[med-svn] [Git][med-team/seqan2][master] split arch/indep install

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / seqan2


Commits:
7c5c8fa0 by Michael R. Crusoe at 2018-02-17T09:23:07-08:00
split arch/indep install

- - - - -


2 changed files:

- debian/changelog
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+seqan2 (2.4.0+dfsg-7) unstable; urgency=medium
+
+  * Split override_dh_install into -arch and -indep
+
+ -- Michael R. Crusoe   Sat, 17 Feb 2018 09:22:51 
-0800
+
 seqan2 (2.4.0+dfsg-6) unstable; urgency=medium
 
   * Retry building on mips*; patch adapted from Adrian Bunk 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -65,14 +65,18 @@ override_dh_auto_build-indep:
-e "s=@CMAKE_INSTALL_FULL_INCLUDEDIR@=/usr/include=g" \
util/pkgconfig/seqan.pc.in > seqan-2.pc
 
-override_dh_install:
-   dh_install
+override_dh_install-indep:
+   dh_install --indep
# Delete additional LICENSE files
-   find $(CURDIR)/debian/$(pkgapps) -type f -name LICENSE -delete || 
/bin/true
if [ -d $(CURDIR)/debian/$(pkgdev) ] ; then \
find $(CURDIR)/debian/$(pkgdev) -type f -name LICENSE -delete ; \
find $(CURDIR)/debian/$(pkgdev) -type f -name "*.pyc" -delete ; \
fi
+
+override_dh_install-arch:
+   dh_install --arch
+   # Delete additional LICENSE files
+   find $(CURDIR)/debian/$(pkgapps) -type f -name LICENSE -delete || 
/bin/true
find $(CURDIR)/debian/$(pkgapps)/usr/lib/seqan/bin -type f \
-name "*.sh" | xargs chmod a+x
find $(CURDIR)/debian/$(pkgapps)/usr/share/commonwl -type f \



View it on GitLab: 
https://salsa.debian.org/med-team/seqan2/commit/7c5c8fa0390700463bdba2f893f7f18711b5a28d

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[med-svn] [Git][med-team/seqan2] Pushed new tag debian/2.4.0+dfsg-7

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag debian/2.4.0+dfsg-7 at Debian Med / seqan2

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[med-svn] [Git][med-team/macs][master] Added a new test directory for autopkgtest along with some sample data

[Aikaterini Kalou]

Aikaterini Kalou pushed to branch master at Debian Med / macs


Commits:
2cc4ef8c by kkalou-guest at 2018-02-19T00:14:51+02:00
Added a new test directory for autopkgtest along with some sample data

- - - - -


7 changed files:

- + README.test
- + debian/examples/aluY.chr1.bed
- + debian/examples/gerp.chr1.bed
- + debian/macs-example-data.install
- + debian/macs.examples
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=
README.test
=
--- /dev/null
+++ b/README.test
@@ -0,0 +1,12 @@
+otes on how this package can be tested.
+
+
+This package can be tested by executing
+
+   sh run-unit-test
+
+in order to confirm its integrity.
+
+Notes : the sample data are recovered from; https://github.com/arq5x/  They 
are both ‘.BED’ 
+file extensions. However the macs package install instructions is
+using the ‘BAM’ extension format. If anyone has any recommendation on where to 
find sample data in this format it will be much appreciated :)


=
debian/examples/aluY.chr1.bed
=
The diff for this file was not included because it is too large.

=
debian/examples/gerp.chr1.bed
=
The diff for this file was not included because it is too large.

=
debian/macs-example-data.install
=
--- /dev/null
+++ b/debian/macs-example-data.install
@@ -0,0 +1,4 @@
+debian/examples/aluY.chr1.bed usr/share/doc/macs/examples
+debian/examples/gerp.chr1.bed  usr/share/doc/macs/examples
+debian/README.test usr/share/doc/macs
+debian/tests/run-unit-test usr/share/doc/macs


=
debian/macs.examples
=
--- /dev/null
+++ b/debian/macs.examples
@@ -0,0 +1,3 @@
+examples/*
+debian/examples/*
+release/common/*.tree


=
debian/tests/control
=
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=
debian/tests/run-unit-test
=
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+set -x
+
+pkg="macs"
+
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+macs2 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01
+macs2 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1



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https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357

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[med-svn] [Git][med-team/rsem][master] 6 commits: DEP3

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / rsem


Commits:
ec10db04 by Andreas Tille at 2018-02-18T20:28:25+01:00
DEP3

- - - - -
2d292817 by Andreas Tille at 2018-02-18T20:30:00+01:00
Remove samtools mentioning from d/copyright

- - - - -
74dd92d3 by Andreas Tille at 2018-02-18T20:33:39+01:00
cme fix dpkg-control

- - - - -
da59abab by Andreas Tille at 2018-02-18T20:34:31+01:00
debhelper 11

- - - - -
b85e15d2 by Andreas Tille at 2018-02-18T21:01:53+01:00
Remove unused --parallel

- - - - -
a430e852 by Andreas Tille at 2018-02-18T21:04:48+01:00
do not parse d/changelog; upload to experimental

- - - - -


6 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/patches/use_debian_packaged_samtools.patch
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,12 +1,15 @@
-rsem (1.3.0+dfsg-1) UNRELEASED; urgency=medium
+rsem (1.3.0+dfsg-1) experimental; urgency=medium
 
   * New upstream version
   * d/watch:
  - version=4
  - xz compression
   * remove code copy of samtools-1.3
+  * cme fix dpkg-control
+  * debhelper 11
+  * d/rules: do not parse d/changelog
 
- -- Andreas Tille   Fri, 09 Dec 2016 14:26:08 +0100
+ -- Andreas Tille   Sun, 18 Feb 2018 20:34:37 +0100
 
 rsem (1.2.31+dfsg-1) unstable; urgency=medium
 


=
debian/compat
=
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -3,8 +3,8 @@ Maintainer: Debian Med Packaging Team 
,
Andreas Tille 
 Section: science
-Priority: extra
-Build-Depends: debhelper (>= 9),
+Priority: optional
+Build-Depends: debhelper (>= 11~),
zlib1g-dev,
libncurses5-dev,
libboost-dev,
@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 9),
 # bowtie is a run-time dependency available on only a few systems, not actually
 # needed for building but it prevents the creation of uninstallable packages
bowtie | bowtie2
-Standards-Version: 3.9.8
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rsem.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/rsem.git
 Homepage: http://deweylab.biostat.wisc.edu/rsem/


