[med-svn] r11422 - in trunk/packages/pdb2pqr/tags: . 1.8-1/debian 1.8-1/debian/patches
Manuel Prinz
manuel at alioth.debian.org
Thu Jun 21 15:34:53 UTC 2012
Author: manuel
Date: 2012-06-21 15:34:53 +0000 (Thu, 21 Jun 2012)
New Revision: 11422
Added:
trunk/packages/pdb2pqr/tags/1.8-1/
trunk/packages/pdb2pqr/tags/1.8-1/debian/README.Debian
trunk/packages/pdb2pqr/tags/1.8-1/debian/changelog
trunk/packages/pdb2pqr/tags/1.8-1/debian/compat
trunk/packages/pdb2pqr/tags/1.8-1/debian/control
trunk/packages/pdb2pqr/tags/1.8-1/debian/copyright
trunk/packages/pdb2pqr/tags/1.8-1/debian/patches/fix-hashbangs.patch
trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.dirs
trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.install
trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.links
trunk/packages/pdb2pqr/tags/1.8-1/debian/rules
Removed:
trunk/packages/pdb2pqr/tags/1.8-1/debian/README.Debian
trunk/packages/pdb2pqr/tags/1.8-1/debian/changelog
trunk/packages/pdb2pqr/tags/1.8-1/debian/compat
trunk/packages/pdb2pqr/tags/1.8-1/debian/control
trunk/packages/pdb2pqr/tags/1.8-1/debian/copyright
trunk/packages/pdb2pqr/tags/1.8-1/debian/patches/fix-hashbangs.patch
trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.dirs
trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.install
trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.links
trunk/packages/pdb2pqr/tags/1.8-1/debian/propka.dirs
trunk/packages/pdb2pqr/tags/1.8-1/debian/propka.install
trunk/packages/pdb2pqr/tags/1.8-1/debian/rules
Log:
[svn-buildpackage] Tagging pdb2pqr 1.8-1
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/README.Debian
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/README.Debian 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/README.Debian 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,16 +0,0 @@
-PROPKA
-======
-
-PDB2PQR can use PROPKA to protonate the structure it converts. If you want to
-use the propka binary as a stand-alone application, you have to install the
-"propka" package. This is not needed if you just want to run PROPKA during a
-PDB2PQR run.
-
-Web Service
-===========
-
-The Debian package of PDB2PQR currently does not provide the parts that are
-necessary to run PDB2PQR as a web service. If you think that the PDB2PQR
-web service should be available as a package, please file a wishlist bug.
-
- -- Manuel Prinz Sat, 29 Jan 2011 22:53:19 +0100
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/README.Debian (from rev 11414, trunk/packages/pdb2pqr/trunk/debian/README.Debian)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/README.Debian (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/README.Debian 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,17 @@
+PROPKA
+======
+
+PDB2PQR can use PROPKA to protonate the structure it converts. PROPKA is
+packaged along with the PDB2PQR in this package.
+
+ -- Manuel Prinz Thu, 21 Jun 2012 15:57:01 +0200
+
+
+Web Service
+===========
+
+The Debian package of PDB2PQR currently does not provide the parts that are
+necessary to run PDB2PQR as a web service. If you think that the PDB2PQR
+web service should be available as a package, please file a wishlist bug.
+
+ -- Manuel Prinz Sat, 29 Jan 2011 22:53:19 +0100
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/changelog
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/changelog 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/changelog 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,28 +0,0 @@
-pdb2pqr (1.8-1) UNRELEASED; urgency=low
-
- [ Andreas Tille ]
- * debian/upstream: Add publication information
-
- [ Manuel Prinz ]
- * 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 <tille at debian.org> Wed, 16 May 2012 09:32:56 +0200
-
-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
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/changelog (from rev 11419, trunk/packages/pdb2pqr/trunk/debian/changelog)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/changelog (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/changelog 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,30 @@
+pdb2pqr (1.8-1) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * debian/upstream: Add publication information
+
+ [ Manuel Prinz ]
+ * New upstream version. Updated debian/copyright.
+ * 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.
+ * Merged pdb2pqr and propka packages as they are more interconnected since
+ this upstream version. Updated README.Debian accordingly.
