apbs (1.2.1b-1) debian-dir only changes

Summary

 debian/README.source                                 |    7 
 debian/apbs.1                                        |   45 ++++
 debian/apbs.install                                  |    1 
 debian/changelog                                     |  164 ++++++++++++++
 debian/compat                                        |    1 
 debian/control                                       |   36 +++
 debian/copyright                                     |  209 +++++++++++++++++++
 debian/patches/00list                                |    3 
 debian/patches/03_skip_expensive_tests.dpatch        |   25 ++
 debian/patches/04_remove_install-exec-am_rule.dpatch |   25 ++
 debian/patches/06_quicktest.dpatch                   |   39 +++
 debian/rules                                         |   37 +++
 debian/watch                                         |    4 
 13 files changed, 596 insertions(+)

    
download this patch

Patch contents

--- apbs-1.2.1b.orig/debian/apbs.1
+++ apbs-1.2.1b/debian/apbs.1
@@ -0,0 +1,45 @@
+.TH "APBS" "1" "July 2009" "apbs" "User Commands"
+.SH NAME
+abps \- Adaptive Poisson Boltzmann Solver
+.SH SYNOPSIS
+.B apbs
+.RB [ options ]
+.I parameters-file
+.SH DESCRIPTION
+The \fBapbs\fR command calculates electrostatic potentials, energies,
+and forces using both multigrid and finite element methods.
+.SH OPTIONS
+At the moment, the following options are supported:
+.TP
+.BI \-\-output\-file=< name >
+Enables output logging to the path listed in <\fIname\fR>.  Uses flat-file
+format if \fB\-\-output\-format\fR is not used.
+.TP
+.BI \-\-output\-format=< type >
+Specifies format for logging.  Options for <\fItype\fR> are either "\fIxml\fR"
+or "\fIflat\fR".
+.TP
+.B \-\-help
+Display this help information.
+.TP
+.B \-\-version
+Display the current \fBapbs\fR version.
+.SH EXAMPLES
+.B apbs apbs.in > apbs.out 2> apbs.err
+.SH CITATION
+Please cite APBS as follows:
+.PP
+.RS 4
+Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+nanosystems: application to microtubules and the ribosome. Proc.
+Natl. Acad. Sci. USA 98, 10037-10041 2001.
+.RE
+.SH "SEE ALSO"
+For more information read the user guide and/or the tutorial found online at
+.IR http://apbs.wustl.edu/ .
+.SH AUTHORS
+.B apbs
+was written by Nathan A\. Baker <\&baker@biochem.wustl.edu\&>.
+.PP
+This manual page was written by Daniel Leidert <\&daniel.leidert@wgdd.de\&>
+for the Debian project (but may be used by others).
--- apbs-1.2.1b.orig/debian/watch
+++ apbs-1.2.1b/debian/watch
@@ -0,0 +1,4 @@
+# See uscan(1) for format
+
+version=3
+http://sf.net/apbs/apbs-([\d\.]+[a-c]?)-source\.tar\.gz
--- apbs-1.2.1b.orig/debian/README.source
+++ apbs-1.2.1b/debian/README.source
@@ -0,0 +1,7 @@
+apbs source for Debian
+----------------------
+
+This package uses the `dpatch' patch management solution. See
+/usr/share/doc/dpatch/README.source.gz.