=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -30,45 +30,6 @@ License: GPL-3
  On Debian systems, the full text of the GNU General Public
  License version 3 can be found in the file
  `/usr/share/common-licenses/GPL-3'.
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz
-
-Files: samtools-1.3/*
-Copyright: © 2008–2016, Genome Research Ltd. (GRL)
-   © 2003–2006, 2008–2011, by Heng Li 
-   © 2009–2012 Broad Institute
-   © 2010 Illumina, Inc.
-   © 2012–2013 Peter Cock, The James Hutton Institute.
-License: MIT
-Comment: Modified version of samtools included as per upstream
-
-Files: samtools-1.3/win32/xcurses.h
-Copyright: Public Domain
-License: public-domain
- This file is part of PDCurses (http://pdcurses.sourceforge.net/),
- which is in the public domain.
-
-Files: samtools-1.3/win32/z*.h
-Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler
-License: zlib
- This software is provided 'as-is', without any express or implied
- warranty.  In no event will the authors be held liable for any damages
- arising from the use of this software.
- .
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
- .
-  1. The origin of this software must not be misrepresented; you must not
- claim that you wrote the original software. If you use this software
- in a product, an acknowledgment in the product documentation would be
- appreciated but is not required.
-  2. Altered source versions must be plainly marked as such, and must not be
- misrepresented as being the original software.
-  3. This notice may not be removed or altered from any source distribution.
- .
-  Jean-loup GaillyMark Adler
-  jl...@gzip.org  mad...@alumni.caltech.edu
 
 License: MIT
  Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -88,4 +49,3 @@ License: MIT
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  THE SOFTWARE.
-

[med-svn] [Git][med-team/rsem] Pushed new tag upstream/1.3.0+dfsg

[Andreas Tille]

Andreas Tille pushed new tag upstream/1.3.0+dfsg at Debian Med / rsem

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[med-svn] [Git][med-team/rsem] Pushed new tag debian/1.3.0+dfsg-1

[Andreas Tille]

Andreas Tille pushed new tag debian/1.3.0+dfsg-1 at Debian Med / rsem

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[med-svn] [Git][med-team/vcftools] Pushed new tag upstream/0.1.15

[Andreas Tille]

Andreas Tille pushed new tag upstream/0.1.15 at Debian Med / vcftools

---
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[med-svn] [Git][med-team/vcftools][master] 7 commits: New upstream version 0.1.15

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / vcftools


Commits:
f02450ec by Andreas Tille at 2018-02-18T18:55:00+01:00
New upstream version 0.1.15
- - - - -
0f8bee46 by Andreas Tille at 2018-02-18T18:55:04+01:00
Update upstream source from tag upstream/0.1.15

Update to upstream version 0.1.15
with Debian dir acb4b38d06bd8475e06fa9a817c70a00f2dff661
- - - - -
20d0dbd4 by Andreas Tille at 2018-02-18T18:58:34+01:00
New upstream version

- - - - -
9f4fb636 by Andreas Tille at 2018-02-18T18:59:17+01:00
Standards-Version: 4.1.3

- - - - -
73619a00 by Andreas Tille at 2018-02-18T18:59:57+01:00
debhelper 11

- - - - -
5e20507f by Andreas Tille at 2018-02-18T20:07:54+01:00
do not parse d/changelog

- - - - -
06470013 by Andreas Tille at 2018-02-18T20:13:59+01:00
Upload to unstable

- - - - -


30 changed files:

- + .tarball-version
- README.md
- configure.ac
- debian/changelog
- debian/compat
- debian/control
- debian/patches/manpage.patch
- debian/rules
- src/cpp/Makefile.am
- src/cpp/parameters.cpp
- src/cpp/parameters.h
- src/cpp/variant_file.h
- src/cpp/variant_file_format_convert.cpp
- src/cpp/variant_file_output.cpp
- src/cpp/vcftools.1
- src/cpp/vcftools.cpp
- src/perl/FaSlice.pm
- src/perl/Makefile.am
- src/perl/Vcf.pm
- src/perl/fill-aa
- src/perl/fill-an-ac
- src/perl/fill-fs
- src/perl/fill-ref-md5
- src/perl/tab-to-vcf
- src/perl/vcf-annotate
- src/perl/vcf-compare
- src/perl/vcf-concat
- src/perl/vcf-consensus
- src/perl/vcf-contrast
- src/perl/vcf-convert


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/vcftools/compare/c213a3e7c3273f4b3db90a98f8dbc5b1249df695...064700138ce380595f17a5677cb192ea73e9c990

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[med-svn] [Git][med-team/vcftools] Pushed new tag debian/0.1.15-1

[Andreas Tille]

Andreas Tille pushed new tag debian/0.1.15-1 at Debian Med / vcftools

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[med-svn] [Git][med-team/vcftools][upstream] New upstream version 0.1.15

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / vcftools


Commits:
f02450ec by Andreas Tille at 2018-02-18T18:55:00+01:00
New upstream version 0.1.15
- - - - -


30 changed files:

- + .tarball-version
- README.md
- configure.ac
- src/cpp/Makefile.am
- src/cpp/parameters.cpp
- src/cpp/parameters.h
- src/cpp/variant_file.h
- src/cpp/variant_file_format_convert.cpp
- src/cpp/variant_file_output.cpp
- src/cpp/vcftools.1
- src/cpp/vcftools.cpp
- src/perl/FaSlice.pm
- src/perl/Makefile.am
- src/perl/Vcf.pm
- src/perl/fill-aa
- src/perl/fill-an-ac
- src/perl/fill-fs
- src/perl/fill-ref-md5
- src/perl/tab-to-vcf
- src/perl/vcf-annotate
- src/perl/vcf-compare
- src/perl/vcf-concat
- src/perl/vcf-consensus
- src/perl/vcf-contrast
- src/perl/vcf-convert
- src/perl/vcf-fix-newlines
- src/perl/vcf-fix-ploidy
- + src/perl/vcf-haplotypes
- src/perl/vcf-indel-stats
- src/perl/vcf-isec


The diff was not included because it is too large.


