas Tille ]
   * Install hisat2_extract_splice_sites.py
   * Recommends: bcftools, samtools
 .
   [ Michael R. Crusoe ]
   * Skip the new python3-hisat2 package while we wait for 2.1.0-3 to go
 through the NEW queue.
   * Include SIMD everywhere headers and enable building on all architectures.
   * debhelper-compat 12
   * Remove trailing whitespace in debian/control
   * Ported Python scripts to Python 3 using 2to3. Closes: #943125
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Accepted libbio-db-embl-perl 1.7.4-2 (source) into unstable

[Michael R. Crusoe]

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Hash: SHA512

Format: 1.8
Date: Fri, 03 Jan 2020 20:47:04 +0100
Source: libbio-db-embl-perl
Architecture: source
Version: 1.7.4-2
Distribution: unstable
Urgency: medium
Maintainer: Michael R. Crusoe 
Changed-By: Michael R. Crusoe 
Closes: 948083
Changes:
 libbio-db-embl-perl (1.7.4-2) unstable; urgency=medium
 .
   * Add missing Breaks+Replaces: libbio-perl-perl (<< 1.7.3) (Closes: #948083)
   * Correct VCS-Git URL
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Accepted libbio-db-hts-perl 3.01-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 03 Jan 2020 22:21:07 +0100
Source: libbio-db-hts-perl
Architecture: source
Version: 3.01-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-hts-perl (3.01-3) unstable; urgency=medium
 .
   * Team upload.
   * Fix tests with missing dependencies. (Closes #948097)
   * Multi-Arch: same
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Accepted libbio-db-ncbihelper-perl 1.7.6-1 (source) into unstable

[Michael R. Crusoe]

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Date: Sat, 04 Jan 2020 12:44:54 +0100
Source: libbio-db-ncbihelper-perl
Architecture: source
Version: 1.7.6-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-ncbihelper-perl (1.7.6-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted smalt 0.7.6-9 (source) into unstable

[Michael R. Crusoe]

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Date: Fri, 03 Jan 2020 11:44:39 +0100
Source: smalt
Architecture: source
Version: 0.7.6-9
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 938501
Changes:
 smalt (0.7.6-9) unstable; urgency=medium
 .
   * Team upload.
 .
   [ Andreas Tille ]
   * Use 2to3 to port to Python3
 Closes: #938501
   * debhelper-compat 12
   * Standards-Version: 4.4.1
   * Remove trailing whitespace in debian/changelog
   * Use secure URI in debian/watch.
   * Use secure URI in Homepage field.
   * Set upstream metadata fields: Archive, Bug-Submit.
   * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
 .
   [ Michael R. Crusoe ]
   * Fixed the remaining Python3 issues in test scripts
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Accepted python-pysam 0.15.3+ds-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Fri, 03 Jan 2020 21:25:33 +0100
Source: python-pysam
Architecture: source
Version: 0.15.3+ds-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 947426
Changes:
 python-pysam (0.15.3+ds-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream release. Not yet dropping py2 due to paleomix and pbsuite
   * debhelper-compat 12
   * Standards-Version: 4.4.0
   * Trim trailing whitespace.
   * Use secure URI in Homepage field.
   * Set upstream metadata fields: Repository.
   * New patch to remove symbols that were dropped in htslib 1.10:
 hts_utell, hts_useek (Closes: #947426)
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Accepted libbio-db-ncbihelper-perl 1.7.4-1 (source all) into unstable, unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 28 Dec 2019 20:45:34 +0100
Source: libbio-db-ncbihelper-perl
Binary: libbio-db-ncbihelper-perl
Architecture: source all
Version: 1.7.4-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Description:
 libbio-db-ncbihelper-perl - collection of routines useful for queries to NCBI 
databases
Closes: 940258
Changes:
 libbio-db-ncbihelper-perl (1.7.4-1) unstable; urgency=low
 .
   * Initial release. (Closes: #940258)
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Accepted libbio-variation-perl 1.7.4-1 (source all) into unstable, unstable

[Michael R. Crusoe]

