[med-svn] r7599 - in trunk/packages/pdb2pqr/tags: . 1.7-2/debian

Manuel Prinz manuel at alioth.debian.org
Tue Aug 30 22:29:32 UTC 2011


Author: manuel
Date: 2011-08-30 22:29:31 +0000 (Tue, 30 Aug 2011)
New Revision: 7599

Added:
   trunk/packages/pdb2pqr/tags/1.7-2/
   trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog
   trunk/packages/pdb2pqr/tags/1.7-2/debian/control
   trunk/packages/pdb2pqr/tags/1.7-2/debian/rules
Removed:
   trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog
   trunk/packages/pdb2pqr/tags/1.7-2/debian/control
   trunk/packages/pdb2pqr/tags/1.7-2/debian/rules
Log:
[svn-buildpackage] Tagging pdb2pqr 1.7-2

Deleted: trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog	2011-08-26 13:24:12 UTC (rev 7556)
+++ trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog	2011-08-30 22:29:31 UTC (rev 7599)
@@ -1,5 +0,0 @@
-pdb2pqr (1.7-1) unstable; urgency=low
-
-  * New upstream release. Closes: #416269, #420734.
-
- -- Manuel Prinz <manuel at debian.org>  Sun, 30 Jan 2011 11:53:54 +0100

Copied: trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog (from rev 7598, trunk/packages/pdb2pqr/trunk/debian/changelog)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog	                        (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.7-2/debian/changelog	2011-08-30 22:29:31 UTC (rev 7599)
@@ -0,0 +1,12 @@
+pdb2pqr (1.7-2) unstable; urgency=low
+
+  * Pass -fPIC to compiler on all architectures. Closes: 636204. LP: 791313.
+  * Bumped Standards-Version to 3.9.2. No changes needed.
+
+ -- Manuel Prinz <manuel at debian.org>  Wed, 31 Aug 2011 00:22:15 +0200
+
+pdb2pqr (1.7-1) unstable; urgency=low
+
+  * New upstream release. Closes: #416269, #420734.
+
+ -- Manuel Prinz <manuel at debian.org>  Sun, 30 Jan 2011 11:53:54 +0100

Deleted: trunk/packages/pdb2pqr/tags/1.7-2/debian/control
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/control	2011-08-26 13:24:12 UTC (rev 7556)
+++ trunk/packages/pdb2pqr/tags/1.7-2/debian/control	2011-08-30 22:29:31 UTC (rev 7599)
@@ -1,56 +0,0 @@
-Source: pdb2pqr
-Section: science
-Priority: optional
-Maintainer: DebiChem Team <debichem-devel at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>, Manuel Prinz <manuel at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.0.50~), gfortran, swig, xmlto, openbabel,
- python-support, python-dev, python-numpy,
- autoconf, automake, libtool, autotools-dev
-Standards-Version: 3.9.1
-XS-Python-Version: 2.6
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pdb2pqr/trunk/
-Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/
-
-Package: pdb2pqr
-XB-Python-Version: ${python:Versions}
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy
-Suggests: apbs
-Enhances: autodocktools
-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.
- 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-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends}
-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.
-
-Package: propka
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: pdb2pqr
-Description: Modify the protonation state of protein structures
- PropKa is a tool to modify the protonation state of a protein structure
- in the Protein Data Bank (PDB) format to match a given pKa value.
- It can also be used to refine NMR structures, which often yield 
- inaccurate pKa values for some residues.
- .
- The PROPKA method is described in Hui Li, Andrew D. Robertson, and
- Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of 
- Protein pKa Values" Proteins, 2005, 61, 704-721

Copied: trunk/packages/pdb2pqr/tags/1.7-2/debian/control (from rev 7597, trunk/packages/pdb2pqr/trunk/debian/control)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.7-2/debian/control	                        (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.7-2/debian/control	2011-08-30 22:29:31 UTC (rev 7599)
@@ -0,0 +1,56 @@
+Source: pdb2pqr
+Section: science
+Priority: optional
+Maintainer: DebiChem Team <debichem-devel at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>, Manuel Prinz <manuel at debian.org>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), gfortran, swig, xmlto, openbabel,
+ python-support, python-dev, python-numpy,
+ autoconf, automake, libtool, autotools-dev
+Standards-Version: 3.9.2
+XS-Python-Version: 2.6
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/pdb2pqr/trunk/
+Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/
+
+Package: pdb2pqr
+XB-Python-Version: ${python:Versions}
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy
+Suggests: apbs
+Enhances: autodocktools
+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.
+ 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-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+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.
+
+Package: propka
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: pdb2pqr
+Description: Modify the protonation state of protein structures
+ PropKa is a tool to modify the protonation state of a protein structure
+ in the Protein Data Bank (PDB) format to match a given pKa value.
+ It can also be used to refine NMR structures, which often yield 
+ inaccurate pKa values for some residues.
+ .
+ The PROPKA method is described in Hui Li, Andrew D. Robertson, and
+ Jan H. Jensen "Very Fast Empirical Prediction and Interpretation of 
+ Protein pKa Values" Proteins, 2005, 61, 704-721