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[med-svn] [Git][med-team/vcftools][pristine-tar] pristine-tar data for vcftools_0.1.15.orig.tar.gz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / vcftools


Commits:
01212760 by Andreas Tille at 2018-02-18T18:55:04+01:00
pristine-tar data for vcftools_0.1.15.orig.tar.gz

- - - - -


2 changed files:

- + vcftools_0.1.15.orig.tar.gz.delta
- + vcftools_0.1.15.orig.tar.gz.id


Changes:

=
vcftools_0.1.15.orig.tar.gz.delta
=
Binary files /dev/null and b/vcftools_0.1.15.orig.tar.gz.delta differ


=
vcftools_0.1.15.orig.tar.gz.id
=
--- /dev/null
+++ b/vcftools_0.1.15.orig.tar.gz.id
@@ -0,0 +1 @@
+e1caf313aeb46af436acb41397bc337e1ff6562e



View it on GitLab: 
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[med-svn] [Git][med-team/tm-align][pristine-tar] pristine-tar data for tm-align_20170708+dfsg.orig.tar.xz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / tm-align


Commits:
02d4197d by Andreas Tille at 2018-02-18T17:31:33+01:00
pristine-tar data for tm-align_20170708+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + tm-align_20170708+dfsg.orig.tar.xz.delta
- + tm-align_20170708+dfsg.orig.tar.xz.id


Changes:

=
tm-align_20170708+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/tm-align_20170708+dfsg.orig.tar.xz.delta differ


=
tm-align_20170708+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/tm-align_20170708+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+f026c9e5505ea1d0ffdd418b821b18d564e621dd



View it on GitLab: 
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[med-svn] [Git][med-team/tm-align] Pushed new tag upstream/20170708+dfsg

[Andreas Tille]

Andreas Tille pushed new tag upstream/20170708+dfsg at Debian Med / tm-align

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[med-svn] [Git][med-team/tm-align] Pushed new tag debian/20170708+dfsg-1

[Andreas Tille]

Andreas Tille pushed new tag debian/20170708+dfsg-1 at Debian Med / tm-align

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[med-svn] [Git][med-team/stacks][pristine-tar] pristine-tar data for stacks_2.0Beta8c+dfsg.orig.tar.xz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / stacks


Commits:
b51bba07 by Andreas Tille at 2018-02-18T16:57:06+01:00
pristine-tar data for stacks_2.0Beta8c+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + stacks_2.0Beta8c+dfsg.orig.tar.xz.delta
- + stacks_2.0Beta8c+dfsg.orig.tar.xz.id


Changes:

=
stacks_2.0Beta8c+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/stacks_2.0Beta8c+dfsg.orig.tar.xz.delta differ


=
stacks_2.0Beta8c+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/stacks_2.0Beta8c+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+681801b5cd10fa8c9d9e59dd0123482273e10d4a



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[med-svn] [Git][med-team/stacks][upstream] New upstream version 2.0Beta8c+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / stacks


Commits:
8c824c31 by Andreas Tille at 2018-02-18T16:56:31+01:00
New upstream version 2.0Beta8c+dfsg
- - - - -


15 changed files:

- ChangeLog
- Makefile.am
- Makefile.in
- README
- config.h.in
- configure
- configure.ac
- − htslib/INSTALL
- − htslib/LICENSE
- − htslib/Makefile
- − htslib/NEWS
- − htslib/README
- − htslib/bgzf.c
- − htslib/bgzip.c
- − htslib/cram/cram.h


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/stacks/commit/8c824c312b38672fcbf2bf9a789eab16e0aa516d

---
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[med-svn] [Git][med-team/stacks] Pushed new tag upstream/2.0Beta8c+dfsg

[Andreas Tille]

Andreas Tille pushed new tag upstream/2.0Beta8c+dfsg at Debian Med / stacks

---
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[med-svn] [Git][med-team/stacks] Pushed new tag debian/2.0Beta8c+dfsg-1

[Andreas Tille]

Andreas Tille pushed new tag debian/2.0Beta8c+dfsg-1 at Debian Med / stacks

---
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[med-svn] [Git][med-team/stacks][master] 9 commits: Remove code copy of htslib

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / stacks


Commits:
648191e9 by Andreas Tille at 2018-02-18T16:56:07+01:00
Remove code copy of htslib

- - - - -
8c824c31 by Andreas Tille at 2018-02-18T16:56:31+01:00
New upstream version 2.0Beta8c+dfsg
- - - - -
dfc7c55a by Andreas Tille at 2018-02-18T16:57:06+01:00
Update upstream source from tag upstream/2.0Beta8c+dfsg

Update to upstream version 2.0Beta8c+dfsg
with Debian dir 995637f6532a888b6669e076b338bfc581ff2eb9
- - - - -
76f9f9a5 by Andreas Tille at 2018-02-18T17:00:50+01:00
New upstream version

- - - - -
d020c143 by Andreas Tille at 2018-02-18T17:02:08+01:00
Adapt patches

- - - - -
38b46685 by Andreas Tille at 2018-02-18T17:14:28+01:00
use Debian packaged version of htslib

- - - - -
b1e36797 by Andreas Tille at 2018-02-18T17:14:44+01:00
Standards-Version: 4.1.3

- - - - -
45ddbffc by Andreas Tille at 2018-02-18T17:15:02+01:00
debhelper 11

- - - - -
61167c94 by Andreas Tille at 2018-02-18T17:22:13+01:00
Upload to unstable

- - - - -


23 changed files:

- ChangeLog
- Makefile.am
- Makefile.in
- README
- config.h.in
- configure
- configure.ac
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/patches/script-exe-paths
- debian/patches/series
- + debian/patches/use_debian_packaged_htslib.patch
- debian/watch
- − htslib/INSTALL
- − htslib/LICENSE
- − htslib/Makefile
- − htslib/NEWS
- − htslib/README
- − htslib/bgzf.c
- − htslib/bgzip.c
- − htslib/cram/cram.h


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/stacks/compare/e42a4010eb90f169a62c128686d5593142dc895d...61167c94ccb05ed7c88d442d30d453cdad6b6f63