+
+ -- Manuel Prinz <manuel at debian.org> Thu, 21 Jun 2012 16:21:50 +0200
+
+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/1.8-1/debian/compat
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/compat 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/compat 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1 +0,0 @@
-7
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/compat (from rev 11414, trunk/packages/pdb2pqr/trunk/debian/compat)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/compat (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/compat 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1 @@
+9
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/control
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/control 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/control 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,57 +0,0 @@
-Source: pdb2pqr
-Section: science
-Priority: optional
-Maintainer: Debian Med <debian-med-packaging 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: 3.9.3
-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/
-
-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
-XB-Python-Version: ${python:Versions}
-Architecture: any
-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
- 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/1.8-1/debian/control (from rev 11414, trunk/packages/pdb2pqr/trunk/debian/control)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/control (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/control 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,49 @@
+Source: pdb2pqr
+Section: science
+Priority: optional
+Maintainer: Debian Med <debian-med-packaging 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 (>= 9), gfortran, swig, xmlto, openbabel,
+ autoconf, automake, libtool, autotools-dev, python-dev, python-numpy,
+Standards-Version: 3.9.3
+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/
+
+Package: pdb2pqr
+XB-Python-Version: ${python:Versions}
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy
+Suggests: apbs
+Enhances: autodocktools
+Provides: propka
+Conflicts: propka
+Replaces: propka
+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
+ .
+ This package also includes PropKa, a tool to modify the protonation state of
+ protein structures 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.
+
+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.
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/copyright
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/copyright 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/copyright 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,132 +0,0 @@
-This package was debianized by Steffen Moeller <moeller at debian.org> on Thu, 20 Dec 2007 16:27:31 +0100.
-
-It was downloaded from http://sourceforge.net/projects/pdb2pqr/.
-
-Copies of NumPy, ZSI and JMol were removed from the tarball, originally found
-in the contrib/ and jmol/ directories. See also the get-orig-source target in
-debian/rules.
-
-Copyrights:
-
- Copyright © 2002-2010 Nathan A. Baker
- Copyright © 2009 Tommy Carstensen
- Copyright © 2004 becker
- Copyright © 2006 Mike Bradley
- Copyright © 1999-2004 Cambridge Crystallographic Data Centre
- Copyright © 2009 Tommy Carstensen
- Copyright © 2002-2010 Paul Czodrowski
- Copyright © Andrew Dalke <dalke at bioreason.com>
- Copyright © 2005-2010 Todd Dolinsky
- Copyright © 2000 EMBL
- Copyright © 1992-2008 Free Software Foundation, Inc.
- Copyright © 1993 Noah Friedman <friedman at prep.ai.mit.edu>
- Copyright © 2010 Wes Goodman
- Copyright © 2010 Bob Hanson (JMol code, removed)
- Copyright © David J. Heisterberg
- Copyright © 1994-2000 Michael Holst
- Copyright © 2007-2010 Yong Huang
- Copyright © 2004-2005 Hui Li
- Copyright © 2005,2010 Jan H. Jensen
- Copyright © 2000-2010 Gerhard Klebe
- Copyright © 2000-2004 Daniel Kuhn
- Copyright © 2010 Predrag Kukic (kukaq)
- Copyright © 2006 Jan Labanowski
- Copyright © 1991 Massachusetts Institute of Technology
- Copyright © 2007 Julie C. Mitchell
- Copyright © 2002-2010 Jens Erik Nielsen
- Copyright © The Ohio Supercomputer Center, Columbus
- Copyright © 2004 Philipps-University, Marburg
- Copyright © J. Ren
- Copyright © 2000-2004 Stefan Schmitt
- Copyright © 2008 Dave Sept
- Copyright © 2002-2003 UCSD/HHMI
- Copyright © 2003-2008 University College Dublin
- Copyright © 2007-2010 Samir Unni
- Copyright © 2004-2007 Washington University St. Louis
- Copyright © 2004 Nils Weskamp
-
-Licenses:
-
- PDB2PQR [BSD 3-clause]:
-
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without modification,
- are permitted provided that the following conditions are met:
-
- * Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice,
- this list of conditions and the following disclaimer in the documentation
- and/or other materials provided with the distribution.