Deleted: trunk/packages/pdb2pqr/tags/1.7-2/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules	2011-08-26 13:24:12 UTC (rev 7556)
+++ trunk/packages/pdb2pqr/tags/1.7-2/debian/rules	2011-08-30 22:29:31 UTC (rev 7599)
@@ -1,49 +0,0 @@
-#!/usr/bin/make -f
-# -*- mode: makefile; coding: utf-8 -*-
-
-PACKAGE  := $(firstword $(shell dh_listpackages))
-VERSION  := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }')
-UPSTREAM := $(shell echo "$(VERSION)"   | sed 's/-.\+$$//')
-
-%:
-	dh $@
-
-# Disable tests, as they need an internet connection to download files
-override_dh_auto_test:
-
-override_dh_auto_install:
-# Fix !#/bin/env shebang: substitute with #!/usr/bin/python
-	sed -i -e '1c#!/usr/bin/python' pdb2pka/inputgen_pKa.py
-# Install Debian-provided stuff
-#   Install wrappers
-	for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \
-		sed -e "s, at SCRIPT@,$${app}," debian/wrapper.sh \
-			>debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \
-		chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \
-	done
-#   Install man pages
-	xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
-	xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml
-	xmlto -o debian/propka/usr/share/man/man1/  man debian/propka.1.xml
-	dh_auto_install
-
-override_dh_fixperms:
-	dh_fixperms
-	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py
-	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py
-	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
-	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py
-	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
-	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
-
-.PHONY: get-orig-source
-get-orig-source:
-	rm -rf get-orig-source
-	mkdir -p get-orig-source
-	uscan --no-conf --no-symlink --force-download --download-current-version --destdir=get-orig-source
-	tar xzf get-orig-source/$(PACKAGE)-$(UPSTREAM).tar.gz -C get-orig-source \
-		--exclude="contrib" \
-		--exclude="jmol"
-	mv get-orig-source/$(PACKAGE)-$(UPSTREAM) get-orig-source/$(PACKAGE)-$(UPSTREAM).repack
-	GZIP='--best --no-name' tar czf ../$(PACKAGE)_$(UPSTREAM).orig.tar.gz -C get-orig-source $(PACKAGE)-$(UPSTREAM).repack
-	rm -rf get-orig-source

Copied: trunk/packages/pdb2pqr/tags/1.7-2/debian/rules (from rev 7596, trunk/packages/pdb2pqr/trunk/debian/rules)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.7-2/debian/rules	                        (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.7-2/debian/rules	2011-08-30 22:29:31 UTC (rev 7599)
@@ -0,0 +1,53 @@
+#!/usr/bin/make -f
+# -*- mode: makefile; coding: utf-8 -*-
+
+PACKAGE  := $(firstword $(shell dh_listpackages))
+VERSION  := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }')
+UPSTREAM := $(shell echo "$(VERSION)"   | sed 's/-.\+$$//')
+
+%:
+	dh $@
+
+# Compile with -fPIC on all platforms (fix for #636204)
+override_dh_auto_configure:
+	dh_auto_configure -- CFLAGS="$(dpkg-buildflags --get CFLAGS) -fPIC" FFLAGS="$(dpkg-buildflags --get FFLAGS) -fPIC"
+
+# Disable tests, as they need an internet connection to download files
+override_dh_auto_test:
+
+override_dh_auto_install:
+# Fix !#/bin/env shebang: substitute with #!/usr/bin/python
+	sed -i -e '1c#!/usr/bin/python' pdb2pka/inputgen_pKa.py
+# Install Debian-provided stuff
+#   Install wrappers
+	for app in /usr/share/pdb2pqr/pdb2pqr.py /usr/share/pdb2pqr/src/psize.py; do \
+		sed -e "s, at SCRIPT@,$${app}," debian/wrapper.sh \
+			>debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \
+		chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \
+	done
+#   Install man pages
+	xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
+	xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml
+	xmlto -o debian/propka/usr/share/man/man1/  man debian/propka.1.xml
+	dh_auto_install
+
+override_dh_fixperms:
+	dh_fixperms
+	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py
+	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py
+	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
+	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py
+	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
+	chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
+
+.PHONY: get-orig-source
+get-orig-source:
+	rm -rf get-orig-source
+	mkdir -p get-orig-source
+	uscan --no-conf --no-symlink --force-download --download-current-version --destdir=get-orig-source
+	tar xzf get-orig-source/$(PACKAGE)-$(UPSTREAM).tar.gz -C get-orig-source \
+		--exclude="contrib" \
+		--exclude="jmol"
+	mv get-orig-source/$(PACKAGE)-$(UPSTREAM) get-orig-source/$(PACKAGE)-$(UPSTREAM).repack
+	GZIP='--best --no-name' tar czf ../$(PACKAGE)_$(UPSTREAM).orig.tar.gz -C get-orig-source $(PACKAGE)-$(UPSTREAM).repack
+	rm -rf get-orig-source




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