[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
More information about the debian-med-commit
mailing list