+
+ -- Daniel Leidert (dale) <daniel.leidert@wgdd.de>, July 2009
--- apbs-1.2.1b.orig/debian/rules
+++ apbs-1.2.1b/debian/rules
@@ -0,0 +1,37 @@
+#!/usr/bin/make -f
+
+-include /usr/share/mpi-default-dev/debian_defaults
+
+include /usr/share/cdbs/1/class/autotools.mk
+include /usr/share/cdbs/1/rules/buildcore.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/rules/utils.mk
+include /usr/share/cdbs/1/rules/dpatch.mk
+
+FFLAGS = -Wall -g
+FFLAGS += $(DEB_OPT_FLAG)
+
+DEB_CONFIGURE_EXTRA_FLAGS := --prefix=/usr
+# because of a bug in the confifgure script, --enable-tools will *disable*
+# building the tools (sf.net #1910799); however turn it off now, because
+# tools/arpack/ardriv.f will lead to an FTBFS (sf.net #1910846)
+DEB_CONFIGURE_EXTRA_FLAGS += --disable-tools
+DEB_CONFIGURE_EXTRA_FLAGS += --with-fetk-include=/usr/include --with-fetk-library=/usr/lib
+DEB_CONFIGURE_EXTRA_FLAGS += --with-blas=-lblas
+DEB_CONFIGURE_EXTRA_FLAGS += --with-arpack=/usr/lib
+# only use MPI if /usr/share/mpi-default-dev/debian_defaults is available
+ifdef ARCH_DEFAULT_MPI_IMPL
+DEB_CONFIGURE_EXTRA_FLAGS += --with-$(ARCH_DEFAULT_MPI_IMPL)=/usr/lib/$(ARCH_DEFAULT_MPI_IMPL)
+DEB_CONFIGURE_SCRIPT_ENV += CC="/usr/bin/mpicc.$(ARCH_DEFAULT_MPI_IMPL)" F77="/usr/bin/mpif77.$(ARCH_DEFAULT_MPI_IMPL)"
+endif
+DEB_CONFIGURE_SCRIPT_ENV += FFLAGS="$(FFLAGS)"
+
+DEB_MAKE_INSTALL_TARGET := -C $(CURDIR)/bin install DESTDIR=$(CURDIR)/debian/tmp
+DEB_MAKE_CHECK_TARGET := -C $(CURDIR)/examples/ quicktest APBS=$(CURDIR)/bin/apbs APBSBIN=$(CURDIR)/bin/apbs
+
+DEB_INSTALL_MANPAGES_apbs := debian/apbs.1
+
+clean::
+	rm -f tools/manip/psize.pyc
+
+common-binary-post-install-arch:: list-missing
--- apbs-1.2.1b.orig/debian/copyright
+++ apbs-1.2.1b/debian/copyright
@@ -0,0 +1,209 @@
+This package was debianized by Michael Banck <mbanck@debian.org> on
+Thu, 29 Jun 2006 17:10:18 +0200.
+
+It was downloaded from:
+
+   http://downloads.sourceforge.net/apbs/.
+
+Upstream Author:
+
+   Nathan A. Baker <baker@biochem.wustl.edu>
+
+Copyright Holder:
+
+   Copyright (C) 2002-2009 Washington University in St. Louis.
+   Portions Copyright (C) 2002-2009 Nathan A. Baker.
+   Portions Copyright (C) 2007 Patrice Koehl.
+   Portions Copyright (C) 1999-2002 The Regents of the University of California.
+   Portions Copyright (C) 1995 Michael Holst.
+
+   PMG: (contrib/**)
+   Copyright (C) 1994-2008 Michael Holst.
+
+   ZSI, wsdl2python, wstools: (contrib/opal/ZSI/)
+   Copyright (C) 2003 The Regents of the University of California.
+   Copyright (C) 2002-2003 Rich Salz.
+   Copyright (C) 2001 Zolera Systems, Inc.
+   Copyright (C) 2001 Zope Corporation and Contributors.
+   Copyright (C) 1999 Stefan Schwarzer.
+
+License: BSD-C3 (/usr/share/common-licenses/BSD)
+
+   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 Washington University in St. Louis 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
+
+
+License for many files
+in contrib/ (e.g. PMG): LGPL2.1+ (/usr/share/common-licenses/LGPL)
+
+   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.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with this library; if not, write to the Free Software Foundation,
+   Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301  USA.
+
+License for most of the ZSI
+in contrib/opal/ZSI/: MIT/X
+
+   Permission is hereby granted, free of charge, to any person obtaining a
+   copy of this software and associated documentation files (the "Software"),
+   to deal in the Software without restriction, including without limitation
+   the rights to use, copy, modify, merge, publish, distribute, and/or
+   sell copies of the Software, and to permit persons to whom the Software
+   is furnished to do so, provided that the above copyright notice(s) and
+   this permission notice appear in all copies of the Software and that
+   both the above copyright notice(s) and this permission notice appear in
+   supporting documentation.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+   OF THIRD PARTY RIGHTS. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR HOLDERS
+   INCLUDED IN THIS NOTICE BE LIABLE FOR ANY CLAIM, OR ANY SPECIAL INDIRECT
+   OR CONSEQUENTIAL DAMAGES, OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+   OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+   OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+   OR PERFORMANCE OF THIS SOFTWARE.
+
+   Except as contained in this notice, the name of a copyright holder
+   shall not be used in advertising or otherwise to promote the sale, use
+   or other dealings in this Software without prior written authorization
+   of the copyright holder.