- * Neither the names of University College Dublin, Washington University in
- St. Louis, or University of Marburg nor the names of its contributors may
- be used to endorse or promote products derived from this software without
- specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
- IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
- INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
- OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
- OF THE POSSIBILITY OF SUCH DAMAGE.
-
- PropKa [BSD 3-clause] (Files under ./propka/):
-
- PROPKA USER LICENSE AGREEMENT
-
- PropKa: a program for protein pKa predictions
- Copyright (c) 2005, Jan H. Jensen and Hui Li
-
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
-
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
- * Neither the name of the University of Copenhagen nor the names of its
- contributors may be used to endorse or promote products derived from
- this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
- A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
- OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
- TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
- PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
- LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
- Clique [LGPL-2]: (Files under ./pdb2pka/substruct/clique/)
-
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Library General Public
- License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later version.
-
- This library 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
- Library General Public License for more details.
-
- On Debian systems, the complete text of the GNU Library General Public License
- can be found in /usr/share/common-licenses/LGPL-2.
-
- mkinstalldirs [Public Domain]: (Files **/config/mkinstalldirs)
-
-
-The Debian packaging is © 2007-2010 Manuel Prinz <manuel at debian.org>
-and Steffen Moeller <moeller at debian.org> and is licensed under the GPL,
-see `/usr/share/common-licenses/GPL'.
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/copyright (from rev 11413, trunk/packages/pdb2pqr/trunk/debian/copyright)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/copyright (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/copyright 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,116 @@
+This package was debianized by Steffen Moeller <moeller at debian.org> on Thu, 20 Dec 2007 16:27:31 +0100.
+
+It was downloaded from http://sourceforge.net/projects/pdb2pqr/.
+
+Copies of NumPy, ZSI and JMol were removed from the tarball, originally found
+in the contrib/ and jmol/ directories. See also the get-orig-source target in
+debian/rules.
+
+Copyrights:
+
+ Copyright © 2002-2010 Nathan A. Baker
+ Copyright © 2009 Tommy Carstensen
+ Copyright © 2004 becker
+ Copyright © 2006 Mike Bradley
+ Copyright © 1999-2004 Cambridge Crystallographic Data Centre
+ Copyright © 2009 Tommy Carstensen
+ Copyright © 2002-2010 Paul Czodrowski
+ Copyright © Andrew Dalke <dalke at bioreason.com>
+ Copyright © 2005-2010 Todd Dolinsky
+ Copyright © 2000 EMBL
+ Copyright © 1992-2008 Free Software Foundation, Inc.
+ Copyright © 1993 Noah Friedman <friedman at prep.ai.mit.edu>
+ Copyright © 2010 Wes Goodman
+ Copyright © 2010 Bob Hanson (JMol code, removed)
+ Copyright © David J. Heisterberg
+ Copyright © 1994-2000 Michael Holst
+ Copyright © 2007-2010 Yong Huang
+ Copyright © 2004-2005 Hui Li
+ Copyright © 2005,2010 Jan H. Jensen
+ Copyright © 2000-2010 Gerhard Klebe
+ Copyright © 2000-2004 Daniel Kuhn
+ Copyright © 2010 Predrag Kukic (kukaq)
+ Copyright © 2006 Jan Labanowski
+ Copyright © 1991 Massachusetts Institute of Technology
+ Copyright © 2007 Julie C. Mitchell
+ Copyright © 2002-2010 Jens Erik Nielsen
+ Copyright © The Ohio Supercomputer Center, Columbus
+ Copyright © 2011-2012 Mats H. M. Olsson
+ Copyright © 2004 Philipps-University, Marburg
+ Copyright © J. Ren
+ Copyright © 2000-2004 Stefan Schmitt
+ Copyright © 2008 Dave Sept
+ Copyright © 2002-2003 UCSD/HHMI
+ Copyright © 2003-2008 University College Dublin
+ Copyright © 2007-2010 Samir Unni
+ Copyright © 2011-2012 Chresten R. Sondergard
+ Copyright © 2004-2007 Washington University St. Louis
+ Copyright © 2004 Nils Weskamp
+
+
+Licenses:
+
+ PDB2PQR [BSD 3-clause]:
+
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ * Neither the names of University College Dublin, Washington University in
+ St. Louis, or University of Marburg nor the names of its contributors may
+ be used to endorse or promote products derived from this software without
+ specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
+ IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
+ INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+ OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ OF THE POSSIBILITY OF SUCH DAMAGE.
