[med-svn] r14581 - in trunk/packages/R: . r-bioc-rsamtools r-bioc-rsamtools/trunk r-bioc-rsamtools/trunk/debian r-bioc-rsamtools/trunk/debian/patches r-bioc-rsamtools/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Wed Sep 4 09:25:52 UTC 2013
Author: tille
Date: 2013-09-04 09:25:52 +0000 (Wed, 04 Sep 2013)
New Revision: 14581
Added:
trunk/packages/R/r-bioc-rsamtools/
trunk/packages/R/r-bioc-rsamtools/trunk/
trunk/packages/R/r-bioc-rsamtools/trunk/debian/
trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test
trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat
trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright
trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/
trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/series
trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
trunk/packages/R/r-bioc-rsamtools/trunk/debian/rules
trunk/packages/R/r-bioc-rsamtools/trunk/debian/source/
trunk/packages/R/r-bioc-rsamtools/trunk/debian/source/format
trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch
Log:
Add packaging for Rsamtools
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1,5 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by loading it into R with the command
+‘library(Rsamtools)’ in order to confirm its integrity.
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1,8 @@
+r-bioc-rsamtools (1.12.4-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+ TODO: Depends:
+ Biostrings: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biostrings/trunk/ (uploaded to new)
+ GenomicRanges: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/ (uploaded to new)
+
+ -- Andreas Tille <tille at debian.org> Wed, 04 Sep 2013 11:11:22 +0200
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/compat 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1,28 @@
+Source: r-bioc-rsamtools
+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
+Build-Depends: debhelper (>= 9),
+ cdbs,
+ r-base-dev,
+ r-cran-bitops,
+ r-bioc-biocgenerics,
+ r-bioc-iranges
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
+Homepage: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
+
+Package: r-bioc-rsamtools
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-cran-bitops,
+ r-bioc-biocgenerics,
+ r-bioc-iranges
+Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
+ This package provides an interface to the 'samtools', 'bcftools', and
+ 'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
+ binary variant call (BCF) and compressed indexed tab-delimited (tabix)
+ files.
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/copyright 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1,107 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Rsamtools
+Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org>
+Source: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
+
+Files: *
+Copyright: © 2006-2013 Martin Morgan, Hervé Pagès
+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-rsamtools/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/series (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/series 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1 @@
+use_debian_packaged_zlib.patch
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Wed, 04 Sep 2013 11:11:22 +0200
+Description: If the systems includes zlib natively there is no point in
+ requiring the import of zlibbioc
+
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -14,7 +14,7 @@ License: Artistic-2.0 + file LICENSE
+ LazyLoad: yes
+ Depends: methods, IRanges (>= 1.15.35), GenomicRanges (>= 1.11.38),
+ Biostrings (>= 2.25.6)
+-Imports: methods, utils, IRanges, GenomicRanges, Biostrings, zlibbioc,
++Imports: methods, utils, IRanges, GenomicRanges, Biostrings,
+ bitops, BiocGenerics (>= 0.1.3)
+ Suggests: ShortRead (>= 1.13.19), GenomicFeatures,
+ TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, pasillaBamSubset,
+--- a/NAMESPACE
++++ b/NAMESPACE
+@@ -1,7 +1,5 @@
+ useDynLib(Rsamtools, .registration=TRUE)
+
+-import(zlibbioc)
+-
+ importFrom(bitops, bitAnd)
+
+ importFrom(utils, read.table) # normalizePath --> base in R-2.13
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/rules 2013-09-04 09:25:52 UTC (rev 14581)
@@ -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-rsamtools/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/source/format (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/source/format 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch 2013-09-04 09:25:52 UTC (rev 14581)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+ http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html .*/Rsamtools_([\d\.]+)\.tar\.gz
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