[med-svn] r17153 - in trunk/packages/R: . r-bioc-genomicalignments r-bioc-genomicalignments/trunk r-bioc-genomicalignments/trunk/debian r-bioc-genomicalignments/trunk/debian/source r-bioc-genomicalignments/trunk/debian/tests

Andreas Tille tille at moszumanska.debian.org
Fri Jun 13 13:53:55 UTC 2014


Author: tille
Date: 2014-06-13 13:53:55 +0000 (Fri, 13 Jun 2014)
New Revision: 17153

Added:
   trunk/packages/R/r-bioc-genomicalignments/
   trunk/packages/R/r-bioc-genomicalignments/trunk/
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/compat
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/docs
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/source/
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/source/format
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/control
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/run-unit-test
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/watch
Log:
This is a precondition for r-bioc-biovizbase and r-bioc-gviz; needs BiocParallel first


Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/README.test	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,10 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage("GenomicAlignments")
+EOT
+
+in order to confirm its integrity.

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,8 @@
+r-bioc-genomicalignments (1.0.1-1) UNRELEASED; urgency=medium
+
+  * Initial release (closes: #?)
+  This is a precondition for r-bioc-biovizbase and r-bioc-gviz
+  TODO:  Needs to package r-bioc-biocparallel first
+      http://bioconductor.org/packages/release/bioc/html/BiocParallel.html
+
+ -- Andreas Tille <tille at debian.org>  Sun, 08 Jun 2014 18:33:04 +0200

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/compat	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1 @@
+9

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,38 @@
+Source: r-bioc-genomicalignments
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: gnu-r
+Priority: optional
+XS-Testsuite: autopkgtest
+Build-Depends: debhelper (>= 9),
+               cdbs,
+               r-base-dev,
+               r-bioc-BiocGenerics,
+               r-bioc-iranges,
+               r-bioc-genomicranges,
+               r-bioc-biostrings,
+               r-bioc-rsamtools,
+               r-bioc-bsgenome,
+               r-bioc-biocparallel
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
+Homepage: http://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html
+
+Package: r-bioc-genomicalignments
+Architecture: all
+Depends: ${R:Depends},
+         ${misc:Depends},
+         r-bioc-BiocGenerics,
+         r-bioc-iranges,
+         r-bioc-genomicranges,
+         r-bioc-biostrings,
+         r-bioc-rsamtools,
+         r-bioc-bsgenome,
+         r-bioc-biocparallel
+Description: BioConductor representation and manipulation of short genomic alignments
+ This BioCOnductor package provides efficient containers for storing and
+ manipulating short genomic alignments (typically obtained by aligning
+ short reads to a reference genome). This includes read counting,
+ computing the coverage, junction detection, and working with the
+ nucleotide content of the alignments.

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,106 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: GenomicAlignments
+Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org>
+Source: http://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html
+
+Files: *
+Copyright: © 2006-2014 Hervè Pagès, Valerie Obenchain, Martin Morgan 
+License: Artistic-2.0
+
+Files: debian/*
+Copyright: 2013 Andreas Tille <tille at debian.org>
+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.

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/docs	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1 @@
+debian/README.test

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk


Property changes on: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/source/format	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/control	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/tests/run-unit-test	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,6 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage("GenomicAlignments")
+EOT
+

Added: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/watch	2014-06-13 13:53:55 UTC (rev 17153)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+ http://www.bioconductor.org/packages/release/bioc/html/GenomicAlignments.html .*/GenomicAlignments_([\d\.]+)\.tar\.gz




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