---
View it on GitLab: 
https://salsa.debian.org/med-team/stacks/compare/e42a4010eb90f169a62c128686d5593142dc895d...61167c94ccb05ed7c88d442d30d453cdad6b6f63
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[med-svn] [Git][med-team/ssake][pristine-tar] pristine-tar data for ssake_4.0.orig.tar.gz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / ssake


Commits:
430a7d3c by Andreas Tille at 2018-02-18T16:27:13+01:00
pristine-tar data for ssake_4.0.orig.tar.gz

- - - - -


2 changed files:

- + ssake_4.0.orig.tar.gz.delta
- + ssake_4.0.orig.tar.gz.id


Changes:

=
ssake_4.0.orig.tar.gz.delta
=
Binary files /dev/null and b/ssake_4.0.orig.tar.gz.delta differ


=
ssake_4.0.orig.tar.gz.id
=
--- /dev/null
+++ b/ssake_4.0.orig.tar.gz.id
@@ -0,0 +1 @@
+c9d7951dc3780835107a19493e3e8bd5c7c71667



View it on GitLab: 
https://salsa.debian.org/med-team/ssake/commit/430a7d3c631abfab8e6783e836a5eb26a734a4bc

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[med-svn] [Git][med-team/ssake] Pushed new tag debian/4.0-1

[Andreas Tille]

Andreas Tille pushed new tag debian/4.0-1 at Debian Med / ssake

---
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[med-svn] [Git][med-team/ssake] Pushed new tag upstream/4.0

[Andreas Tille]

Andreas Tille pushed new tag upstream/4.0 at Debian Med / ssake

---
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[med-svn] [Git][med-team/squizz][master] 2 commits: debhelper 11 (+ dh_auto_test --no-parallel)

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / squizz


Commits:
52c32b20 by Andreas Tille at 2018-02-18T16:17:23+01:00
debhelper 11 (+ dh_auto_test --no-parallel)

- - - - -
230be386 by Andreas Tille at 2018-02-18T16:18:01+01:00
Spelling

- - - - -


5 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/patches/disable-swissprot-test.patch
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,6 @@
 squizz (0.99d+dfsg-2) UNRELEASED; urgency=medium
 
-  * Check why debhelper compat level 10 makes test fail
+  * debhelper 11 (+ dh_auto_test --no-parallel)
 
  -- Andreas Tille   Sun, 18 Feb 2018 15:27:33 +0100
 


=
debian/compat
=
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Uploaders: Olivier Sallou ,
Andreas Tille 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10)
+Build-Depends: debhelper (>= 11~)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/squizz.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/squizz.git


=
debian/patches/disable-swissprot-test.patch
=
--- a/debian/patches/disable-swissprot-test.patch
+++ b/debian/patches/disable-swissprot-test.patch
@@ -1,4 +1,4 @@
-Subject: Disable tests using copyrigthed seq
+Subject: Disable tests using copyrighted seq
 Description: upstream constains copyrighted sequence,
  removed form packaged. This patch removes tests using this
  sequence


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -10,3 +10,6 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
dh $@
+
+override_dh_auto_test:
+   dh_auto_test --no-parallel



View it on GitLab: 
https://salsa.debian.org/med-team/squizz/compare/434f5638460090b9735311345f1ff55a0a1350a8...230be386b231a81319d76d74d2349784c6388f66

---
View it on GitLab: 
https://salsa.debian.org/med-team/squizz/compare/434f5638460090b9735311345f1ff55a0a1350a8...230be386b231a81319d76d74d2349784c6388f66
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[med-svn] [Git][med-team/sra-sdk] Pushed new tag debian/2.8.2-5+dfsg-1

[Andreas Tille]

Andreas Tille pushed new tag debian/2.8.2-5+dfsg-1 at Debian Med / sra-sdk

---
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[med-svn] [Git][med-team/sra-sdk][pristine-tar] pristine-tar data for sra-sdk_2.8.2-5+dfsg.orig.tar.xz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / sra-sdk


Commits:
ea514c52 by Andreas Tille at 2018-02-18T08:58:29+01:00
pristine-tar data for sra-sdk_2.8.2-5+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + sra-sdk_2.8.2-5+dfsg.orig.tar.xz.delta
- + sra-sdk_2.8.2-5+dfsg.orig.tar.xz.id


Changes:

=
sra-sdk_2.8.2-5+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/sra-sdk_2.8.2-5+dfsg.orig.tar.xz.delta differ


=
sra-sdk_2.8.2-5+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/sra-sdk_2.8.2-5+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+c8edb7c282aad0666a1b60ac14efb22568a4621a



View it on GitLab: 
https://salsa.debian.org/med-team/sra-sdk/commit/ea514c528852eadd08e52fa08db47b8e067bf66c

---
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[med-svn] [Git][med-team/sra-sdk] Pushed new tag upstream/2.8.2-5+dfsg

[Andreas Tille]

Andreas Tille pushed new tag upstream/2.8.2-5+dfsg at Debian Med / sra-sdk

---
View it on GitLab: 
https://salsa.debian.org/med-team/sra-sdk/tree/upstream/2.8.2-5+dfsg
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[med-svn] [Git][med-team/squizz][master] Check why debhelper compat level 10 makes test fail

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / squizz


Commits:
434f5638 by Andreas Tille at 2018-02-18T15:28:00+01:00
Check why debhelper compat level 10 makes test fail

- - - - -


4 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+squizz (0.99d+dfsg-2) UNRELEASED; urgency=medium
+
+  * Check why debhelper compat level 10 makes test fail
+
+ -- Andreas Tille   Sun, 18 Feb 2018 15:27:33 +0100
+
 squizz (0.99d+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=
debian/compat
=
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+10


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -4,8 +4,7 @@ Uploaders: Olivier Sallou ,
Andreas Tille 
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
-   dh-autoreconf
+Build-Depends: debhelper (>= 10)
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/squizz.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/squizz.git


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -9,4 +9,4 @@
 export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-   dh $@ --with autoreconf
+   dh $@



View it on GitLab: 
https://salsa.debian.org/med-team/squizz/commit/434f5638460090b9735311345f1ff55a0a1350a8

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[med-svn] [Git][med-team/squizz] Pushed new tag debian/0.99b+dfsg-3

[Andreas Tille]

