[med-svn] r2328 - in trunk/packages/R: . r-other-bio3d r-other-bio3d/trunk r-other-bio3d/trunk/debian

Sat Jul 26 17:22:18 UTC 2008

Author: smoe-guest
Date: 2008-07-26 17:22:18 +0000 (Sat, 26 Jul 2008)
New Revision: 2328

Added:
   trunk/packages/R/r-other-bio3d/
   trunk/packages/R/r-other-bio3d/trunk/
   trunk/packages/R/r-other-bio3d/trunk/debian/
   trunk/packages/R/r-other-bio3d/trunk/debian/README.Debian
   trunk/packages/R/r-other-bio3d/trunk/debian/changelog
   trunk/packages/R/r-other-bio3d/trunk/debian/compat
   trunk/packages/R/r-other-bio3d/trunk/debian/control
   trunk/packages/R/r-other-bio3d/trunk/debian/copyright
   trunk/packages/R/r-other-bio3d/trunk/debian/files
   trunk/packages/R/r-other-bio3d/trunk/debian/rules
   trunk/packages/R/r-other-bio3d/trunk/debian/watch
Log:
Found this excellent package for protein structure visualisation and analysis in R. Amazing.


Added: trunk/packages/R/r-other-bio3d/trunk/debian/README.Debian
===================================================================

--- trunk/packages/R/r-other-bio3d/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/README.Debian	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1,14 @@
+... and I always thought that R would not be good for protein structure
+analysis. This fine work has completely escaped my routine scanning,
+albeit being properly published in bioinformatics. Let this Debian
+packaging help its dissemination a bit.
+
+When using the package, please cite
+
+	 Bio3D: An R package for the comparative analysis of protein
+	 structures.  Grant, Rodrigues, ElSawy, McCammon, Caves, (2006)
+	 Bioinformatics 22, 2695-2696
+
+in your publications.
+
+-- Steffen Moeller <moeller at debian.org>  Sat, 26 Jul 2008 19:19:11 +0200

Added: trunk/packages/R/r-other-bio3d/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/changelog	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1,5 @@
+r-other-bio3d (1.0-5-1) unstable; urgency=low
+
+  * Initial release.
+
+ -- Steffen Moeller <moeller at debian.org>  Sat, 26 Jul 2008 19:08:08 +0200

Added: trunk/packages/R/r-other-bio3d/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/compat	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1 @@
+5

Added: trunk/packages/R/r-other-bio3d/trunk/debian/control
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/control	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/control	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1,24 @@
+Source: r-other-bio3d
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Uploaders: Dirk Eddelbuettel <edd at debian.org>
+Build-Depends: debhelper (>> 5), cdbs, r-base-dev (>= 2.7.1)
+Standards-Version: 3.8.0
+Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/
+
+Package: r-other-bio3d
+Architecture: all
+Depends: ${shlibs:Depends}, r-base-core (>= 2.7.1)
+Suggests: r-cran-ncdf
+Description: GNU R package for biological structure analysis
+ The bio3d package contains utilities to process, organize and explore
+ protein structure, sequence and dynamics data.  Features include the
+ ability to read and write structure, sequence and dynamic trajectory
+ data, perform atom summaries, atom selection, re-orientation,
+ superposition, rigid core identification, clustering, torsion analysis,
+ distance matrix analysis, structure and sequence conservation analysis,
+ and principal component analysis (PCA).  In addition, various utility
+ functions are provided to enable the statistical and graphical power of
+ the R environment to work with biological sequence and structural data.
+ Please refer to the Url below for more information.

Added: trunk/packages/R/r-other-bio3d/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/copyright	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1,18 @@
+This is the Debian GNU/Linux r-other-bio3d package of the R library
+bio3d, performing statistical analyses and graphical visualisations
+on protein structures.  Bio3d is written and maintained by Barry
+Grant <bgrant at mccammon.ucsd.edu>. He owns the copyright 2006-2008 and
+distributes bio3d under the terms of the GNU Public License version 2
+or later.
+
+This package was created by Steffen Moeller <moeller at debian.org>, based on
+work for the r-cran-rodbc package of Dirk Eddelbuettel <edd at debian.org>.
+
+The sources were downloaded from http://mccammon.ucsd.edu/~bgrant/bio3d.
+
+The package was renamed from its upstream name 'bio3d' to 'r-other-bio3d'
+to highlight the fact that is it a package for R and in neither of the
+CRAN, OmegaHat or the BioConductor archives.
+
+On a Debian GNU/Linux system, the GPL license is included in the file
+/usr/share/common-licenses/GPL.

Added: trunk/packages/R/r-other-bio3d/trunk/debian/files
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/files	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/files	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1 @@
+r-other-bio3d_1.0-5-1_all.deb science optional

Added: trunk/packages/R/r-other-bio3d/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/rules	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+# 							-*- makefile -*-
+# debian/rules file for the Debian/GNU Linux r-cran-qtl package
+# Copyright 2003-2006 by Dirk Eddelbuettel <edd at debian.org>
+
+debRreposname := other
+include /usr/share/R/debian/r-cran.mk


Property changes on: trunk/packages/R/r-other-bio3d/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/R/r-other-bio3d/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/watch	2008-07-26 17:22:18 UTC (rev 2328)
@@ -0,0 +1,3 @@
+version=3
+http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_(.*).tar.gz
+