+
+License for most of the wstools
+in contrib/opal/ZSI/ZSI/wstools: Zope Public License (ZPL) Version 2.0
+
+   This software is Copyright (C) Zope Corporation (tm) and
+   Contributors. All rights reserved.
+
+   This license has been certified as open source. It has also
+   been designated as GPL compatible by the Free Software
+   Foundation (FSF).
+
+   Redistribution and use in source and binary forms, with or
+   without modification, are permitted provided that the
+   following conditions are met:
+
+   1. Redistributions in source code must retain the above
+      copyright notice, this list of conditions, and the following
+      disclaimer.
+
+   2. 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.
+
+   3. The name Zope Corporation (tm) must not be used to
+      endorse or promote products derived from this software
+      without prior written permission from Zope Corporation.
+
+   4. The right to distribute this software or to use it for
+      any purpose does not give you the right to use Servicemarks
+      (sm) or Trademarks (tm) of Zope Corporation. Use of them is
+      covered in a separate agreement (see
+      http://www.zope.com/Marks).
+
+   5. If any files are modified, you must cause the modified
+      files to carry prominent notices stating that you changed
+      the files and the date of any change.
+
+   THIS SOFTWARE IS PROVIDED BY ZOPE CORPORATION ``AS IS''
+   AND ANY EXPRESSED 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 ZOPE CORPORATION OR ITS 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.
+
+License for most of the wsdl2python tools
+in contrib/opal/ZSI/ZSI/: 
+
+   Redistribution and use in source and binary forms, with or
+   without modification, are permitted provided that the following
+   conditions are met:
+
+   (1) Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+
+   (2) 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.
+
+   (3) Neither the name of the University of California, Lawrence Berkeley
+       National Laboratory, U.S. Dept. of Energy 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.
+
+   You are under no obligation whatsoever to provide any bug fixes,
+   patches, or upgrades to the features, functionality or performance of
+   the source code ("Enhancements") to anyone; however, if you choose to
+   make your Enhancements available either publicly, or directly to
+   Lawrence Berkeley National Laboratory, without imposing a separate
+   written license agreement for such Enhancements, then you hereby grant
+   the following license: a non-exclusive, royalty-free perpetual license
+   to install, use, modify, prepare derivative works, incorporate into
+   other computer software, distribute, and sublicense such Enhancements
+   or derivative works thereof, in binary and source code form.
+
+==============================================================================
+
+Please cite your use of APBS as:
+
+   Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of
+   nanosystems: application to microtubules and the ribosome. Proc.
+   Natl. Acad. Sci. USA 98, 10037-10041 2001.
+
+==============================================================================
+
+The Debian packaging is Coypright (C) 2006-2009 by the debichem team
+<debichem-devel@lists.alioth.debian.org> and subject to the GNU General
+Public License (GPL) version 2, or at your option, any later version.
--- apbs-1.2.1b.orig/debian/compat
+++ apbs-1.2.1b/debian/compat
@@ -0,0 +1 @@
+5
--- apbs-1.2.1b.orig/debian/control
+++ apbs-1.2.1b/debian/control
@@ -0,0 +1,36 @@
+Source: apbs
+Section: science
+Priority: optional
+Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
+Uploaders: Michael Banck <mbanck@debian.org>,
+ Daniel Leidert (dale) <daniel.leidert@wgdd.de>
+Build-Depends: cdbs, debhelper (>> 5), autotools-dev, dpatch, bc,
+ gfortran, libarpack2-dev, libblas-dev, libmaloc-dev, mpi-default-dev (>= 0.3),
+ python-minimal
+Standards-Version: 3.8.3
+Homepage: http://apbs.sourceforge.net
+Vcs-Browser: http://svn.debian.org/wsvn/debichem/
+Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/apbs/
+DM-Upload-Allowed: yes
+
+Package: apbs
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Adaptive Poisson Boltzmann Solver
+ APBS is a software package for the numerical solution of the
+ Poisson-Boltzmann equation (PBE), one of the most popular continuum
+ models for describing electrostatic interactions between molecular
+ solutes in salty, aqueous media.  Continuum electrostatics plays an
+ important role in several areas of biomolecular simulation, including:
+ .
+   * simulation of diffusional processes to determine ligand-protein and
+     protein-protein binding kinetics,
+   * implicit solvent molecular dynamics of biomolecules ,
+   * solvation and binding energy calculations to determine
+     ligand-protein and protein-protein equilibrium binding constants
+     and aid in rational drug design,
+   * and biomolecular titration studies.