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Hash: SHA256

Format: 1.8
Date: Mon, 9 Dec 2019 16:39:30 +0100
Source: libbio-variation-perl
Binary: libbio-variation-perl
Architecture: source all
Version: 1.7.4-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Team 
Changed-By: Michael R. Crusoe 
Description:
 libbio-variation-perl - BioPerl variation-related functionality
Closes: 946468
Changes:
 libbio-variation-perl (1.7.4-1) unstable; urgency=low
 .
   * Initial release. (Closes: #946468)
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Accepted iva 1.0.9+ds-7 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 25 Dec 2019 12:37:15 +0100
Source: iva
Architecture: source
Version: 1.0.9+ds-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 iva (1.0.9+ds-7) unstable; urgency=medium
 .
   * Team upload.
   * debian/patches/samtools1.10: fix the samtools version logic
   * debhelper-compat 12
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Accepted libbio-procedural-perl 1.7.4-1 (source all) into unstable, unstable

[Michael R. Crusoe]

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Hash: SHA256

Format: 1.8
Date: Fri, 6 Dec 2019 14:53:51 +0100
Source: libbio-procedural-perl
Binary: libbio-procedural-perl
Architecture: source all
Version: 1.7.4-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Description:
 libbio-procedural-perl - Simple low-dependency procedural interfaces to BioPerl
Closes: 946272
Changes:
 libbio-procedural-perl (1.7.4-1) unstable; urgency=low
 .
   * Initial release. (Closes: #946272)
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Accepted libbio-db-embl-perl 1.7.4-1 (source all) into unstable, unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 28 Dec 2019 20:44:31 +0100
Source: libbio-db-embl-perl
Binary: libbio-db-embl-perl
Architecture: source all
Version: 1.7.4-1
Distribution: unstable
Urgency: low
Maintainer: Michael R. Crusoe 
Changed-By: Michael R. Crusoe 
Description:
 libbio-db-embl-perl - Database object interface for EMBL entry retrieval
Closes: 940254
Changes:
 libbio-db-embl-perl (1.7.4-1) unstable; urgency=low
 .
   * Initial release. (Closes: #940254)
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Accepted python-pomegranate 0.12.0+dfsg-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 02 Jan 2020 14:42:51 +0100
Source: python-pomegranate
Architecture: source
Version: 0.12.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Python Modules Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-pomegranate (0.12.0+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Add a patch to fix i386 test rounding error
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Accepted bcftools 1.10.2-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 02 Jan 2020 13:58:57 +0100
Source: bcftools
Architecture: source
Version: 1.10.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 bcftools (1.10.2-2) unstable; urgency=medium
 .
   * Fix build on i386 by using SSE2
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Accepted python-pomegranate 0.12.0+dfsg-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 02 Jan 2020 08:57:53 +0100
Source: python-pomegranate
Architecture: source
Version: 0.12.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Python Modules Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-pomegranate (0.12.0+dfsg-1) unstable; urgency=medium
 .
   [ Andreas Tille ]
   * Team upload.
   * Properly renamed version due to removal of autogenerated files (+dfsg 
suffix)
 .
   [ Michael R. Crusoe ]
   * Switch to downloading from GitHub
   * Add Testsuite: autopkgtest-pkg-python
   * Mark the -doc package as Multi-Arch: foreign
   * Added build-dep on python3-pandas for the tests
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Accepted mypy 0.761-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 01 Jan 2020 22:04:59 +0100
Source: mypy
Architecture: source
Version: 0.761-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 mypy (0.761-1) unstable; urgency=medium
 .
   * Demote riscv64 to -O0
   * Demote hppa to -O2
   * New upstream version
   * Remove stubgen-fix.patch, it was applied upstream
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Accepted snakemake 5.9.1-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 01 Jan 2020 16:06:43 +0100
Source: snakemake
Architecture: source
Version: 5.9.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 snakemake (5.9.1-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream release.
   * Exclude new test 'test_env_modules' as it isn't for us.
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Accepted libbio-db-swissprot-perl 1.7.4-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 01 Jan 2020 13:00:17 +0100
