[med-svn] [r-bioc-ebseq] 02/02: initial Debianization
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 17 02:11:03 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository r-bioc-ebseq.
commit 35ebd1814a4fb2231a1f4a52bc7c0962b1e38370
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date: Mon Feb 16 19:44:05 2015 -0500
initial Debianization
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 16 ++++++++
debian/copyright | 105 +++++++++++++++++++++++++++++++++++++++++++++++
debian/rules | 4 ++
debian/source/format | 1 +
debian/upstream/metadata | 14 +++++++
debian/watch | 4 ++
8 files changed, 150 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..fa30dd6
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-bioc-ebseq (1.6.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #778586)
+
+ -- Michael R. Crusoe <mcrusoe at msu.edu> Mon, 16 Feb 2015 19:26:42 -0500
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..960bb44
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,16 @@
+Source: r-bioc-ebseq
+Section: gnu-r
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>
+Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-gplots, r-cran-gplots
+Standards-Version: 3.9.6
+Homepage: https://www.biostat.wisc.edu/~kendzior/EBSEQ/
+
+Package: r-bioc-ebseq
+Architecture: all
+Depends: ${R:Depends}, ${misc:Depends}, r-cran-gplots, r-cran-gplots
+Description: R package for RNA-Seq Differential Expression Analysis
+ r-bioc-ebseq is an R package for identifying genes and isoforms differentially
+ expressed (DE) across two or more biological conditions in an RNA-seq
+ experiment.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..d4e037c
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,105 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: EBSeq
+Source: http://www.bioconductor.org/packages/2.14/bioc/src/contrib/EBSeq_1.4.0.tar.gz
+
+Files: *
+Copyright: © 2013-2014 Ning Leng <nleng at wisc.edu>
+License: Artistic-2.0
+
+Files: debian/*
+Copyright: © 2015 Michigan State University
+License: Artistic-2.0
+
+License: Artistic-2.0
+ The "Artistic License"
+ .
+ Preamble
+ .
+ 1. You may make and give away verbatim copies of the source form of the
+ Standard Version of this Package without restriction, provided that
+ you duplicate all of the original copyright notices and associated
+ disclaimers.
+ .
+ 2. You may apply bug fixes, portability fixes and other modifications
+ derived from the Public Domain or from the Copyright Holder. A
+ Package modified in such a way shall still be considered the Standard
+ Version.
+ .
+ 3. You may otherwise modify your copy of this Package in any way,
+ provided that you insert a prominent notice in each changed file stating
+ how and when you changed that file, and provided that you do at least
+ ONE of the following:
+ .
+ a) place your modifications in the Public Domain or otherwise make them
+ Freely Available, such as by posting said modifications to Usenet or
+ an equivalent medium, or placing the modifications on a major archive
+ site such as uunet.uu.net, or by allowing the Copyright Holder to include
+ your modifications in the Standard Version of the Package.
+ .
+ b) use the modified Package only within your corporation or organization.
+ .
+ c) rename any non-standard executables so the names do not conflict
+ with standard executables, which must also be provided, and provide
+ a separate manual page for each non-standard executable that clearly
+ documents how it differs from the Standard Version.
+ .
+ d) make other distribution arrangements with the Copyright Holder.
+ .
+ 4. You may distribute the programs of this Package in object code or
+ executable form, provided that you do at least ONE of the following:
+ .
+ a) distribute a Standard Version of the executables and library files,
+ together with instructions (in the manual page or equivalent) on where
+ to get the Standard Version.
+ .
+ b) accompany the distribution with the machine-readable source of
+ the Package with your modifications.
+ .
+ c) give non-standard executables non-standard names, and clearly
+ document the differences in manual pages (or equivalent), together
+ with instructions on where to get the Standard Version.
+ .
+ d) make other distribution arrangements with the Copyright Holder.
+ .
+ 5. You may charge a reasonable copying fee for any distribution of this
+ Package. You may charge any fee you choose for support of this Package.
+ You may not charge a fee for this Package itself. However, you may
+ distribute this Package in aggregate with other (possibly commercial)
+ programs as part of a larger (possibly commercial) software distribution
+ provided that you do not advertise this Package as a product of your
+ own. You may embed this Package's interpreter within an executable of
+ yours (by linking); this shall be construed as a mere form of
+ aggregation, provided that the complete Standard Version of the
+ interpreter is so embedded.
+ .
+ 6. The scripts and library files supplied as input to or produced as
+ output from the programs of this Package do not automatically fall under
+ the copyright of this Package, but belong to whoever generated them, and
+ may be sold commercially, and may be aggregated with this Package. If
+ such scripts or library files are aggregated with this Package via the
+ so-called "undump" or "unexec" methods of producing a binary executable
+ image, then distribution of such an image shall neither be construed as
+ a distribution of this Package nor shall it fall under the restrictions
+ of Paragraphs 3 and 4, provided that you do not represent such an
+ executable image as a Standard Version of this Package.
+ .
+ 7. C subroutines (or comparably compiled subroutines in other
+ languages) supplied by you and linked into this Package in order to
+ emulate subroutines and variables of the language defined by this
+ Package shall not be considered part of this Package, but are the
+ equivalent of input as in Paragraph 6, provided these subroutines do
+ not change the language in any way that would cause it to fail the
+ regression tests for the language.
+ .
+ 8. Aggregation of this Package with a commercial distribution is always
+ permitted provided that the use of this Package is embedded; that is,
+ when no overt attempt is made to make this Package's interfaces visible
+ to the end user of the commercial distribution. Such use shall not be
+ construed as a distribution of this Package.
+ .
+ 9. The name of the Copyright Holder may not be used to endorse or promote
+ products derived from this software without specific prior written permission.
+ .
+ 10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+ WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..524887f
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,14 @@
+Reference:
+ Author: Leng, Ning and Dawson, John A. and Thomson, James A. and Ruotti,
+Victor and Rissman, Anna I. and Smits, Bart M. G. and Haag, Jill D. and Gould,
+Michael N. and Stewart, Ron M. and Kendziorski, Christina
+ Title: 'EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq
+experiments'
+ Journal: Bioinformatics
+ Year: 2013
+ Volume: 29
+ Number: 8
+ Pages: 1035-1043
+ DOI: http://dx.doi.org/10.1093/bioinformatics/btt087
+ URL: http://bioinformatics.oxfordjournals.org/content/29/8/1035.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/29/8/1035.full.pdf+html
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..c875dac
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+ http://www.bioconductor.org/packages/release/bioc/html/EBSeq.html .*/EBSeq_([\d\.]+)\.tar\.gz
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