[med-svn] r1991 - in trunk/packages/pdb2pqr/trunk/debian: . patches

smoe-guest at alioth.debian.org smoe-guest at alioth.debian.org
Sun Jun 8 15:41:54 UTC 2008


Author: smoe-guest
Date: 2008-06-08 15:41:53 +0000 (Sun, 08 Jun 2008)
New Revision: 1991

Added:
   trunk/packages/pdb2pqr/trunk/debian/patches/
   trunk/packages/pdb2pqr/trunk/debian/patches/build-gcc-4.3.patch
   trunk/packages/pdb2pqr/trunk/debian/patches/series
   trunk/packages/pdb2pqr/trunk/debian/pdb2pqr-examples.examples
Removed:
   trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.examples
Modified:
   trunk/packages/pdb2pqr/trunk/debian/README.Debian
   trunk/packages/pdb2pqr/trunk/debian/changelog
   trunk/packages/pdb2pqr/trunk/debian/control
   trunk/packages/pdb2pqr/trunk/debian/copyright
   trunk/packages/pdb2pqr/trunk/debian/rules
Log:
* separate package for examples (needs some optimisation to
  install into /usr/share/doc/pdb2pqr/examples
* patches for gcc-4.3 compatibility
* introduced quilt
* Rewriting of debian/README.Debian


Modified: trunk/packages/pdb2pqr/trunk/debian/README.Debian
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian	2008-06-06 09:58:19 UTC (rev 1990)
+++ trunk/packages/pdb2pqr/trunk/debian/README.Debian	2008-06-08 15:41:53 UTC (rev 1991)
@@ -1,13 +1,16 @@
-The packaging of PDB2PQR was stimulated by the AutoDockTools
-and their dependency on it to visualise properties of the
-protein. And yes, if you have interest in this package, please
-help with completing the packaging.
+Two Debian developers have met to work the packaging of PDB2PQR for
+their favorite Linux distribution. For one, the packaging of PDB2PQR was
+stimulated by his packaging of the AutoDockTools and their dependency
+on it to visualise properties of the protein. The other uses PDB2PQR
+for his mostly day-time profession.
 
-Upstream does not seem to have prepared the installation of
-their work into distinct directories. No time was yet allocated to
-address this.
-
 The code to offer pdb2pqr as a web service was omitted. The extensions
 directory was added as a documentation.
 
- -- Steffen Moeller  Fri, 23 May 2008 14:58:07 +0200
+The adv-tests of the build process are not performed to allow the
+build-process to be executed offline. This would be required for
+compliance with the DFSG. The regular build process fetches a protein
+structure from PDB and one should instread probably better provide a patch 
+that uses a structure from the examples directory directly.
+
+ -- Steffen Moeller and Manuel Prinz  Sat, 07 Jun 2008 22:02:05 +0200

Modified: trunk/packages/pdb2pqr/trunk/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog	2008-06-06 09:58:19 UTC (rev 1990)
+++ trunk/packages/pdb2pqr/trunk/debian/changelog	2008-06-08 15:41:53 UTC (rev 1991)
@@ -1,3 +1,18 @@
+pdb2pqr (1.3.0-2) UNRELEASED; urgency=low
+
+  [ Steffen ]
+  * First upload to 'unstable'
+  * Introduced quilt patch system for compatibility with gcc-4.3
+  * Disabled adv-tests to allow package build process without
+    internet access.
+
+  [ Manuel ]
+  * Various improvements for lintian-cleanliness and beyond
+    - wrote man pages
+    - package names as prefix in debian/*
+
+ -- Manuel Prinz <debian at pinguinkiste.de>  Sat, 07 Jun 2008 22:03:19 +0200
+
 pdb2pqr (1.3.0-1) experimental; urgency=low
 
   * Initial release (Closes: #416269)