Source: libbio-db-swissprot-perl
Architecture: source
Version: 1.7.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-swissprot-perl (1.7.4-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted libdeflate 1.5-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 01 Jan 2020 11:45:12 +0100
Source: libdeflate
Architecture: source
Version: 1.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libdeflate (1.5-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted last-align 1045-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Tue, 31 Dec 2019 08:42:29 +0100
Source: last-align
Architecture: source
Version: 1045-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 last-align (1045-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
   * Updated simde patches
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Accepted libbio-db-refseq-perl 1.7.4-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Mon, 30 Dec 2019 21:21:28 +0100
Source: libbio-db-refseq-perl
Architecture: source
Version: 1.7.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-refseq-perl (1.7.4-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted last-align 1044-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sun, 22 Dec 2019 20:19:58 -0700
Source: last-align
Architecture: source
Version: 1044-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 946850
Changes:
 last-align (1044-2) unstable; urgency=medium
 .
   * Team upload.
   * Enable building on any architecture via simde. (Closes: #946850)
   * For any-amd64 and any-i386: compile multiple times with reducing levels of
 SIMD instruction support and ship a dispatching script to pick the best
 one for the user at run-time.
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Accepted pbcopper 1.3.0+dfsg-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sun, 29 Dec 2019 18:58:05 +0100
Source: pbcopper
Architecture: source
Version: 1.3.0+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 947717
Changes:
 pbcopper (1.3.0+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Add the SIMD everywhere headers so we can build on all archs again
 Closes: #947717
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Accepted qtltools 1.2+dfsg-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 25 Dec 2019 22:27:16 +0100
Source: qtltools
Architecture: source
Version: 1.2+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 qtltools (1.2+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * debian/rules: on mipsel, skip debug info to fit into 4 GB of memory
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Accepted macs 2.2.6-3 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sat, 28 Dec 2019 12:57:18 +0100
Source: macs
Architecture: source
Version: 2.2.6-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 macs (2.2.6-3) unstable; urgency=medium
 .
   * Skip command line tests on arm64 ppc64el s390x.
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Accepted libbio-db-refseq-perl 1.7.3-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sat, 28 Dec 2019 09:43:21 +0100
Source: libbio-db-refseq-perl
Architecture: source
Version: 1.7.3-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Changes:
 libbio-db-refseq-perl (1.7.3-2) unstable; urgency=medium
 .
   * Be explicit about libhttp-message-perl dependency.
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Accepted libssw 1.1-7 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Thu, 26 Dec 2019 16:59:08 +0100
Source: libssw
Architecture: source
Version: 1.1-7
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libssw (1.1-7) unstable; urgency=medium
 .
   * debian/patches/malloc: Include definition for malloc & free
   * debian/include/simde: sync with upstream 2019-12-27
 (098d150385ba618f945f953bc4d5ae306fd22f2e)
   * debian/libssw0.symbols: start tracking the library symbols
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Accepted libdeflate 1.4-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sat, 28 Dec 2019 12:00:11 +0100
Source: libdeflate
Architecture: source
Version: 1.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libdeflate (1.4-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted libbio-db-refseq-perl 1.7.3-1 (source all) into unstable, unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Fri, 6 Dec 2019 14:33:36 +0100
Source: libbio-db-refseq-perl
Binary: libbio-db-refseq-perl
Architecture: source all
Version: 1.7.3-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med team 
Changed-By: Michael R. Crusoe 
Description:
 libbio-db-refseq-perl - Database object interface for RefSeq retrieval
Closes: 946269
Changes:
 libbio-db-refseq-perl (1.7.3-1) unstable; urgency=low
 .
   * Initial release. (Closes: #946269)
