[med-svn] r14484 - in trunk/packages/R: . r-bioc-rtracklayer r-bioc-rtracklayer/trunk r-bioc-rtracklayer/trunk/debian r-bioc-rtracklayer/trunk/debian/source
Andreas Tille
tille at alioth.debian.org
Thu Aug 22 12:42:09 UTC 2013
Author: tille
Date: 2013-08-22 12:42:08 +0000 (Thu, 22 Aug 2013)
New Revision: 14484
Added:
trunk/packages/R/r-bioc-rtracklayer/
trunk/packages/R/r-bioc-rtracklayer/trunk/
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/README.test
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/compat
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/source/
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/source/format
trunk/packages/R/r-bioc-rtracklayer/trunk/debian/watch
Log:
Inject some inclomplete packaging with incomplete copyright and missing BUild-Depoends
Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/README.test (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/README.test 2013-08-22 12:42:08 UTC (rev 14484)
@@ -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-rtracklayer/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/changelog 2013-08-22 12:42:08 UTC (rev 14484)
@@ -0,0 +1,5 @@
+r-bioc-rtracklayer (1.20.4-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???).
+
+ -- Andreas Tille <tille at debian.org> Thu, 22 Aug 2013 14:01:29 +0200
Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/compat (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/compat 2013-08-22 12:42:08 UTC (rev 14484)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/control 2013-08-22 12:42:08 UTC (rev 14484)
@@ -0,0 +1,25 @@
+Source: r-bioc-rtracklayer
+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
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rtracklayer/trunk/
+Homepage: http://bioconductor.org/packages/2.12/bioc/html/rtracklayer.html
+
+Package: r-bioc-rtracklayer
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends}
+Description: GNU R interface to genome browsers and their annotation tracks
+ Extensible framework for interacting with multiple genome browsers
+ (currently UCSC built-in) and manipulating annotation tracks in various
+ formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+ built-in). The user may export/import tracks to/from the supported
+ browsers, as well as query and modify the browser state, such as the
+ current viewport.
+
Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/copyright 2013-08-22 12:42:08 UTC (rev 14484)
@@ -0,0 +1,110 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: rtracklayer
+Upstream-Contact: Michael Lawrence <michafla at gene.com>
+Source: http://bioconductor.org/packages/2.12/bioc/html/rtracklayer.html
+
+Files: *
+Copyright: © 2006-2013 Michael Lawrence, Vince Carey, Robert Gentleman
+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.
+
+ The End
Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/rules 2013-08-22 12:42:08 UTC (rev 14484)
@@ -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-rtracklayer/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/source/format (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/source/format 2013-08-22 12:42:08 UTC (rev 14484)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/R/r-bioc-rtracklayer/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-rtracklayer/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-bioc-rtracklayer/trunk/debian/watch 2013-08-22 12:42:08 UTC (rev 14484)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+ http://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html .*/rtracklayer_([\d\.]+)\.tar\.gz
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