[med-svn] [r-bioc-mergeomics] 04/05: Initial debian/

Fri Nov 18 22:13:07 UTC 2016

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bob.dybian-guest pushed a commit to branch master
in repository r-bioc-mergeomics.

commit 6622e8decbe4039245643f3b5fe2c81e79265532
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Fri Nov 18 22:18:57 2016 +0100

    Initial debian/
---
 debian/changelog         |  5 +++++
 debian/compat            |  1 +
 debian/control           | 24 ++++++++++++++++++++++++
 debian/copyright         | 30 ++++++++++++++++++++++++++++++
 debian/rules             |  5 +++++
 debian/source/format     |  1 +
 debian/tests/bioc        |  4 ++++
 debian/tests/control     |  5 +++++
 debian/upstream/metadata | 11 +++++++++++
 debian/watch             |  3 +++
 10 files changed, 89 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..df700de
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-bioc-mergeomics (1.2.0-1) UNRELEASED; urgency=medium
+
+  * Initial release (Closes: #xxxxxx)
+
+ -- Dylan Aïssi <bob.dybian at gmail.com>  Fri, 18 Nov 2016 21:53:34 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..8212b29
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: r-bioc-mergeomics
+Section: gnu-r
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Dylan Aïssi <bob.dybian at gmail.com>
+Build-Depends: debhelper (>= 9), dh-r, r-base-dev
+Standards-Version: 3.9.8
+Homepage: https://bioconductor.org/packages/Mergeomics/
+Vcs-Browser: https://anonscm.debian.org/git/debian-med/r-bioc-mergeomics.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/r-bioc-mergeomics.git
+
+Package: r-bioc-mergeomics
+Architecture: all
+Depends: ${R:Depends}, ${shlibs:Depends}, ${misc:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
+Description: Integrative network analysis of omics data
+ The Mergeomics pipeline serves as a flexible framework for integrating
+ multidimensional omics-disease associations, functional genomics,
+ canonical pathways and gene-gene interaction networks to generate
+ mechanistic hypotheses. It includes two main parts:
+ 1) Marker set enrichment analysis (MSEA);
+ 2) Weighted Key Driver Analysis (wKDA).
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..fd5e4df
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,30 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Mergeomics
+Upstream-Contact: Zeyneb Kurt <zeyneb at ucla.edu>
+Source: https://bioconductor.org/packages/Mergeomics/
+
+Files: *
+Copyright: 2016 Ville-Petteri Makinen, Le Shu, Yuqi Zhao, Zeyneb Kurt, Bin Zhang, Xia Yang
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2016 Dylan Aïssi <bob.dybian at gmail.com>
+License: GPL-2+
+
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the full text of the GNU General Public License
+ version 3 can be found in `/usr/share/common-licenses/GPL-2'.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..529c38a
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+
+%:
+	dh $@ --buildsystem R
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/tests/bioc b/debian/tests/bioc
new file mode 100644
index 0000000..533584e
--- /dev/null
+++ b/debian/tests/bioc
@@ -0,0 +1,4 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save -e 'BiocGenerics:::testPackage("Mergeomics")'
+
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..93554ac
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,5 @@
+Tests: bioc
+Depends: @, r-cran-runit, r-bioc-biocgenerics
+Restrictions: allow-stderr
+
+
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..04e9cb9
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,11 @@
+Archive: Bioconductor
+Contact: Zeyneb Kurt
+Name: Mergeomics
+Reference:
+  - Author: Le Shu and Yuqi Zhao and Zeyneb Kurt and Sean Geoffrey Byars and Taru Tukiainen and Johannes Kettunen and Luz D. Orozco and Matteo Pellegrini and Aldons J. Lusis and Samuli Ripatti and Bin Zhang and Michael Inouye and Ville-Petteri Mäkinen and Xia Yang
+    Title: "Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems"
+    Journal: BMC Genomics
+    Year: 2016
+    DOI: 10.1186/s12864-016-3198-9
+    URL: http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3198-9
+    eprint: http://bmcgenomics.biomedcentral.com/track/pdf/10.1186/s12864-016-3198-9
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..3e404f5
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+opts=downloadurlmangle=s?^(.*)\.\.?https:$1packages/release/bioc? \
+https://bioconductor.org/packages/release/bioc/html/Mergeomics.html .*/Mergeomics_(.*).tar.gz

-- 
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