Modified: trunk/packages/pdb2pqr/trunk/debian/control
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/control	2008-06-06 09:58:19 UTC (rev 1990)
+++ trunk/packages/pdb2pqr/trunk/debian/control	2008-06-08 15:41:53 UTC (rev 1991)
@@ -1,10 +1,10 @@
 Source: pdb2pqr
-Section: non-free/science
+Section: science
 Priority: optional
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Steffen Moeller <moeller at debian.org>, Manuel Prinz <debian at pinguinkiste.de>
-Build-Depends: debhelper (>= 5.0.38), python-central (>= 0.5.6), cdbs (>= 0.4.49), python-all-dev (>= 2.3.5-11), swig, python-numpy, gfortran, autotools-dev
+Build-Depends: debhelper (>= 5.0.38), python-central (>= 0.5.6), cdbs (>= 0.4.49), python-all-dev (>= 2.3.5-11), swig, python-numpy, gfortran, autotools-dev, quilt
 Standards-Version: 3.7.3
 XS-Python-Version: 2.5
 XS-Autobuild: yes
@@ -19,11 +19,19 @@
 Suggests: apbs
 Description: Preparation of protein structures for electrostatics calculations
  PDB2PQR is a Python software package that automates many of the common
- tasks of preparing structures for continuum electrostatics calculations,
- providing a platform-independent utility for converting protein files
+ tasks of preparing structures for continuum electrostatics calculations.
+ It thus provides a platform-independent utility for converting protein files
  in PDB format to PQR format. These tasks include:
   * Adding a limited number of missing heavy atoms to biomolecular structures
   * Determining side-chain pKas
   * Placing missing hydrogens
   * Optimizing the protein for favorable hydrogen bonding
   * Assigning charge and radius parameters from a variety of force fields
+
+Package: pdb2pqr-examples
+Architecture: any
+Recommends: pdb2pqr
+Description: example files accompanying pdb2pqr
+ Files containing protein structures tend to become large very quickly and
+ most users of this package will refrain from their installation, particularly
+ on larger clusters.

Modified: trunk/packages/pdb2pqr/trunk/debian/copyright
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/copyright	2008-06-06 09:58:19 UTC (rev 1990)
+++ trunk/packages/pdb2pqr/trunk/debian/copyright	2008-06-08 15:41:53 UTC (rev 1991)
@@ -84,5 +84,6 @@
 	NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 	SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-The Debian packaging is (C) 2007, Steffen Moeller <moeller at debian.org> and
-is licensed under the GPL, see `/usr/share/common-licenses/GPL'.
+The Debian packaging is (C) 2007, Manuel Prinz <debian at pinguinkiste.de>
+and Steffen Moeller <moeller at debian.org> and is licensed under the GPL,
+see `/usr/share/common-licenses/GPL'.

Added: trunk/packages/pdb2pqr/trunk/debian/patches/build-gcc-4.3.patch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/build-gcc-4.3.patch	                        (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/build-gcc-4.3.patch	2008-06-08 15:41:53 UTC (rev 1991)
@@ -0,0 +1,10 @@
+--- pdb2pqr-1.3.0.orig/pdb2pka/pMC_mult.h
++++ pdb2pqr-1.3.0/pdb2pka/pMC_mult.h
+@@ -8,6 +8,7 @@
+ 
+ #include <string>
+ #include <vector>
++#include <stdlib.h>
+ #include <math.h>
+ #include <time.h>
+ 

Added: trunk/packages/pdb2pqr/trunk/debian/patches/series
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/patches/series	2008-06-08 15:41:53 UTC (rev 1991)
@@ -0,0 +1 @@
+build-gcc-4.3.patch

Copied: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr-examples.examples (from rev 1990, trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.examples)
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr-examples.examples	                        (rev 0)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr-examples.examples	2008-06-08 15:41:53 UTC (rev 1991)
@@ -0,0 +1 @@
+examples/*

Deleted: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.examples
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.examples	2008-06-06 09:58:19 UTC (rev 1990)
+++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.examples	2008-06-08 15:41:53 UTC (rev 1991)
@@ -1 +0,0 @@
-examples/*

Modified: trunk/packages/pdb2pqr/trunk/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules	2008-06-06 09:58:19 UTC (rev 1990)
+++ trunk/packages/pdb2pqr/trunk/debian/rules	2008-06-08 15:41:53 UTC (rev 1991)
@@ -3,9 +3,12 @@
 
 include /usr/share/cdbs/1/class/autotools.mk
 include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
 
 # Enable checks
-DEB_MAKE_CHECK_TARGET = test adv-test
+#DEB_MAKE_CHECK_TARGET = test adv-test
+# adv-test demands outgoing internet access, which may not be available
+DEB_MAKE_CHECK_TARGET = test
 
 # Do not execute "install" target. We'll take care of that since
 # upstream's build system installs *everything* to $prefix (if set)




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