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Accepted kallisto 0.46.1+dfsg-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 25 Dec 2019 12:05:55 +0100
Source: kallisto
Architecture: source
Version: 0.46.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 kallisto (0.46.1+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * mark kallisto-examples as Multi-Arch: foreign
   * debian/patches/spelling: fix typo
   * debian/patches/htslib1.3: use kseq.h from htslib, not the bundled version
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Accepted reapr 1.0.18+dfsg-5 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Thu, 26 Dec 2019 16:22:02 +0100
Source: reapr
Architecture: source
Version: 1.0.18+dfsg-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 reapr (1.0.18+dfsg-5) unstable; urgency=medium
 .
   * Team upload.
   * debhelper-compat 12
   * Secure URI in copyright format
   * Use secure URI in Homepage field.
   * Move source package lintian overrides to debian/source.
   * Update renamed lintian tag names in lintian overrides.
   * debian/rules: fix incorrect-path-for-interpreter
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Accepted delly 0.8.1-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 25 Dec 2019 11:22:47 +0100
Source: delly
Architecture: source
Version: 0.8.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 delly (0.8.1-3) unstable; urgency=medium
 .
   * Team upload.
   * debhelper-compat 12
   * Standards-Version: 4.4.1
   * debian/rules: build with openmp
   * debian/upstream/metadata: added DOI
   * debian/patches/hardening: Compile using CPPFLAGS
   * debian/patches/hts1.3: small patch for libhts3 compat
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Accepted hopscotch-map 2.2.1-1 (source amd64) into unstable, unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Thu, 12 Dec 2019 13:38:02 +0100
Source: hopscotch-map
Binary: libtsl-hopscotch-map-dev
Architecture: source amd64
Version: 2.2.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 libtsl-hopscotch-map-dev - C++ fast hash map and hash set using hopscotch 
hashing
Closes: 946638
Changes:
 hopscotch-map (2.2.1-1) unstable; urgency=medium
 .
   * Initial release (Closes: #946638)
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Accepted libvcflib 1.0.1+dfsg-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Thu, 26 Dec 2019 15:54:27 +0100
Source: libvcflib
Architecture: source
Version: 1.0.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libvcflib (1.0.1+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * -tools: add ${perl:Depends}
   * libvcflib{1,-dev}: add Multi-Arch: same
   * Standards-Version: 4.4.1
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Accepted htslib 1.10.2-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sat, 21 Dec 2019 14:15:05 -0700
Source: htslib
Architecture: source
Version: 1.10.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 htslib (1.10.2-2) unstable; urgency=medium
 .
   * htslib-test: breaks+replaces libhts-private-dev
   * libhts3: breaks libtabixpp << 1.0.0-5
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Accepted samtools 1.10-3 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 25 Dec 2019 17:15:23 +0100
Source: samtools
Architecture: source
Version: 1.10-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 samtools (1.10-3) unstable; urgency=medium
 .
   * Team upload.
   * Allow tests to fail on mipsel due to lack of memory
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Accepted bcftools 1.10.2-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 25 Dec 2019 17:58:32 +0100
Source: bcftools
Architecture: source
Version: 1.10.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 bcftools (1.10.2-1) unstable; urgency=medium
 .
   * New upstream version
   * debhelper-compat 12
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Accepted samtools 1.10-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Wed, 25 Dec 2019 14:54:48 +0100
Source: samtools
Architecture: source
Version: 1.10-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 samtools (1.10-2) unstable; urgency=medium
 .
   * Team upload.
   * Samtools breaks older iva and bio-tradis
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Accepted macs 2.2.6-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Fri, 20 Dec 2019 13:24:14 -0800
Source: macs
Architecture: source
Version: 2.2.6-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 macs (2.2.6-2) unstable; urgency=medium
 .
   * Run even more tests.
   * Patch from upstream to fix test that fails with Python 3.8.1rc1+
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Accepted python-biopython 1.76+dfsg-1 (source) into unstable