Andreas Tille pushed new tag debian/0.99b+dfsg-3 at Debian Med / squizz

---
View it on GitLab: 
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[med-svn] [Git][med-team/squizz][pristine-tar] pristine-tar data for squizz_0.99d+dfsg.orig.tar.xz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / squizz


Commits:
8d6b91df by Andreas Tille at 2018-02-18T08:54:45+01:00
pristine-tar data for squizz_0.99d+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + squizz_0.99d+dfsg.orig.tar.xz.delta
- + squizz_0.99d+dfsg.orig.tar.xz.id


Changes:

=
squizz_0.99d+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/squizz_0.99d+dfsg.orig.tar.xz.delta differ


=
squizz_0.99d+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/squizz_0.99d+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+cae296dbc3d5cf87927a2bc1b99b324a12413950



View it on GitLab: 
https://salsa.debian.org/med-team/squizz/commit/8d6b91dfc35a92f19e5f006d4225bfc42db4b191

---
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[med-svn] [Git][med-team/squizz] Pushed new tag upstream/0.99d+dfsg

[Andreas Tille]

Andreas Tille pushed new tag upstream/0.99d+dfsg at Debian Med / squizz

---
View it on GitLab: 
https://salsa.debian.org/med-team/squizz/tree/upstream/0.99d+dfsg
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[med-svn] [Git][med-team/squizz][master] 9 commits: add versioned Depends from libsquizz

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / squizz


Commits:
710db72e by Andreas Tille at 2016-09-09T12:04:40+02:00
add versioned Depends from libsquizz

- - - - -
f2d80783 by Andreas Tille at 2016-09-09T12:05:17+02:00
remove broken symbols file - feel free to re-add a corrected one

- - - - -
dc3ffcfe by Andreas Tille at 2016-09-09T12:07:56+02:00
hardening=+all

- - - - -
2794b921 by Andreas Tille at 2016-09-09T12:09:50+02:00
Drop breaks itself, upload to unstable

- - - - -
f8e5b25c by Andreas Tille at 2018-02-18T08:54:42+01:00
New upstream version 0.99d+dfsg
- - - - -
fd021b39 by Andreas Tille at 2018-02-18T08:54:45+01:00
Update upstream source from tag upstream/0.99d+dfsg

Update to upstream version 0.99d+dfsg
with Debian dir 8accb8afeae7d9616baa25112f61a9fd229f1656
- - - - -
445955b8 by Andreas Tille at 2018-02-18T08:55:51+01:00
New upstream version

- - - - -
d645de37 by Andreas Tille at 2018-02-18T08:56:20+01:00
cme fix dpkg-control

- - - - -
a3116a9d by Andreas Tille at 2018-02-18T15:25:58+01:00
Realise that debian/compat  9 will break tests due to not set $srcdir 
variable

- - - - -


30 changed files:

- ChangeLog
- Makefile.in
- configure
- configure.ac
- debian/changelog
- debian/control
- − debian/libsquizz.symbols
- debian/rules
- lib/align.h
- lib/align/clustal.h
- lib/align/fasta2.h
- lib/align/mega.h
- lib/align/msf.h
- lib/align/nexusi.h
- lib/align/parse.h
- lib/align/phylip.h
- lib/align/phylipi.h
- lib/align/phylips.h
- lib/align/stock.h
- lib/compat.h
- lib/config.h.in
- lib/extern/file.h
- lib/extern/text.h
- lib/sequence.h
- lib/sequence/codata.h
- lib/sequence/embl.h
- lib/sequence/embll.c
- lib/sequence/embll.l
- lib/sequence/embly.c
- lib/sequence/embly.y


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/squizz/compare/67d78865a608893d2fe3c45bb75f201e1d3011d3...a3116a9dd6fea01c01852664ffd6c72157b91019

---
View it on GitLab: 
https://salsa.debian.org/med-team/squizz/compare/67d78865a608893d2fe3c45bb75f201e1d3011d3...a3116a9dd6fea01c01852664ffd6c72157b91019
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[med-svn] [Git][med-team/squizz][upstream] New upstream version 0.99d+dfsg

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / squizz


Commits:
f8e5b25c by Andreas Tille at 2018-02-18T08:54:42+01:00
New upstream version 0.99d+dfsg
- - - - -


30 changed files:

- ChangeLog
- Makefile.in
- configure
- configure.ac
- lib/align.h
- lib/align/clustal.h
- lib/align/fasta2.h
- lib/align/mega.h
- lib/align/msf.h
- lib/align/nexusi.h
- lib/align/parse.h
- lib/align/phylip.h
- lib/align/phylipi.h
- lib/align/phylips.h
- lib/align/stock.h
- lib/compat.h
- lib/config.h.in
- lib/extern/file.h
- lib/extern/text.h
- lib/sequence.h
- lib/sequence/codata.h
- lib/sequence/embl.h
- lib/sequence/embll.c
- lib/sequence/embll.l
- lib/sequence/embly.c
- lib/sequence/embly.y
- lib/sequence/fasta.h
- lib/sequence/gcg.h
- lib/sequence/gde.h
- lib/sequence/genbank.h


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/squizz/commit/f8e5b25c36534bf082f64f3599d89108db1eed38

---
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https://salsa.debian.org/med-team/squizz/commit/f8e5b25c36534bf082f64f3599d89108db1eed38
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[med-svn] [Git][med-team/squizz] Pushed new tag debian/0.99d+dfsg-1

[Andreas Tille]

Andreas Tille pushed new tag debian/0.99d+dfsg-1 at Debian Med / squizz

---
View it on GitLab: 
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[med-svn] [Git][med-team/bcftools][upstream] New upstream version 1.7

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / bcftools


Commits:
c5c1bb21 by Andreas Tille at 2018-02-17T14:52:30+01:00
New upstream version 1.7
- - - - -


16 changed files:

- Makefile
- NEWS
- bcftools.h
- consensus.c
- convert.c
- convert.h
- csq.c
- doc/bcftools.1
- doc/bcftools.html
- doc/bcftools.txt
- filter.c
- + misc/fix-broken-GATK-Double-vs-Integer
- misc/plot-roh.py
- misc/plot-vcfstats
- misc/run-roh.pl
- plugins/fill-tags.c


