Author: manuel Date: 2012-05-20 17:35:42 +0000 (Sun, 20 May 2012) New Revision: 10914
Added: trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch Removed: trunk/packages/pdb2pqr/trunk/debian/propka.docs Modified: trunk/packages/pdb2pqr/trunk/debian/changelog trunk/packages/pdb2pqr/trunk/debian/control trunk/packages/pdb2pqr/trunk/debian/patches/series trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install trunk/packages/pdb2pqr/trunk/debian/propka.dirs trunk/packages/pdb2pqr/trunk/debian/propka.install trunk/packages/pdb2pqr/trunk/debian/rules Log: Updated package to new upstream version Modified: trunk/packages/pdb2pqr/trunk/debian/changelog =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/changelog 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/changelog 2012-05-20 17:35:42 UTC (rev 10914) @@ -7,6 +7,10 @@ * New upstream version * Updated Standards-Version to 3.9.3. No changes needed. * Changed Maintainer to Debian Med team. + * Pass -fPIC to CXXFLAGS. Thanks to Konstantinos Margaritis for the patch! + Closes: 654240. LP: 935357. + * Updated PROPKA packaging to new version. (It's written in Python now.) + * Added fix-hashbangs.patch. -- Andreas Tille <[email protected]> Wed, 16 May 2012 09:32:56 +0200 Modified: trunk/packages/pdb2pqr/trunk/debian/control =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/control 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/control 2012-05-20 17:35:42 UTC (rev 10914) @@ -9,7 +9,7 @@ python-support, python-dev, python-numpy, autoconf, automake, libtool, autotools-dev Standards-Version: 3.9.3 -XS-Python-Version: 2.6 +XS-Python-Version: 2.7 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/pdb2pqr/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/pdb2pqr/trunk/ Homepage: http://pdb2pqr.poissonboltzmann.org/pdb2pqr/ @@ -42,8 +42,9 @@ on larger clusters. Package: propka +XB-Python-Version: ${python:Versions} Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends} Suggests: pdb2pqr Description: Modify the protonation state of protein structures PropKa is a tool to modify the protonation state of a protein structure Added: trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch (rev 0) +++ trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch 2012-05-20 17:35:42 UTC (rev 10914) @@ -0,0 +1,24 @@ +--- pdb2pqr-1.8.repack.orig/pdb2pka/inputgen_pKa.py ++++ pdb2pqr-1.8.repack/pdb2pka/inputgen_pKa.py +@@ -1,4 +1,4 @@ +-#!/bin/env python ++#!/usr/bin/python + # + # $Id: inputgen_pKa.py 974 2011-06-30 14:58:03Z jens_nielsen $ + # +--- pdb2pqr-1.8.repack.orig/propka30/Source/corresponding_atoms.py ++++ pdb2pqr-1.8.repack/propka30/Source/corresponding_atoms.py +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/python3.0 ++#!/usr/bin/python + + # + # * This library is free software; you can redistribute it and/or +--- pdb2pqr-1.8.repack.orig/propka30/Source/rotate.py ++++ pdb2pqr-1.8.repack/propka30/Source/rotate.py +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/python3.0 ++#!/usr/bin/python + # + # * This library is free software; you can redistribute it and/or + # * modify it under the terms of the GNU Lesser General Public Modified: trunk/packages/pdb2pqr/trunk/debian/patches/series =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/patches/series 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/patches/series 2012-05-20 17:35:42 UTC (rev 10914) @@ -1 +1,2 @@ fix-includes.patch +fix-hashbangs.patch Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs 2012-05-20 17:35:42 UTC (rev 10914) @@ -1,6 +1,5 @@ /usr/bin /usr/lib/pdb2pqr/pdb2pka/substruct -/usr/lib/pdb2pqr/propka /usr/share/doc/pdb2pqr /usr/share/man/man1 /usr/share/pdb2pqr/dat Modified: trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install 2012-05-20 17:35:42 UTC (rev 10914) @@ -7,8 +7,6 @@ pdb2pka/*.py usr/share/pdb2pqr/pdb2pka pdb2pka/ligandclean/*.py usr/share/pdb2pqr/pdb2pka/ligandclean pdb2pka/substruct/*.py usr/share/pdb2pqr/pdb2pka/substruct -propka/*.py usr/share/pdb2pqr/propka # Binary parts pdb2pka/_pMC_mult.so usr/lib/pdb2pqr/pdb2pka pdb2pka/substruct/Algorithms.so usr/lib/pdb2pqr/pdb2pka/substruct -propka/_propkalib.so usr/lib/pdb2pqr/propka Modified: trunk/packages/pdb2pqr/trunk/debian/propka.dirs =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/propka.dirs 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/propka.dirs 2012-05-20 17:35:42 UTC (rev 10914) @@ -1 +1,2 @@ /usr/bin +/usr/share/propka Deleted: trunk/packages/pdb2pqr/trunk/debian/propka.docs =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/propka.docs 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/propka.docs 2012-05-20 17:35:42 UTC (rev 10914) @@ -1,4 +0,0 @@ -propka/AUTHORS -propka/ChangeLog -propka/NEWS -propka/README Modified: trunk/packages/pdb2pqr/trunk/debian/propka.install =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/propka.install 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/propka.install 2012-05-20 17:35:42 UTC (rev 10914) @@ -1 +1 @@ -propka/propka usr/bin +propka30/* usr/share/propka Modified: trunk/packages/pdb2pqr/trunk/debian/rules =================================================================== --- trunk/packages/pdb2pqr/trunk/debian/rules 2012-05-20 17:03:42 UTC (rev 10913) +++ trunk/packages/pdb2pqr/trunk/debian/rules 2012-05-20 17:35:42 UTC (rev 10914) @@ -5,19 +5,33 @@ VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }') UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//') +# Compile with -fPIC on all platforms (fix for #636204, #654240) +CFLAGS = $(shell dpkg-buildflags --get CFLAGS) -fPIC -I/usr/share/pyshared/numpy/core/include/numpy +CXXFLAGS = $(shell dpkg-buildflags --get CXXFLAGS) -fPIC -I/usr/share/pyshared/numpy/core/include/numpy +FFLAGS = $(shell dpkg-buildflags --get FFLAGS) -fPIC + %: dh $@ -# Compile with -fPIC on all platforms (fix for #636204) +override_dh_auto_clean: + ( cd pdb2pka && \ + if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \ + if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi ) + dh_auto_clean + override_dh_auto_configure: - dh_auto_configure -- CFLAGS="$(dpkg-buildflags --get CFLAGS) -fPIC" FFLAGS="$(dpkg-buildflags --get FFLAGS) -fPIC" + dh_auto_configure -- CFLAGS="$(CFLAGS)" CXXFLAGS="$(CXXFLAGS)" FFLAGS="$(FFLAGS)" + ( cd pdb2pka && \ + cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \ + cp -a pMC_mult.py pMC_mult.py.saved && \ + swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i ) # 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 +### 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 \ @@ -25,11 +39,16 @@ >debian/pdb2pqr/usr/bin/$$(basename $${app} .py) && \ chmod 0755 debian/pdb2pqr/usr/bin/$$(basename $${app} .py); \ done + for app in usr/share/propka/propka.py; do \ + sed -e "s,@SCRIPT@,$${app}," debian/wrapper.sh \ + >debian/propka/usr/bin/$$(basename $${app} .py) && \ + chmod 0755 debian/propka/usr/bin/$$(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 +# dh_auto_install override_dh_fixperms: dh_fixperms _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
