[med-svn] r4239 - trunk/packages/R/r-other-bio3d/trunk/debian

Charles Plessy plessy at alioth.debian.org
Thu Oct 22 04:26:23 UTC 2009 

Author: plessy
Date: 2009-10-22 04:26:22 +0000 (Thu, 22 Oct 2009)
New Revision: 4239

Added:
   trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml
Removed:
   trunk/packages/R/r-other-bio3d/trunk/debian/files
Modified:
   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/watch
Log:
New upstream release, and package refreshing.

  * Mended debian/watch thanks to Yan Morin (Closes: #551414).
  * Conforms to Policy 3.8.3:
    - Changed section to gnu-r (debian/control).
    - Added VCS fields (debian/control).
    - Incremented Standards-Version (debian/control).
  * Switched to Debhelper 7 (debian/control, debian/compat).
  * Depend on ${misc:Depends}, not on ${shlibs:Depends} (debian/compat).
  * Added myself to Uploaders (debian/control).
  * Added various upstream informations in debian/upstream-metadata.yaml.
  * Deleted debian/files, not needed.
  * Converted debian/copyright to experimental machine-readable format.


Modified: trunk/packages/R/r-other-bio3d/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/changelog	2009-10-22 01:20:40 UTC (rev 4238)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/changelog	2009-10-22 04:26:22 UTC (rev 4239)
@@ -1,3 +1,20 @@
+r-other-bio3d (1.0-6-1) unstable; urgency=low
+
+  * New upstream release.
+  * Mended debian/watch thanks to Yan Morin (Closes: #551414).
+  * Conforms to Policy 3.8.3:
+    - Changed section to gnu-r (debian/control).
+    - Added VCS fields (debian/control).
+    - Incremented Standards-Version (debian/control).
+  * Switched to Debhelper 7 (debian/control, debian/compat).
+  * Depend on ${misc:Depends}, not on ${shlibs:Depends} (debian/compat).
+  * Added myself to Uploaders (debian/control).
+  * Added various upstream informations in debian/upstream-metadata.yaml.
+  * Deleted debian/files, not needed.
+  * Converted debian/copyright to experimental machine-readable format.
+
+ -- Charles Plessy <plessy at debian.org>  Thu, 22 Oct 2009 13:07:32 +0900
+
 r-other-bio3d (1.0-5-1.1) unstable; urgency=low
 
   * Non-maintainer upload

Modified: trunk/packages/R/r-other-bio3d/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/compat	2009-10-22 01:20:40 UTC (rev 4238)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/compat	2009-10-22 04:26:22 UTC (rev 4239)
@@ -1 +1 @@
-5
+7

Modified: trunk/packages/R/r-other-bio3d/trunk/debian/control
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/control	2009-10-22 01:20:40 UTC (rev 4238)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/control	2009-10-22 04:26:22 UTC (rev 4239)
@@ -1,15 +1,17 @@
 Source: r-other-bio3d
-Section: science
+Section: gnu-r
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>> 5), cdbs, r-base-dev (>= 2.7.1)
-Standards-Version: 3.8.0
+Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <plessy at debian.org>
+Build-Depends: debhelper (>> 7), cdbs, r-base-dev
+Standards-Version: 3.8.3
 Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-bio3d/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/R/r-other-bio3d/trunk/
 
 Package: r-other-bio3d
 Architecture: all
-Depends: ${shlibs:Depends}, r-base-core (>= 2.7.1)
+Depends: ${misc:Depends}
 Suggests: r-cran-ncdf, r-cran-rocr, mafft
 Description: GNU R package for biological structure analysis
  The bio3d package contains utilities to process, organize and explore

Modified: trunk/packages/R/r-other-bio3d/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/copyright	2009-10-22 01:20:40 UTC (rev 4238)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/copyright	2009-10-22 04:26:22 UTC (rev 4239)
@@ -1,18 +1,36 @@
-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.
+Name      :  Bio3D
+Contact   :  Barry Grant <bgrant at mccammon.ucsd.edu>
+Source    :  http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_1.0-6.tar.gz
 
+Copyright :  Barry Grant <bgrant at mccammon.ucsd.edu>
+License   :  GPL-2+
+    
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+On a Debian GNU/Linux system, the GPL license version 2 is included in the file
+‘/usr/share/common-licenses/GPL-2’.
+
+
+Files: debian/*
+Copyright: © 2008 Steffen Moeller <moeller at debian.org>
+           © 2009 Charles Plessy   <plessy at debian.org>
+License: GPL-2+
+
 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.

Deleted: trunk/packages/R/r-other-bio3d/trunk/debian/files
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/files	2009-10-22 01:20:40 UTC (rev 4238)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/files	2009-10-22 04:26:22 UTC (rev 4239)
@@ -1 +0,0 @@
-r-other-bio3d_1.0-5-1_all.deb science optional

Added: trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/upstream-metadata.yaml	2009-10-22 04:26:22 UTC (rev 4239)
@@ -0,0 +1,20 @@
+Contact: Barry Grant <bgrant at mccammon.ucsd.edu>
+DOI: 10.1093/bioinformatics/btl461
+Gallery: http://mccammon.ucsd.edu/~bgrant/bio3d/gallery/gallery.html
+Homepage: http://mccammon.ucsd.edu/~bgrant/bio3d/
+Name: Bio3D
+PubMed: 16940322
+Reference: |
+ @article{BarryJ. Grant11012006,
+ author = {Grant, Barry J. and Rodrigues, Ana P. C. and ElSawy, Karim M. and McCammon, J. Andrew and Caves, Leo S. D.},
+ title = {{Bio3d: an R package for the comparative analysis of protein structures}},
+ journal = {Bioinformatics},
+ volume = {22},
+ number = {21},
+ pages = {2695-2696},
+ doi = {10.1093/bioinformatics/btl461},
+ year = {2006},
+ URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/21/2695},
+ eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/22/21/2695.pdf}
+ }
+Wiki: http://bio3d.pbworks.com/

Modified: trunk/packages/R/r-other-bio3d/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-other-bio3d/trunk/debian/watch	2009-10-22 01:20:40 UTC (rev 4238)
+++ trunk/packages/R/r-other-bio3d/trunk/debian/watch	2009-10-22 04:26:22 UTC (rev 4239)
@@ -1,4 +1,3 @@
 version=3
-#http://mccammon.ucsd.edu/~bgrant/bio3d/download/download.html bio3d_(.*).tar.gz
-http://mccammon.ucsd.edu/~bgrant/bio3d/ bio3d_(.*).tar.gz
-#http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_(.*).tar.gz
+http://mccammon.ucsd.edu/~bgrant/bio3d/download/download.html \
+ http://mccammon.ucsd.edu/~bgrant/bio3d/bio3d_(.+)\.tar\.gz

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