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/bcftools/commit/c5c1bb21049ca46de059f6b6377b6e82aa694bad

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[med-svn] [Git][med-team/bcftools][pristine-tar] pristine-tar data for bcftools_1.7.orig.tar.gz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / bcftools


Commits:
97e51d5a by Andreas Tille at 2018-02-17T14:52:44+01:00
pristine-tar data for bcftools_1.7.orig.tar.gz

- - - - -


2 changed files:

- + bcftools_1.7.orig.tar.gz.delta
- + bcftools_1.7.orig.tar.gz.id


Changes:

=
bcftools_1.7.orig.tar.gz.delta
=
Binary files /dev/null and b/bcftools_1.7.orig.tar.gz.delta differ


=
bcftools_1.7.orig.tar.gz.id
=
--- /dev/null
+++ b/bcftools_1.7.orig.tar.gz.id
@@ -0,0 +1 @@
+41ff67bc6002392022b07f5d8929372c48f93a2d



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[med-svn] [Git][med-team/bcftools] Pushed new tag upstream/1.7

[Andreas Tille]

Andreas Tille pushed new tag upstream/1.7 at Debian Med / bcftools

---
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[med-svn] [Git][med-team/bcftools][master] 5 commits: New upstream version 1.7

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / bcftools


Commits:
c5c1bb21 by Andreas Tille at 2018-02-17T14:52:30+01:00
New upstream version 1.7
- - - - -
67800b68 by Andreas Tille at 2018-02-17T14:52:44+01:00
Update upstream source from tag upstream/1.7

Update to upstream version 1.7
with Debian dir a76b653af798bff3ab3dbf7ad0ab0b7f6c7459fd
- - - - -
4471d4e6 by Andreas Tille at 2018-02-17T14:58:50+01:00
New upstream version (most patches are applied)

- - - - -
014ab0fe by Andreas Tille at 2018-02-17T14:59:57+01:00
Standards-Version: 4.1.3

- - - - -
6de82c1d by Andreas Tille at 2018-02-17T15:08:57+01:00
drop useless option --parallel, upload to unstable

- - - - -


18 changed files:

- Makefile
- NEWS
- bcftools.h
- consensus.c
- convert.c
- convert.h
- csq.c
- debian/changelog
- debian/control
- − debian/patches/fix-test_vcf_query.patch
- − debian/patches/make_the_test_cases_conform_to_VCF_specification.patch
- debian/patches/series
- − debian/patches/test-regidx-unsigned-char.patch
- debian/patches/tests-pluginpath.patch
- debian/rules
- doc/bcftools.1
- doc/bcftools.html
- doc/bcftools.txt


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/bcftools/compare/837644a700cf4b4bf171b8b57c8fdb7df6918969...6de82c1d210381386d5ec70808e36b4b6ffd5196

---
View it on GitLab: 
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[med-svn] [Git][med-team/python-schema-salad] Pushed new tag upstream/2.6.20170927145003

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag upstream/2.6.20170927145003 at Debian Med / 
python-schema-salad

---
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[med-svn] [Git][med-team/python-schema-salad][master] add missing python-avro dependency

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / python-schema-salad


Commits:
70c99f23 by Michael R. Crusoe at 2018-02-18T05:29:29-08:00
add missing python-avro dependency

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+python-schema-salad (2.6.20171201034858-3) unstable; urgency=medium
+
+  * Add missing python-avro dependency
+
+ -- Michael R. Crusoe   Sun, 18 Feb 2018 05:27:57 
-0800
+
 python-schema-salad (2.6.20171201034858-2) unstable; urgency=medium
 
   * Team upload


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -2,6 +2,7 @@ Source: python-schema-salad
 Maintainer: Debian Med Packaging Team 

 Uploaders: Michael R. Crusoe 
 Section: python
+Testsuite: autopkgtest-pkg-python
 Priority: optional
 Build-Depends: debhelper (>= 10),
dh-python,
@@ -19,7 +20,7 @@ Build-Depends: debhelper (>= 10),
python-cachecontrol,
python-lockfile,
help2man
-Standards-Version: 4.1.1
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-schema-salad.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/python-schema-salad.git
 Homepage: http://www.commonwl.org
@@ -28,6 +29,7 @@ Package: python-schema-salad
 Architecture: all
 Depends: ${python:Depends},
  ${misc:Depends},
+ python-avro,
  libjs-bootstrap
 Recommends: cwltool
 Description: Schema Annotations for Linked Avro Data (SALAD)



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[med-svn] [Git][med-team/python-schema-salad] Pushed new tag debian/2.6.20171201034858-3

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag debian/2.6.20171201034858-3 at Debian Med / 
python-schema-salad

---
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[med-svn] [Git][med-team/insighttoolkit] Pushed new tag debian/4.13.0-dfsg1-2_exp1

[Gert Wollny]

Gert Wollny pushed new tag debian/4.13.0-dfsg1-2_exp1 at Debian Med / 
insighttoolkit

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[med-svn] [Git][med-team/insighttoolkit][master] 2 commits: d/rules: Add embedded library override

[Gert Wollny]

Gert Wollny pushed to branch master at Debian Med / insighttoolkit


Commits:
bc5153ba by Gert Wollny at 2018-02-18T11:40:47+01:00
d/rules: Add embedded library override

- - - - -
af4e80fa by Gert Wollny at 2018-02-18T11:49:03+01:00
Make another upload to exp

- - - - -


2 changed files:

- debian/changelog
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+insighttoolkit4 (4.13.0-dfsg1-2~exp1) experimental; urgency=medium
+
+  * d/rules: Add embedded library override
+
+ -- Gert Wollny   Sun, 18 Feb 2018 11:48:24 +0100
+
 insighttoolkit4 (4.13.0-dfsg1-1) experimental; urgency=medium
 
   * New upstream version 4.13.0-dfsg1


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -103,6 +103,8 @@ override_dh_auto_test:
LD_LIBRARY_PATH=`pwd`/BUILD/lib:`pwd`/BUILD/Testing/Temporary 
dh_auto_test 
 
 override_dh_lintian:
+   echo "#ITK embeds various patched libraries" > 
debian/$(pkg_lib).lintian-overrides
+   echo "$(pkg_lib): embedded-library" > 
debian/$(pkg_lib).lintian-overrides
echo "$(pkg_lib): package-name-doesnt-match-sonames" > 
debian/$(pkg_lib).lintian-overrides
dh_lintian
 