+ .
+ APBS was designed to efficiently evaluate electrostatic properties for
+ such simulations for a wide range of length scales to enable the
+ investigation of molecules with tens to millions of atoms.
--- apbs-1.2.1b.orig/debian/changelog
+++ apbs-1.2.1b/debian/changelog
@@ -0,0 +1,164 @@
+apbs (1.2.1b-1) unstable; urgency=low
+
+  * New upstream (bugfix) release.
+
+  * debian/control (Standards-Version): Bumped to 3.8.3.
+    (Build-Depends): Replace libmpich1.0-dev with mpi-default-dev.
+  * debian/rules: Added list-missing target.
+    (DEB_CONFIGURE_EXTRA_FLAGS, DEB_CONFIGURE_SCRIPT_ENV): Use the default
+    MPI implementation for the architecture.
+  * debian/watch: Slightly adjusted for upstream version schema.
+
+ -- Daniel Leidert (dale) <daniel.leidert@wgdd.de>  Sun, 13 Dec 2009 15:59:00 +0100
+
+apbs (1.1.0-1) unstable; urgency=low
+
+  * New upstream release.
+
+  * debian/apbs.1: Added citation section.
+    (SEE ALSO): User guide is not available locally anymore.
+  * debian/apbs.doc-base,
+    debian/apbs.dirs: Dropped useless files.
+  * debian/apbs.install: Removed documentation files, because the user guide
+    is not shipped anymore (closes: #508980). The lintian overrides are
+    considered by dh_lintian.
+  * debian/control (Uploaders): Removed LI as requested. Thanks for your work!
+    (Build-Depends): Re-added arpack, which is back in main.
+    (Standards-Version): Bumped to 3.8.2 (no other changes).
+    (Vcs-Svn): Fixed vcs-field-uses-not-recommended-uri-format.
+  * debian/copyright: Updated and completed.
+  * debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Build with arpack.
+  * debian/README.source: Added to comply to policy.
+  * debian/lintian-overrides/apbs: Dropped. License file is not installed
+    anymore.
+  * debian/patches/01_html_documentation.dpatch: Dropped, as there is no
+    documentation installed anymore.
+  * debian/patches/04_remove_install-exec-am_rule.dpatch: Updated/adjusted.
+  * debian/patches/05_reduce_test_suite.dpatch: Dropped (cannot be applied
+    anymore).
+  * debian/patches/00list: Adjusted.
+
+ -- Daniel Leidert (dale) <daniel.leidert@wgdd.de>  Fri, 17 Jul 2009 19:06:05 +0200
+
+apbs (1.0.0-2) unstable; urgency=low
+
+  * debian/patches/06_quicktest.dpatch: New patch, add a `quicktest' target
+    which only runs a couple of small tests.
+  * debian/rules (DEB_MAKE_CHECK_TARGET): Run quicktest instead of test for
+    now.
+  * debian/control (Build-Depends): Removed libarpack2-dev. (closes: #497722)
+  * debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Removed --with-arpack.
+
+ -- Michael Banck <mbanck@debian.org>  Thu, 04 Sep 2008 00:00:41 +0200
+
+apbs (1.0.0-1) unstable; urgency=low
+
+  * New upstream release.
+    + No longer contains a corrupted tarball (closes: #473822).
+  * debian/patches/04_remove_install-exec-am_rule.dpatch: Refreshed.
+  * debian/patches/05_reduce_test_suite.dpatch: New patch, remove most of the
+    coordinates for the ion test to save time (closes: 475064).
+
+ -- Michael Banck <mbanck@debian.org>  Tue, 10 Jun 2008 14:25:47 +0200
+
+apbs (0.5.1-2) unstable; urgency=low
+
+  * Acknowledge NMU 0.5.1-1.1 (closes: #462263). Thanks to Colin Tuckley.
+
+  [ Daniel Leidert ]
+  * debian/apbs.1: Added.
+  * debian/apbs.doc-base (Section): Adjusted accordingly to latest doc-base
+    policy.
+  * debian/apbs.install: Install lintian override.
+  * debian/compat: Raised to level 5.
+  * debian/control: Homepage field transition. Added Vcs fields. Added
+    DM-Upload-Allowed field for DM status.
+    (Maintainer): Set to the debichem team address. Moved Michael to
+    Uploaders.
+    (Uploaders): Added myself and LI Daobing.
