unanimity (3.3.0+dfsg-2.1) [PTS] [DDPO]

NEW: VCS has unreleased changes: 3.4.1+git20180307.02aa264+dfsg-1 > 3.3.0+dfsg-2.1

Git: https://salsa.debian.org/med-team/unanimity.git
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Branch: master
Path: debian/changelog
Browser: https://salsa.debian.org/med-team/unanimity
Last scan: 2020-05-22 07:18:11+00
Next scan: 2020-05-28 16:42:00+00

Debian changelog in Git:

unanimity (3.4.1+git20180307.02aa264+dfsg-1) UNRELEASED; urgency=medium

  * Afif removed himself from Uploaders (thanks for your previous work, Afif)
  * New upstream version
    Attention: This is the last release of unanimity obtained from Git
    (see README.source)
    Closes: #939506
  * debhelper-compat 12
  * Standards-Version: 4.4.1
  * Use 2to3 to port from Python2 to Python3
    Closes: #938751
  * debian/copyright: use spaces rather than tabs to start continuation
    lines.
  TODO:

  1. With latest libpbcopper:
[ 56%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o
cd /build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/src && /usr/bin/c++   -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/include -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/generated -I/    build/unanimity-3.4.1+git20180307.02aa264+dfsg/src  -g -O2 -fdebug-prefix-map=/build/unanimity-3.4.1+git20180307.02aa264+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -           D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs   -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o -c /    build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp
In file included from /usr/include/pbcopper/data/ReadId.h:13,
                 from /usr/include/pbcopper/data/Read.h:19,
                 from /usr/include/pbcopper/data/MappedRead.h:10,
                 from /usr/include/pbbam/BamRecord.h:19,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/IPoaModel.h:8,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/arrow/ArrowModel.h:5,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp:8:
/usr/include/pbcopper/data/Interval.h:24:7: error: redefinition of ‘class PacBio::Data::Interval’
   24 | class Interval
      |       ^~~~~~~~
In file included from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/ReferenceWindow.h:10,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/Consensus.h:10,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/WindowResult.h:7,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/IConsensusModel.h:5,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/genomicconsensus/experimental/ConsensusModelFactory.h:9,
                 from /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp:3:
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/include/pacbio/data/Interval.h:20:7: note: previous definition of ‘class PacBio::Data::Interval’
   20 | class Interval
      |       ^~~~~~~~
make[3]: *** [src/CMakeFiles/unanimity.dir/build.make:79: src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o] Error 1

  --> The definition in /include/pacbio/data/Interval.h is NOT good - we need the one of include/pacbio/data/Interval.h  !
  
  2. If 1. is solved
[ 90%] Building CXX object src/CMakeFiles/ccs.dir/main/ccs.cpp.o
cd /build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/src && /usr/bin/c++   -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/include -I/build/unanimity-3.4.1+git20180307.02aa264+dfsg/build/generated -I/    build/unanimity-3.4.1+git20180307.02aa264+dfsg/src  -g -O2 -fdebug-prefix-map=/build/unanimity-3.4.1+git20180307.02aa264+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -           D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs   -fPIC -std=c++14 -o CMakeFiles/ccs.dir/main/ccs.cpp.o -c /build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp: In function ‘int Runner(const PacBio::CLI::Results&)’:
/build/unanimity-3.4.1+git20180307.02aa264+dfsg/src/main/ccs.cpp:571:38: error: ‘move’ was not declared in this scope
  571 |                     read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),
      |                                      ^~~~


 -- Andreas Tille <tille@debian.org>  Thu, 19 Dec 2019 08:17:37 +0100

This branch is 21 commits ahead of tag debian/3.3.0+dfsg-2.1

Git log:

commit 838929ad639e69df5344752d6b9b1dba17a1eb4a
Author: Andreas Tille <tille@debian.org>
Date:   Fri Jan 24 14:32:20 2020 +0100

    Add open issues to changelog as todo

commit 8ac78dda0954c3d1e1b68a255675f0da1a655af0
Author: Andreas Tille <tille@debian.org>
Date:   Thu Dec 19 21:05:35 2019 +0100

    Fix some issues in gcc9

commit 07c8d23df1c301d191517b36b1e6d88a3f5dea82
Author: Andreas Tille <tille@debian.org>
Date:   Thu Dec 19 08:59:46 2019 +0100

    Close proper bugs

commit 5adf3be5b73b35cb9f1a279e6816972285aa9547
Author: Andreas Tille <tille@debian.org>
Date:   Thu Dec 19 08:17:31 2019 +0100

    debian/copyright: use spaces rather than tabs to start continuation lines.
    