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---
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[med-svn] [Git][med-team/itksnap][itk-transition] Correct stupid error

[Gert Wollny]

Gert Wollny pushed to branch itk-transition at Debian Med / itksnap


Commits:
101015c6 by Gert Wollny at 2018-02-18T11:11:21+01:00
Correct stupid error

- - - - -


1 changed file:

- debian/.gitlab-ci.yml


Changes:

=
debian/.gitlab-ci.yml
=
--- a/debian/.gitlab-ci.yml
+++ b/debian/.gitlab-ci.yml
@@ -9,7 +9,7 @@ build:
 - grep "^deb .* sid "  /etc/apt/sources.list | sed -e "s/ sid / 
experimental /" >> /etc/apt/sources.list
 - cat /etc/apt/sources.list
 - apt-get update && apt-get -y install devscripts git-buildpackage
-- apt-get -t experimental libinsighttoolkit4-dev
+- apt-get -t experimental install libinsighttoolkit4-dev
 - mk-build-deps --tool "apt -y -o Debug::pkgProblemResolver=yes 
--no-install-recommends" --install -r debian/control 
   script:
 - git checkout pristine-tar 



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https://salsa.debian.org/med-team/itksnap/commit/101015c6d4736995f67f55fa16729cf35111b196

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[med-svn] [Git][med-team/itksnap][itk-transition] Correct creation of experimental entry

[Gert Wollny]

Gert Wollny pushed to branch itk-transition at Debian Med / itksnap


Commits:
a5fa2913 by Gert Wollny at 2018-02-18T11:08:26+01:00
Correct creation of experimental entry

- - - - -


1 changed file:

- debian/.gitlab-ci.yml


Changes:

=
debian/.gitlab-ci.yml
=
--- a/debian/.gitlab-ci.yml
+++ b/debian/.gitlab-ci.yml
@@ -6,7 +6,7 @@ build:
   before_script:
 - cat /etc/apt/sources.list
 - echo "adding experimental" 
-- grep "^deb .* sid "  /etc/apt/sources.list | sed -e "s/ sid 
/experimental/" >> /etc/apt/sources.list
+- grep "^deb .* sid "  /etc/apt/sources.list | sed -e "s/ sid / 
experimental /" >> /etc/apt/sources.list
 - cat /etc/apt/sources.list
 - apt-get update && apt-get -y install devscripts git-buildpackage
 - apt-get -t experimental libinsighttoolkit4-dev



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[med-svn] [Git][med-team/itksnap][itk-transition] Debugging output

[Gert Wollny]

Gert Wollny pushed to branch itk-transition at Debian Med / itksnap


Commits:
b7d380e1 by Gert Wollny at 2018-02-18T11:06:54+01:00
Debugging output

- - - - -


1 changed file:

- debian/.gitlab-ci.yml


Changes:

=
debian/.gitlab-ci.yml
=
--- a/debian/.gitlab-ci.yml
+++ b/debian/.gitlab-ci.yml
@@ -4,7 +4,10 @@ build:
   stage: build
   
   before_script:
+- cat /etc/apt/sources.list
+- echo "adding experimental" 
 - grep "^deb .* sid "  /etc/apt/sources.list | sed -e "s/ sid 
/experimental/" >> /etc/apt/sources.list
+- cat /etc/apt/sources.list
 - apt-get update && apt-get -y install devscripts git-buildpackage
 - apt-get -t experimental libinsighttoolkit4-dev
 - mk-build-deps --tool "apt -y -o Debug::pkgProblemResolver=yes 
--no-install-recommends" --install -r debian/control 



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https://salsa.debian.org/med-team/itksnap/commit/b7d380e1eaf862077574d5554d0b1c8f763ca679

---
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[med-svn] [Git][med-team/itksnap][itk-transition] Whitepace cleanup

[Gert Wollny]

Gert Wollny pushed to branch itk-transition at Debian Med / itksnap


Commits:
510a06a5 by Gert Wollny at 2018-02-18T11:04:40+01:00
Whitepace cleanup

- - - - -


1 changed file:

- debian/.gitlab-ci.yml


Changes:

=
debian/.gitlab-ci.yml
=
--- a/debian/.gitlab-ci.yml
+++ b/debian/.gitlab-ci.yml
@@ -5,7 +5,7 @@ build:
   
   before_script:
 - grep "^deb .* sid "  /etc/apt/sources.list | sed -e "s/ sid 
/experimental/" >> /etc/apt/sources.list
-- apt-get update && apt-get -y install devscripts git-buildpackage 
+- apt-get update && apt-get -y install devscripts git-buildpackage
 - apt-get -t experimental libinsighttoolkit4-dev
 - mk-build-deps --tool "apt -y -o Debug::pkgProblemResolver=yes 
--no-install-recommends" --install -r debian/control 
   script:



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https://salsa.debian.org/med-team/itksnap/commit/510a06a56f465f3163dec967659d2cf8ba8d2f3f

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[med-svn] [Git][med-team/lambda-align][master] Fix AutoPkgTests

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / lambda-align


Commits:
d1546206 by Michael R. Crusoe at 2018-02-18T02:02:14-08:00
Fix AutoPkgTests

- - - - -


3 changed files:

- debian/changelog
- debian/tests/control
- debian/tests/run-tests


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+lambda-align (1.0.3-2) unstable; urgency=medium
+
+  * Fix AutoPkgTests, tested locally with debci
+
+ -- Michael R. Crusoe   Sun, 18 Feb 2018 02:00:59 
-0800
+
 lambda-align (1.0.3-1) unstable; urgency=medium
 
   [ Steffen Moeller ]


=
debian/tests/control
=
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1,3 +1,3 @@
 Tests: run-tests
-Depends: lambda-align, openssl, gzip, coreutils, diffutils
+Depends: @, @builddeps@, openssl, gzip, coreutils, diffutils
 Restrictions: allow-stderr