+    (Standards-Version): Updated to latest 3.7.3 (no other changes).
+    (Build-Depends): Raised debhelper to v5. Added libarpack2-dev. Added
+    libmpich1.0-dev for MPI support. Added python-minimal for some tests.
+  * debian/copyright: Fixed old-fsf-address-in-copyright-file issue. Updated
+    copyright information. Added exception.
+  * debian/rules: Install the newly added apbs.1 manpage.
+    (DEB_CONFIGURE_EXTRA_FLAGS): Enable building with arpack (not useful atm
+    without tools). Set prefix.
+    (DEB_CONFIGURE_EXTRA_FLAGS, DEB_CONFIGURE_SCRIPT_ENV): Enable MPI.
+    (DEB_MAKE_INSTALL_TARGET): Only install from bin/ as long as we don't use
+    the rest.
+  * debian/watch: Updated to fit new source archive naming.
+  * debian/lintian-overrides/apbs: Added. The documentation contains the
+    license in several formats.
+
+  [ LI Daobing ]
+  * FTBFS if built twice in a row (Closes: #424100)
+
+ -- Daniel Leidert (dale) <daniel.leidert@wgdd.de>  Mon, 10 Mar 2008 08:46:53 +0100
+
+apbs (0.5.1-1.1) unstable; urgency=low
+
+  * Non-maintainer upload
+  * Build depend on libblas-dev instead of refblas3-dev (closes: #462263)
+  * Add gfortran to Build Depends: to fix FTBFS in clean chroot
+
+ -- Colin Tuckley <colint@debian.org>  Mon, 28 Jan 2008 11:05:21 +0000
+
+apbs (0.5.1-1) unstable; urgency=low
+
+  * New upstream release.
+
+  [ Daniel Leidert ]
+  * debian/control (Build-Depends): Added dpatch and autotools-dev.
+    (Standards-Version): Changed to latest standards version 3.7.2.
+    (Description): Added Homepage field.
+  * debian/copyright: Fixed download location after apbs has been moved to
+    sourceforge.net.
+  * debian/rules: Changed to use dpatch.mk instead of simple-patchsys.mk.
+    Added buildcore.mk ruleset. Added FFLAGS flags to configure.
+  * debian/watch: Added.
+  * debian/patches/01_html_documentation.dpatch: Added. Replaces
+    debian/patches/01_html_docu.patch.
+  * debian/patches/02_remove_vf2c.dpatch: Added. Replaces
+    debian/patches/02_remove_vf2c.patch.
+  * debian/patches/90_autoreconf.dpatch: Added. Replaces
+    debian/patches/90_autoreconf.patch. Probably closes: #424100.
+  * debian/patches/00list: Added.
+
+  [ Michael Banck ]
+  * debian/patches/01_html_documentation: Updated.
+  * debian/patches/02_remove_vf2c: Removed; no longer needed.
+  * debian/patches/90_autoreconf: Likewise.
+  * debian/control (Build-Depends): Added bc, needed for the test suite.
+  * debian/rules (DEB_CONFIGURE_EXTRA_FLAGS): Added
+    --with-fetk-include=/usr/include --with-fetk-library=/usr/lib
+    --with-blas=-lblas.
+  * debian/rules (DEB_MAKE_CHECK_TARGET): New target, run the test suite.
+  * debian/patches/03_skip_expensive_tests.dpatch: New patch, skip tests which
+    take a lot of memory and CPU.
+  * debian/patches/04_remove_install-exec-am_rule.dpatch: New patch, remove
+    the install-exec-am rule from the top-level Makefile.  We can just install
+    that data manually and it does not support DESTDIR anyway.
+  * debian/apbs.install: Updated location of the user's guide and tutorial in
+    the source tree.  Install license.html as well.
+
+ -- Michael Banck <mbanck@debian.org>  Wed, 18 Jul 2007 15:48:58 +0200
+
+apbs (0.4.0-2) unstable; urgency=low
+
+  * debian/patches: New directory, manage changes to upstream with
+    simple-patchsys.mk.
+  * debian/patches/01_html_docu.patch: New patch, supress link to the
+    programmer's manual we don't ship for now.
+  * debian/patches/02_remove_vf2c.patch: New patch, remove MALOC's own
+    -lvf2c f2c fork from linking.
+  * debian/patches/90_autoreconf.patch: Update libtool; closes: #378211.
