[med-svn] [r-bioc-dnacopy] 02/02: initial Debianization

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository r-bioc-dnacopy.

commit 166e9b0e2e21c4436e4026b5176614b73b624f24
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sat Jun 25 14:52:30 2016 -0700

    initial Debianization
---
 debian/changelog     |  5 +++++
 debian/compat        |  1 +
 debian/control       | 30 ++++++++++++++++++++++++++++++
 debian/copyright     | 20 ++++++++++++++++++++
 debian/rules         |  4 ++++
 debian/source/format |  1 +
 debian/watch         |  4 ++++
 7 files changed, 65 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..32cf412
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-bioc-dnacopy (1.46.0-1) UNRELEASED; urgency=medium
+
+  * Initial release. (Closes: #828189)
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com>  Sat, 25 Jun 2016 13:58:30 -0700
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..1a1ad78
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,30 @@
+Source: r-bioc-dnacopy
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               cdbs,
+               r-base-dev,
+Standards-Version: 3.9.8
+Homepage: http://www.bioconductor.org/packages/DNAcopy/
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-bioc-dnacopy.git
+Vcs-Git: https://anonscm.debian.org/debian-med/r-bioc-dnacopy.git
+
+Package: r-bioc-dnacopy
+Architecture: any
+Depends: ${R:Depends},
+         ${misc:Depends},
+         ${shlibs:Depends}
+Description: R package: DNA copy number data analysis
+ Implements the circular binary segmentation (CBS) algorithm to segment DNA
+ copy number data and identify genomic regions with abnormal copy number.
+ .
+ This package is for analyzing array DNA copy number data, which is usually
+ (but not always) called array Comparative Genomic Hybridization (array CGH)
+ data It implements a methodology for finding change-points in these data which
+ are points after which the (log) test over reference ratios have changed
+ location. This model is that the change-points correspond to positions where
+ the underlying DNA copy number has changed. Therefore, change-points can be
+ used to identify regions of gained and lost copy number. Also provided is a
+ function for making relevant plots of these data.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..15e4bd2
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,20 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: DNAcopy
+Source: http://www.bioconductor.org/packages/release/bioc/html/DNAcopy.html
+
+Files: *
+Copyright: Venkatraman E. Seshan <seshanv at mskcc.org>
+           Adam Olshen
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: © 2016 Michael R. Crusoe <michael.crusoe at gmail.com>
+License: GPL-2.0+
+
+License: GPL-2.0+
+  This code may be freely distributed and modified under the
+  terms of the GNU General Public Licence.  This should
+  be distributed with the code.
+  .
+  On Debian systems, the complete text of the GNU General Public License
+  can be found in  `/usr/share/common-licenses/GPL-2'.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..aeb12b3
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk
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/watch b/debian/watch
new file mode 100644
index 0000000..bb9b363
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
+  http://www.bioconductor.org/packages/release/bioc/html/DNAcopy.html .*/DNAcopy_([\d\.]+)\.tar\.gz

-- 
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