=
debian/tests/run-tests
=
--- a/debian/tests/run-tests
+++ b/debian/tests/run-tests
@@ -1,8 +1,10 @@
-#!/bin/sh -e
+#!/bin/sh -ex
 
 mkdir build
 cd build
-cmake ../
-for binary in $(dpkg -L lambda-align); do ln -s ${binary} bin/; done
+cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON \
+   -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON ../
+for binary in $(dpkg -L lambda-align | grep bin/); do ln -s ${binary} bin/; 
done
+cd tests
 ctest  --parallel $(nproc)
 



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[med-svn] [Git][med-team/lambda-align] Pushed new tag debian/1.0.3-2

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag debian/1.0.3-2 at Debian Med / lambda-align

---
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[med-svn] [Git][med-team/itksnap][master] 2 commits: use itk-transition branch

[Gert Wollny]

Gert Wollny pushed to branch master at Debian Med / itksnap


Commits:
f5139fa0 by Gert Wollny at 2018-02-18T10:55:19+01:00
use itk-transition branch

- - - - -
01b9e4e8 by Gert Wollny at 2018-02-18T10:58:20+01:00
Add CI for master

- - - - -


1 changed file:

- + debian/.gitlab-ci.yml


Changes:

=
debian/.gitlab-ci.yml
=
--- /dev/null
+++ b/debian/.gitlab-ci.yml
@@ -0,0 +1,19 @@
+image: debian:sid
+
+build:
+  stage: build
+  
+  before_script:
+- grep "^deb .* sid "  /etc/apt/sources.list | sed -e "s/ sid 
/experimental/" >> /etc/apt/sources.list
+- apt-get update && apt-get -y install devscripts git-buildpackage 
+#  - apt-get -t experimental libinsighttoolkit4-dev
+- mk-build-deps --tool "apt -y -o Debug::pkgProblemResolver=yes 
--no-install-recommends" --install -r debian/control 
+  script:
+- git checkout pristine-tar 
+- git pull 
+- git checkout master
+- git pull 
+# silence build to not exceed build log size of gitlab-ci
+- gbp buildpackage -uc -us 2>&1 >../build.log
+- tail -n 100 ../build.log
+



View it on GitLab: 
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---
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[med-svn] [Git][med-team/itksnap][itk-transition] use itk-transition branch

[Gert Wollny]

Gert Wollny pushed to branch itk-transition at Debian Med / itksnap


Commits:
f5139fa0 by Gert Wollny at 2018-02-18T10:55:19+01:00
use itk-transition branch

- - - - -


1 changed file:

- + debian/.gitlab-ci.yml


Changes:

=
debian/.gitlab-ci.yml
=
--- /dev/null
+++ b/debian/.gitlab-ci.yml
@@ -0,0 +1,19 @@
+image: debian:sid
+
+build:
+  stage: build
+  
+  before_script:
+- grep "^deb .* sid "  /etc/apt/sources.list | sed -e "s/ sid 
/experimental/" >> /etc/apt/sources.list
+- apt-get update && apt-get -y install devscripts git-buildpackage 
+- apt-get -t experimental libinsighttoolkit4-dev
+- mk-build-deps --tool "apt -y -o Debug::pkgProblemResolver=yes 
--no-install-recommends" --install -r debian/control 
+  script:
+- git checkout pristine-tar 
+- git pull 
+- git checkout itk-transition
+- git pull 
+# silence build to not exceed build log size of gitlab-ci
+- gbp buildpackage -uc -us 2>&1 >../build.log
+- tail -n 100 ../build.log
+



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https://salsa.debian.org/med-team/itksnap/commit/f5139fa090a934f419ff40cfdaa4ee4707daecca

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[med-svn] [Git][med-team/itksnap] Pushed new branch itk-transition

[Gert Wollny]

Gert Wollny pushed new branch itk-transition at Debian Med / itksnap

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[med-svn] [Git][med-team/cwltool][master] even better description

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / cwltool


Commits:
5a7b2ff2 by Michael R. Crusoe at 2018-02-18T01:19:04-08:00
even better description

- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -31,13 +31,17 @@ Provides: cwl-runner
 Architecture: all
 Depends: ${python:Depends},
  ${misc:Depends}
-Description: Common workflow language reference implementation
- This is the reference implementation of the Common Workflow Language. It is
- intended to be feature complete and provide comprehensive validation of CWL
- files as well as provide other tools related to working with CWL.
+Description: Common Workflow Language reference implementation
+ This is the reference implementation of the Common Workflow Language
+ standards.
  .
- This is written and tested for Python 2.7.
+ The CWL open standards are for describing analysis workflows and tools in a
+ way that makes them portable and scalable across a variety of software and
+ hardware environments, from workstations to cluster, cloud, and high
+ performance computing (HPC) environments. CWL is designed to meet the needs of
+ data-intensive science, such as Bioinformatics, Medical Imaging, Astronomy,
+ Physics, and Chemistry.
  .
- The "cwltool" package is the primary Python module containing the reference
- implementation in the "cwltool" module and console executable by the same
- name.
+ The CWL reference implementation (cwltool) is intended to be feature complete
+ and to provide comprehensive validation of CWL files as well as provide other
+ tools related to working with CWL descriptions.



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https://salsa.debian.org/med-team/cwltool/commit/5a7b2ff2e17919f009091925f19d6116a9e952f2

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[med-svn] [Git][med-team/cwltool][master] improve description

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / cwltool


Commits:
6d54204d by Michael R. Crusoe at 2018-02-18T01:08:54-08:00
improve description

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+cwltool (1.0.20180211183944-3) UNRELEASED; urgency=medium
+
+  * Improve package description.
+
+ -- Michael R. Crusoe   Sun, 18 Feb 2018 01:08:48 
-0800
+
 cwltool (1.0.20180211183944-2) unstable; urgency=medium
 
   * Provide the "cwl-runner" virtual package.


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -38,10 +38,6 @@ Description: Common workflow language reference 
implementation
  .
  This is written and tested for Python 2.7.
  .
- The reference implementation consists of two packages. The "cwltool" package
- is the primary Python module containing the reference implementation in the
- "cwltool" module and console executable by the same name.
- .
- The "cwl-runner" package is optional and provides an additional entry point
- under the alias "cwl-runner", which is the implementation-agnostic name for 
the
- default CWL interpreter installed on a host.
+ The "cwltool" package is the primary Python module containing the reference
+ implementation in the "cwltool" module and console executable by the same
+ name.



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