[med-svn] r14488 - in trunk/packages/R: . r-bioc-gviz r-bioc-gviz/trunk r-bioc-gviz/trunk/debian r-bioc-gviz/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Thu Aug 22 16:10:43 UTC 2013
Author: tille
Date: 2013-08-22 16:10:42 +0000 (Thu, 22 Aug 2013)
New Revision: 14488
Added:
trunk/packages/R/r-bioc-gviz/
trunk/packages/R/r-bioc-gviz/trunk/
trunk/packages/R/r-bioc-gviz/trunk/debian/
trunk/packages/R/r-bioc-gviz/trunk/debian/README.test
trunk/packages/R/r-bioc-gviz/trunk/debian/changelog
trunk/packages/R/r-bioc-gviz/trunk/debian/compat
trunk/packages/R/r-bioc-gviz/trunk/debian/control
trunk/packages/R/r-bioc-gviz/trunk/debian/copyright
trunk/packages/R/r-bioc-gviz/trunk/debian/rules
trunk/packages/R/r-bioc-gviz/trunk/debian/source/
trunk/packages/R/r-bioc-gviz/trunk/debian/source/format
trunk/packages/R/r-bioc-gviz/trunk/debian/upstream
trunk/packages/R/r-bioc-gviz/trunk/debian/watch
Log:
Inject initial packaging mentioning all the missing Dependencies in changelog
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/README.test (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/README.test 2013-08-22 16:10:42 UTC (rev 14488)
@@ -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(rtracklayer)’ in order to confirm its integrity.
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/changelog 2013-08-22 16:10:42 UTC (rev 14488)
@@ -0,0 +1,16 @@
+r-bioc-gviz (1.4.5-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???).
+ The following preconditions are needed but missing in Debian
+ rtracklayer: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
+ GenomicRanges: http://www.bioconductor.org/packages/release/bioc/html/GenomicRanges.html
+ IRanges: http://bioconductor.org/packages/2.3/bioc/html/IRanges.html
+ Biostrings: http://www.bioconductor.org/packages/2.2/bioc/html/Biostrings.html
+ BSgenome: http://bioconductor.org/packages/2.4/bioc/html/BSgenome.html
+ Rsamtools: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
+ biomaRt: http://www.bioconductor.org/packages/2.12/bioc/html/biomaRt.html
+ AnnotationDbi: http://www.bioconductor.org/packages/2.9/bioc/html/AnnotationDbi.html
+ GenomicFeatures: http://www.bioconductor.org/packages/2.12/bioc/html/GenomicFeatures.html
+ biovizBase: http://bioconductor.org/packages/2.12/bioc/html/biovizBase.html
+
+ -- Andreas Tille <tille at debian.org> Thu, 22 Aug 2013 14:01:29 +0200
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/compat (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/compat 2013-08-22 16:10:42 UTC (rev 14488)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/control 2013-08-22 16:10:42 UTC (rev 14488)
@@ -0,0 +1,32 @@
+Source: r-bioc-gviz
+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-lattice,
+ r-cran-rcolorbrewer,
+ r-bioc-biobase,
+ r-bioc-biocgenerics
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-gviz/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-gviz/trunk/
+Homepage: http://bioconductor.org/packages/2.12/bioc/html/gviz.html
+
+Package: r-bioc-gviz
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-cran-lattice,
+ r-cran-rcolorbrewer,
+ r-bioc-biobase,
+ r-bioc-biocgenerics
+Description: Plotting data and annotation information along genomic coordinates
+ Genomic data analyses requires integrated visualization of known
+ genomic information and new experimental data. Gviz uses the biomaRt and
+ the rtracklayer packages to perform live annotation queries to Ensembl
+ and UCSC and translates this to e.g. gene/transcript structures in
+ viewports of the grid graphics package. This results in genomic
+ information plotted together with your data.
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/copyright 2013-08-22 16:10:42 UTC (rev 14488)
@@ -0,0 +1,108 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Gviz
+Upstream-Contact: Florian Hahne <florian.hahne at novartis.com>
+Source: http://www.bioconductor.org/packages/2.12/bioc/html/Gviz.html
+
+Files: *
+Copyright: © 2006-2013 Florian Hahne, Steffen Durinck,
+ Robert Ivanek, Arne Mueller, Steve Lianoglou
+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-gviz/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/rules 2013-08-22 16:10:42 UTC (rev 14488)
@@ -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-gviz/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/source/format (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/source/format 2013-08-22 16:10:42 UTC (rev 14488)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/upstream
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/upstream (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/upstream 2013-08-22 16:10:42 UTC (rev 14488)
@@ -0,0 +1,12 @@
+Reference:
+ Author: Michael Lawrence and Robert Gentleman and "Vincent Carey
+ Title: "rtracklayer: an R package for interfacing with genome browsers"
+ Journal: Bioinformatics
+ Year: 2009
+ Volume: 25
+ Number: 14
+ Pages: 1841-1842
+ DOI: 10.1093/bioinformatics/btp328
+ PMID: 19468054
+ URL: http://bioinformatics.oxfordjournals.org/content/25/14/1841.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/25/14/1841.full.pdf+html
Added: trunk/packages/R/r-bioc-gviz/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/watch 2013-08-22 16:10:42 UTC (rev 14488)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+ http://www.bioconductor.org/packages/release/bioc/html/Gviz.html .*/Gviz_([\d\.]+)\.tar\.gz
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