+
+ PropKa [LGPL 2.1 or later] (Files under ./propka30/):
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published by the
+ Free Software Foundation; either version 2.1 of the License, or (at your
+ option) any later version.
+
+ This library 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 Lesser General Public License
+ for more details.
+
+ On Debian systems, you can find a copy of the LGPL license in
+ /usr/share/common-licenses/LGPL-2.1.
+
+ Clique [LGPL-2]: (Files under ./pdb2pka/substruct/clique/)
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+
+ This library 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
+ Library General Public License for more details.
+
+ On Debian systems, the complete text of the GNU Library General Public License
+ can be found in /usr/share/common-licenses/LGPL-2.
+
+ mkinstalldirs [Public Domain]: (Files **/config/mkinstalldirs)
+
+
+The Debian packaging is © 2007-2010 Manuel Prinz <manuel at debian.org>
+and Steffen Moeller <moeller at debian.org> and is licensed under the GPL,
+see `/usr/share/common-licenses/GPL'.
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/patches/fix-hashbangs.patch
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/patches/fix-hashbangs.patch 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,24 +0,0 @@
---- 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
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/patches/fix-hashbangs.patch (from rev 11411, trunk/packages/pdb2pqr/trunk/debian/patches/fix-hashbangs.patch)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/patches/fix-hashbangs.patch (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/patches/fix-hashbangs.patch 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,27 @@
+Subject: Fixes "broken" hashbangs
+From: Manuel Prinz <manuel at debian.org>
+Last-Update: 2012-06-21
+--- 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
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.dirs 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,9 +0,0 @@
-/usr/bin
-/usr/lib/pdb2pqr/pdb2pka/substruct
-/usr/share/doc/pdb2pqr
-/usr/share/man/man1
-/usr/share/pdb2pqr/dat
-/usr/share/pdb2pqr/extensions
-/usr/share/pdb2pqr/pdb2pka/ligandclean
-/usr/share/pdb2pqr/pdb2pka/substruct
-/usr/share/pdb2pqr/src
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.dirs (from rev 11414, trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.dirs)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.dirs (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.dirs 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,10 @@
+/usr/bin
+/usr/lib/pdb2pqr/pdb2pka/substruct
+/usr/share/doc/pdb2pqr
+/usr/share/man/man1
+/usr/share/pdb2pqr/dat
+/usr/share/pdb2pqr/extensions
+/usr/share/pdb2pqr/pdb2pka/ligandclean
+/usr/share/pdb2pqr/pdb2pka/substruct
+/usr/share/pdb2pqr/propka30
+/usr/share/pdb2pqr/src
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.install
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.install 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,12 +0,0 @@
-pdb2pqr.py usr/share/pdb2pqr/
-main.py usr/share/pdb2pqr/
-main_cgi.py usr/share/pdb2pqr/
-dat/* usr/share/pdb2pqr/dat/
-extensions/* usr/share/pdb2pqr/extensions/
-src/* usr/share/pdb2pqr/src/
-pdb2pka/*.py usr/share/pdb2pqr/pdb2pka
-pdb2pka/ligandclean/*.py usr/share/pdb2pqr/pdb2pka/ligandclean
-pdb2pka/substruct/*.py usr/share/pdb2pqr/pdb2pka/substruct
-# Binary parts
-pdb2pka/_pMC_mult.so usr/lib/pdb2pqr/pdb2pka
-pdb2pka/substruct/Algorithms.so usr/lib/pdb2pqr/pdb2pka/substruct
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.install (from rev 11414, trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.install)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.install (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.install 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,13 @@
+pdb2pqr.py usr/share/pdb2pqr/
+main.py usr/share/pdb2pqr/
+main_cgi.py usr/share/pdb2pqr/
+dat/* usr/share/pdb2pqr/dat/
+extensions/* usr/share/pdb2pqr/extensions/
+src/* usr/share/pdb2pqr/src/
+pdb2pka/*.py usr/share/pdb2pqr/pdb2pka
+pdb2pka/ligandclean/*.py usr/share/pdb2pqr/pdb2pka/ligandclean
+pdb2pka/substruct/*.py usr/share/pdb2pqr/pdb2pka/substruct
+propka30/* usr/share/pdb2pqr/propka30/
+# Binary parts
+pdb2pka/_pMC_mult.so usr/lib/pdb2pqr/pdb2pka
+pdb2pka/substruct/Algorithms.so usr/lib/pdb2pqr/pdb2pka/substruct
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.links