+
+ -- Michael Banck <mbanck@debian.org>  Sun, 10 Sep 2006 19:14:24 +0200
+
+apbs (0.4.0-1) unstable; urgency=low
+
+  * Initial release.
+
+ -- Michael Banck <mbanck@debian.org>  Thu, 29 Jun 2006 17:10:18 +0200
+
--- apbs-1.2.1b.orig/debian/apbs.install
+++ apbs-1.2.1b/debian/apbs.install
@@ -0,0 +1 @@
+debian/tmp/usr/bin/* usr/bin/
--- apbs-1.2.1b.orig/debian/patches/03_skip_expensive_tests.dpatch
+++ apbs-1.2.1b/debian/patches/03_skip_expensive_tests.dpatch
@@ -0,0 +1,25 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 03_skip_expensive_tests.dpatch by Michael Banck <mbanck@debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Skip tests which take a lot of memory and CPU.
+
+@DPATCH@
+--- apbs/examples/Makefile.in.orig	2007-07-17 18:06:39.000000000 +0200
++++ apbs/examples/Makefile.in	2007-07-17 18:06:47.000000000 +0200
+@@ -278,13 +278,13 @@
+ test:
+ 	rm -f TESTRESULTS.log
+ 	touch TESTRESULTS.log
+-	cd actin-dimer; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++#	cd actin-dimer; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd alkanes; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd born; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd FKBP; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd hca-bind; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd ion-pmf; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+-	cd ion-protein; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++#	cd ion-protein; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd ionize; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd pka-lig; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
+ 	cd point-pmf; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
--- apbs-1.2.1b.orig/debian/patches/04_remove_install-exec-am_rule.dpatch
+++ apbs-1.2.1b/debian/patches/04_remove_install-exec-am_rule.dpatch
@@ -0,0 +1,25 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04_remove_install-exec-am_rule.dpatch by Michael Banck <mbanck@debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Remove the install-exec-am rule from the top-level Makefile.  We 
+## DP: can just install that data manually and it does not support 
+## DP: DESTDIR anyway.
+
+@DPATCH@
+diff -urNad apbs~/Makefile.in apbs/Makefile.in
+--- apbs~/Makefile.in	2009-04-13 20:47:41.000000000 +0200
++++ apbs/Makefile.in	2009-07-17 18:16:51.000000000 +0200
+@@ -664,12 +664,6 @@
+ install-exec-local:
+ 	-rm -f ./bin/apbs
+ 
+-install-data-local:
+-	mkdir -p ${prefix}/share
+-	-cp -rf examples ${prefix}/share 
+-	-cp -rf doc ${prefix}/share 
+-	-cp -rf tools ${prefix}/share
+-
+ test:
+ 	cd examples; make test
+ # Tell versions [3.59,3.63) of GNU make to not export all variables.
--- apbs-1.2.1b.orig/debian/patches/00list
+++ apbs-1.2.1b/debian/patches/00list
@@ -0,0 +1,3 @@
+03_skip_expensive_tests
+04_remove_install-exec-am_rule
+06_quicktest
--- apbs-1.2.1b.orig/debian/patches/06_quicktest.dpatch
+++ apbs-1.2.1b/debian/patches/06_quicktest.dpatch
@@ -0,0 +1,39 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 06_quicktest.dpatch by Michael Banck <mbanck@debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Add a `quicktest' target which only runs a couple of small tests
+
+@DPATCH@
+--- apbs-1.0.0.orig/examples/Makefile.am
++++ apbs-1.0.0/examples/Makefile.am
+@@ -31,6 +31,13 @@
+ 	cd smbe; make clean
+ 	cd solv; make clean
+ 
++quicktest:
++	rm -f TESTRESULTS.log
++	touch TESTRESULTS.log
++	cd alkanes; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++	cd hca-bind; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++	cd solv; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++        
+ test:
+ 	rm -f TESTRESULTS.log
+ 	touch TESTRESULTS.log
+--- apbs-1.0.0.orig/examples/Makefile.in
++++ apbs-1.0.0/examples/Makefile.in
+@@ -357,6 +360,13 @@
+ 	cd smbe; make clean
+ 	cd solv; make clean
+ 
++quicktest:
++	rm -f TESTRESULTS.log
++	touch TESTRESULTS.log
++	cd alkanes; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++	cd hca-bind; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++	cd solv; make test; cat TESTRESULTS.log >> ../TESTRESULTS.log
++
+ test:
+ 	rm -f TESTRESULTS.log
+ 	touch TESTRESULTS.log