[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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