    Fixes lintian: tab-in-licence-text
    See https://lintian.debian.org/tags/tab-in-licence-text.html for more details.

commit f48ff8063f354beab6e6ef3564f240dc1fdaf41a
Author: Andreas Tille <tille@debian.org>
Date:   Thu Dec 19 08:16:55 2019 +0100

    Switch to Python3 in packaging

commit 60fdd657a4e5aa6a2d590e6bab040a06888836fb
Author: Andreas Tille <tille@debian.org>
Date:   Thu Dec 19 08:15:01 2019 +0100

    Use 2to3 to port from Python2 to Python3

commit ae9de4ef06a862205c33636d9f11c826fc5a5624
Author: Andreas Tille <tille@debian.org>
Date:   Thu Dec 19 08:11:54 2019 +0100

    Update patch

commit ee41f70149a6499ae53fac1f811d932b63eb2a92
Author: Andreas Tille <tille@debian.org>
Date:   Thu Dec 19 08:09:24 2019 +0100

    Standards-Version: 4.4.1

commit b81e03b27a36704486f6b662494e0124344789b5
Author: Andreas Tille <tille@debian.org>
Date:   Wed Dec 18 17:33:16 2019 +0100

    This is the last release of unanimity obtained from Git

commit da3d7e10463fe477fe4ee4d564111f7a1ae048c3
Merge: 30ceca7 7ad208f
Author: Andreas Tille <tille@debian.org>
Date:   Wed Dec 18 17:26:18 2019 +0100

    Update upstream source from tag 'upstream/3.4.1+git20180307.02aa264+dfsg'
    
    Update to upstream version '3.4.1+git20180307.02aa264+dfsg'
    with Debian dir 432b67005a03d7d451c9471ae37be620b517570f

commit 7ad208f73b8ab223b23ce8fe201b72289ba45a22
Author: Andreas Tille <tille@debian.org>
Date:   Wed Dec 18 17:26:15 2019 +0100

    New upstream version 3.4.1+git20180307.02aa264+dfsg

commit 787936774016aef861b0cd50548b486c9da980a7
Author: Andreas Tille <tille@debian.org>
Date:   Wed Dec 18 17:24:56 2019 +0100

    New upstream version 3.4.1+git20180307.02aa264

commit 1f1780ae76a28e6a58f5e43189f0b97ee5f2a1fc
Author: Andreas Tille <tille@debian.org>
Date:   Wed Dec 18 17:01:30 2019 +0100

    New upstream version 4.1.0

commit 30ceca7b890b941ad7c02cc11571c26c62651193
Author: Steffen Möller <moeller@debian.org>
Date:   Tue Oct 15 21:18:44 2019 +0000

    Update metadata

commit f6222abdd0df73740e9940e3335b8f42470e3efa
Author: Andreas Tille <tille@debian.org>
Date:   Tue Sep 17 08:03:42 2019 +0200

    Standards-Version: 4.4.0

commit 6cfd330e13912bd75eba5bbd310373ac94e06e07
Author: Andreas Tille <tille@debian.org>
Date:   Tue Sep 17 08:03:36 2019 +0200

    New upstream version 4.0.0

commit e5b42e2bcb4d85d3daa4e7b8bda0db1fead7f213
Author: Andreas Tille <tille@debian.org>
Date:   Tue Sep 17 08:03:36 2019 +0200

    debhelper-compat 12

commit 56a1ef98aafb6ceb289375d38b8dc49de76e2210
Merge: 83bd0b4 6cfd330
Author: Andreas Tille <tille@debian.org>
Date:   Tue Sep 17 08:03:36 2019 +0200

    Update upstream source from tag 'upstream/4.0.0'
    
    Update to upstream version '4.0.0'
    with Debian dir 7392f70aa1c843bb80ba2da30b3d3a250929e6a0

commit 83bd0b472c3555c44562d390deab305066ebfd30
Author: Andreas Tille <tille@debian.org>
Date:   Tue Sep 17 08:03:35 2019 +0200

    New upstream version

commit 59de564f4b211115b7a9d83a1323c930ecbe65f2
Author: Steffen Möller <moeller@debian.org>
Date:   Fri Feb 15 18:55:01 2019 +0000

    Added new d/u/metadata file
    
    RRIDs only

commit 12e3b3cf164cc10aab4b7ca1eac3cdd6e0c341f3
Author: Andreas Tille <tille@debian.org>
Date:   Thu Feb 7 08:34:45 2019 +0100

    Afif removed himself from Uploaders