[Michael R. Crusoe]

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Hash: SHA512

Format: 1.8
Date: Fri, 20 Dec 2019 11:00:46 -0800
Source: python-biopython
Architecture: source
Version: 1.76+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-biopython (1.76+dfsg-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
   * Remove patches applied upstream:
 fix_doctests, ppc64el_precision, python_3.8_iteration_fix.patch
   * Remove patches missing from debian/patches/series.
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Accepted htslib 1.10.2-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Fri, 20 Dec 2019 09:57:05 -0800
Source: htslib
Architecture: source
Version: 1.10.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 947066
Changes:
 htslib (1.10.2-1) unstable; urgency=medium
 .
   * New upstream version
   * debian/source/options: ignore changes to aclocal.m4 config.h.in configure
   * debian/control: remove libhts-private-dev (Closes: #947066)
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Accepted bowtie2 2.3.5.1-6 (source) into unstable

[Michael R. Crusoe]

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Hash: SHA512

Format: 1.8
Date: Wed, 18 Dec 2019 13:36:56 +0100
Source: bowtie2
Architecture: source
Version: 2.3.5.1-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 925499
Changes:
 bowtie2 (2.3.5.1-6) unstable; urgency=medium
 .
   * Team upload.
   * Remove the -m64 flag; not needed and not as universal as I thought
   * This means we build on arm64. (Closes: #925499)
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Accepted nitime 0.8.1-1 (source all) into unstable, unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 15 Dec 2019 15:32:08 +0100
Source: nitime
Binary: python-nitime-doc python3-nitime
Architecture: source all
Version: 0.8.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 python-nitime-doc - timeseries analysis for neuroscience data (nitime) -- 
documentati
 python3-nitime - timeseries analysis for neuroscience data (nitime)
Closes: 937145
Changes:
 nitime (0.8.1-1) unstable; urgency=medium
 .
   [ Michael R. Crusoe ]
   * Team upload.
   * New upstream version, python3 only. (Closes: #937145)
   * Move package to salsa.debian.org/med-team
 .
   [ Andreas Tille ]
   * Priotity optional
   * debhelper-compat 9 (leave level 9 for backwards compatibility)
   * Standards-Version: 4.4.1
   * Testsuite: autopkgtest-pkg-python
   * Secure URI in copyright format
   * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
   * Remove trailing whitespace in debian/changelog
   * Use secure URI in Homepage field.
   * Set upstream metadata fields: Bug-Database.
   * Remove unused paragraph from d/copryight
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Accepted htslib 1.10.1-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Wed, 18 Dec 2019 12:54:51 +0100
Source: htslib
Architecture: source
Version: 1.10.1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 htslib (1.10.1-2) unstable; urgency=medium
 .
   * Fix binary-arch vs binary-indep builds
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Accepted bowtie2 2.3.5.1-5 (source) into unstable

[Michael R. Crusoe]

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Date: Wed, 18 Dec 2019 12:15:28 +0100
Source: bowtie2
Architecture: source
Version: 2.3.5.1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 bowtie2 (2.3.5.1-5) unstable; urgency=medium
 .
   * Team upload.
   * debian/rules: Remove -santized here as well
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Accepted python-bx 0.8.6-2 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Wed, 18 Dec 2019 12:23:30 +0100
Source: python-bx
Architecture: source
Version: 0.8.6-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 944409
Changes:
 python-bx (0.8.6-2) unstable; urgency=medium
 .
   * Team upload.
   * Add patch for errors on 32 bit systems. Closes: #944409
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Accepted bowtie2 2.3.5.1-4 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Mon, 16 Dec 2019 10:13:27 +0100
Source: bowtie2
Architecture: source
Version: 2.3.5.1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 bowtie2 (2.3.5.1-4) unstable; urgency=medium
 .
   * Team upload.
   * Added patch to correct the 64bit detection logic.
   * Disable -fsanitize builds to save resources
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Accepted python-biopython 1.75+dfsg-4 (source) into unstable

[Michael R. Crusoe]

