[med-svn] r14501 - in trunk/packages/R: . r-bioc-affyio r-bioc-affyio/trunk r-bioc-affyio/trunk/debian r-bioc-affyio/trunk/debian/patches r-bioc-affyio/trunk/debian/source

Fri Aug 23 10:36:15 UTC 2013

Author: tille
Date: 2013-08-23 10:36:15 +0000 (Fri, 23 Aug 2013)
New Revision: 14501

Added:
   trunk/packages/R/r-bioc-affyio/
   trunk/packages/R/r-bioc-affyio/trunk/
   trunk/packages/R/r-bioc-affyio/trunk/debian/
   trunk/packages/R/r-bioc-affyio/trunk/debian/README.test
   trunk/packages/R/r-bioc-affyio/trunk/debian/changelog
   trunk/packages/R/r-bioc-affyio/trunk/debian/compat
   trunk/packages/R/r-bioc-affyio/trunk/debian/control
   trunk/packages/R/r-bioc-affyio/trunk/debian/copyright
   trunk/packages/R/r-bioc-affyio/trunk/debian/patches/
   trunk/packages/R/r-bioc-affyio/trunk/debian/patches/series
   trunk/packages/R/r-bioc-affyio/trunk/debian/patches/use_debian_packaged_zlib.patch
   trunk/packages/R/r-bioc-affyio/trunk/debian/rules
   trunk/packages/R/r-bioc-affyio/trunk/debian/source/
   trunk/packages/R/r-bioc-affyio/trunk/debian/source/format
   trunk/packages/R/r-bioc-affyio/trunk/debian/watch
Log:
Seems we have now reached somehow the bottom of BioConductor dependency tree - affyio ready for upload


Added: trunk/packages/R/r-bioc-affyio/trunk/debian/README.test
===================================================================

--- trunk/packages/R/r-bioc-affyio/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/README.test	2013-08-23 10:36:15 UTC (rev 14501)
@@ -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(affyio)’ in order to confirm its integrity.

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/changelog	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1,5 @@
+r-bioc-affyio (1.28.0-1) UNRELEASED; urgency=low
+
+  * Initial release (closes: #???)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 23 Aug 2013 12:11:49 +0200

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/compat	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1 @@
+9

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/control	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1,24 @@
+Source: r-bioc-affyio
+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,
+               zlib1g-dev,
+               r-base-dev
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-affyio/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-affyio/trunk/
+Homepage: http://bioconductor.org/packages/2.12/bioc/html/affyio.html
+
+Package: r-bioc-affyio
+Architecture: any
+Depends: ${R:Depends},
+         ${shlibs:Depends},
+         ${misc:Depends}
+Description: BioConductor tools for parsing Affymetrix data files
+ This BioConductor package provides routines for parsing Affymetrix data
+ files based upon file format information. Primary focus is on accessing
+ the CEL and CDF file formats.
+

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/copyright	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1,17 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: affyio
+Upstream-Contact: Benjamin Milo Bolstad <bmb at bmbolstad.com>
+Source: http://www.bioconductor.org/packages/2.12/bioc/html/affyio.html
+
+Files: *
+Copyright: © 2006-2013 Benjamin Milo Bolstad <bmb at bmbolstad.com>
+License: LGPL-2.1+
+
+Files: debian/*
+Copyright: 2013 Andreas Tille <tille at debian.org>
+License: LGPL-2.1+
+
+License: LGPL-2.1+
+ On Debian GNU/Linux system you can find the complete text of the
+ LGPL license in '/usr/share/common-licenses/LGPL-2.1'.
+

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/patches/series	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1 @@
+use_debian_packaged_zlib.patch

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/patches/use_debian_packaged_zlib.patch	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/patches/use_debian_packaged_zlib.patch	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1,22 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Fri, 23 Aug 2013 12:11:49 +0200
+Description: If the systems includes zlib natively there is no point in
+ requiring the import of zlibbioc
+
+--- a/NAMESPACE
++++ b/NAMESPACE
+@@ -1,4 +1,3 @@
+ exportPattern("^[^\\.]")
+ useDynLib("affyio")
+-import(zlibbioc)
+ 
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -4,7 +4,6 @@ Title: Tools for parsing Affymetrix data
+ Author: Benjamin Milo Bolstad <bmb at bmbolstad.com>
+ Maintainer: Benjamin Milo Bolstad <bmb at bmbolstad.com>
+ Depends: R (>= 2.6.0), methods
+-Imports: zlibbioc
+ Description: Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.
+ License: LGPL (>= 2)
+ biocViews: Microarray, DataImport, Infrastructure

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/rules	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk
+
+install/$(package)::
+	rm -rf debian/$(package)/usr/lib/R/site-library/$(cranName)/LICENSE


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

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/source/format	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/R/r-bioc-affyio/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-affyio/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/R/r-bioc-affyio/trunk/debian/watch	2013-08-23 10:36:15 UTC (rev 14501)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+ http://www.bioconductor.org/packages/release/bioc/html/affyio.html .*/affyio_([\d\.]+)\.tar\.gz