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.links 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.links 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,3 +0,0 @@
-usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
-usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
-usr/lib/pdb2pqr/propka/_propkalib.so usr/share/pdb2pqr/propka/_propkalib.so
Copied: trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.links (from rev 11414, trunk/packages/pdb2pqr/trunk/debian/pdb2pqr.links)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.links (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/pdb2pqr.links 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,3 @@
+usr/lib/pdb2pqr/pdb2pka/_pMC_mult.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
+usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
+#usr/lib/pdb2pqr/propka/_propkalib.so usr/share/pdb2pqr/propka/_propkalib.so
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/propka.dirs
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.dirs 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/propka.dirs 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,2 +0,0 @@
-/usr/bin
-/usr/share/propka
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/propka.install
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/propka.install 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/propka.install 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1 +0,0 @@
-propka30/* usr/share/propka
Deleted: trunk/packages/pdb2pqr/tags/1.8-1/debian/rules
===================================================================
--- trunk/packages/pdb2pqr/trunk/debian/rules 2012-06-19 17:06:13 UTC (rev 11395)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/rules 2012-06-21 15:34:53 UTC (rev 11422)
@@ -1,73 +0,0 @@
-#!/usr/bin/make -f
-# -*- mode: makefile; coding: utf-8 -*-
-
-PACKAGE := $(firstword $(shell dh_listpackages))
-VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }')
-UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//')
-
-# 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 $@
-
-override_dh_auto_clean:
- ( cd pdb2pka && \
- if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \
- if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi )
- dh_auto_clean
-
-override_dh_auto_configure:
- dh_auto_configure -- CFLAGS="$(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
-# 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 $${app} .py); \
- done
- for app in /usr/share/propka/propka.py; do \
- sed -e "s, at SCRIPT@,$${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
-
-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
- chmod 0755 debian/propka/usr/share/propka/propka.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/1.8-1/debian/rules (from rev 11414, trunk/packages/pdb2pqr/trunk/debian/rules)
===================================================================
--- trunk/packages/pdb2pqr/tags/1.8-1/debian/rules (rev 0)
+++ trunk/packages/pdb2pqr/tags/1.8-1/debian/rules 2012-06-21 15:34:53 UTC (rev 11422)
@@ -0,0 +1,72 @@
+#!/usr/bin/make -f
+# -*- mode: makefile; coding: utf-8 -*-
+
+PACKAGE := $(firstword $(shell dh_listpackages))
+VERSION := $(shell dpkg-parsechangelog | awk '/^Version:/ { print $$2 }')
+UPSTREAM := $(shell echo "$(VERSION)" | sed 's/-.\+$$//')
+
+# Compile with -fPIC on all platforms (fix for #636204, #654240)
+CFLAGS += -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+CPPFLAGS += -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+CXXFLAGS += -fPIC -I/usr/share/pyshared/numpy/core/include/numpy
+FFLAGS += -fPIC
+
+%:
+ dh $@ --with python2
+
+override_dh_auto_clean:
+ ( cd pdb2pka && \
+ if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \
+ if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi )
+ dh_auto_clean
+
+override_dh_auto_configure:
+ dh_auto_configure -- CFLAGS="$(CFLAGS)" CPPFLAGS="$(CPPFLAGS)" CXXFLAGS="$(CXXFLAGS)" FFLAGS="$(FFLAGS)" LDFLAGS="$(LDFLAGS)"
+ ( 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:
+# 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 $${app} .py); \
+ done
+ for app in /usr/share/pdb2pqr/propka30/propka.py; do \
+ sed -e "s, at SCRIPT@,$${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/pdb2pqr/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
+ chmod 0755 debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.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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