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Hash: SHA512

Format: 1.8
Date: Tue, 17 Dec 2019 11:35:41 +0100
Source: python-biopython
Architecture: source
Version: 1.75+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-biopython (1.75+dfsg-4) unstable; urgency=medium
 .
   * Team upload.
   * Patch added to reduce the required precision for one part of the
 test_phenotype_fit.TestPhenoMicro test
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Accepted macs 2.2.6-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Tue, 17 Dec 2019 15:35:50 +0100
Source: macs
Architecture: source
Version: 2.2.6-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 macs (2.2.6-1) unstable; urgency=medium
 .
   [ Andreas Tille ]
   * Drop cython from Build-Depends
 .
   [ Michael R. Crusoe ]
   * New upstream version
   * Set upstream metadata fields: Repository.
   * Remove obsolete fields Name from debian/upstream/metadata.
   * Get sources from GitHub, so we have the tests
   * New upstream version
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Accepted python-biopython 1.75+dfsg-3 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Mon, 16 Dec 2019 22:15:00 +0100
Source: python-biopython
Architecture: source
Version: 1.75+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 python-biopython (1.75+dfsg-3) unstable; urgency=medium
 .
   * Team upload.
   * Restrict where we test phyml for now.
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Accepted libtabixpp 1.1.0-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Mon, 16 Dec 2019 21:43:57 +0100
Source: libtabixpp
Architecture: source
Version: 1.1.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 libtabixpp (1.1.0-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream release.
   * Freshen patches; hardening patch applied upstream
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Accepted raxml 8.2.12+dfsg-2 (source) into unstable

[Michael R. Crusoe]

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Hash: SHA512

Format: 1.8
Date: Mon, 16 Dec 2019 17:54:43 +0100
Source: raxml
Architecture: source
Version: 8.2.12+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 raxml (8.2.12+dfsg-2) unstable; urgency=medium
 .
   * Team upload.
   * Build on non-x86 too, via SIMDE
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Accepted python-biopython 1.75+dfsg-2 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA512

Format: 1.8
Date: Sun, 15 Dec 2019 14:38:14 +0100
Source: python-biopython
Architecture: source
Version: 1.75+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Closes: 937606
Changes:
 python-biopython (1.75+dfsg-2) unstable; urgency=medium
 .
   [ Michael R. Crusoe ]
   * Team upload.
   * Skip PDB_ResidueDepth test, as http://mgltools.scripps.edu/packages/MSMS
 is not yet packaged for Debian
   * Skip test_mmtf{,_online} as https://github.com/rcsb/mmtf-python is not yet
 packaged for Debian
   * Added missing test dependencies: python-unittest2, python{,3}-networkx,
 samtools
   * i386: build-dep on raxml for testing purposes
   * debian/patches/arm64.patch from upstream to fix the PairwiseAligner
   * debian/patches/fix_doctest: from me to fix the Bio.Cluster._cluster 
doctests
 Now the tests are required to pass again.
 .
   [ Andreas Tille ]
   * Drop Python2 package
 Closes: #937606
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Accepted r-cran-r.cache 0.14.0-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sun, 15 Dec 2019 15:07:15 +0100
Source: r-cran-r.cache
Architecture: source
Version: 0.14.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers 
Changed-By: Michael R. Crusoe 
Changes:
 r-cran-r.cache (0.14.0-1) unstable; urgency=medium
 .
   * New Upstream release.
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Accepted r-cran-globals 0.12.5-1 (source) into unstable

[Michael R. Crusoe]

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Format: 1.8
Date: Sun, 15 Dec 2019 15:05:20 +0100
Source: r-cran-globals
Architecture: source
Version: 0.12.5-1
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers 
Changed-By: Michael R. Crusoe 
Changes:
 r-cran-globals (0.12.5-1) unstable; urgency=medium
 .
   * New upstream version
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Accepted samtools 1.10-1 (source) into unstable

[Michael R. Crusoe]

-BEGIN PGP SIGNED MESSAGE-
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Format: 1.8
Date: Mon, 16 Dec 2019 16:17:22 +0100
Source: samtools
Architecture: source
Version: 1.10-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Changes:
 samtools (1.10-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream release.
   * Freshen patches
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samtools_1.10-1_source.buildinfo
Files:
 1162315a1484ee777ce96f543152d3d0 2223 science optional samtools_1.10-1.dsc
 dc147b46cabbb2c168529e474e947b1d 4457760 science optional 
samtools_1.10.orig.tar.gz
 0db2636ace89aff0f2e2f077904d5a1b 20060 science optional 
samtools_1.10-1.debian.tar.xz
 519e0b39fa2e60c8d3bed41f0d7c9f20 8943 science optional 
samtools_1.10-1_source.buildinfo

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