[Debichem-commits] r3552 - in /unstable/apbs/debian: ./ patches/

dleidert-guest at users.alioth.debian.org dleidert-guest at users.alioth.debian.org
Sun Apr 29 21:11:38 UTC 2012


Author: dleidert-guest
Date: Sun Apr 29 21:11:37 2012
New Revision: 3552

URL: http://svn.debian.org/wsvn/debichem/?sc=1&rev=3552
Log:
* debian/apbs.install: Adjusted.
* debian/apbs.manpages: Added to fix binary-without-manpage.
* debian/compat: Increased dh level to 7.
* debian/control: Used wrap-and-sort.
  (Standards-Version): Bumped to recent 3.9.3.
  (Build-Depends): Removed unused cdbs. Added autotools-dev version
  requirements. Lowered required debhelper version.
  (Vcs-Browser): Fixed.
* debian/copyright: Updated. Removed BSD license file reference to fix
  copyright-refers-to-deprecated-bsd-license-file.
* debian/rules: Run autotools_dev template. Added override target for
  dh_install.
* debian/upstream: Added.
* debian/README.source: Dropped obsolete file.
* debian/patches/*.patch: Updated for quilt. Removed executable permissions.
* debian/patches/04_remove_install-exec-am_rule.patch: Dropped. Moved
  patch content to 07_destdir.patch.
* debian/patches/series: Adjusted.

Added:
    unstable/apbs/debian/apbs.manpages
    unstable/apbs/debian/upstream
Removed:
    unstable/apbs/debian/README.source
    unstable/apbs/debian/patches/04_remove_install-exec-am_rule.patch
Modified:
    unstable/apbs/debian/apbs.install
    unstable/apbs/debian/changelog
    unstable/apbs/debian/compat
    unstable/apbs/debian/control
    unstable/apbs/debian/copyright
    unstable/apbs/debian/patches/03_skip_expensive_tests.patch   (contents, props changed)
    unstable/apbs/debian/patches/06_quicktest.patch   (contents, props changed)
    unstable/apbs/debian/patches/07_destdir.patch
    unstable/apbs/debian/patches/08_distclean.patch
    unstable/apbs/debian/patches/09_acinclude_fix.patch
    unstable/apbs/debian/patches/series
    unstable/apbs/debian/rules

Modified: unstable/apbs/debian/apbs.install
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/apbs.install?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/apbs.install (original)
+++ unstable/apbs/debian/apbs.install Sun Apr 29 21:11:37 2012
@@ -1,1 +1,1 @@
-debian/tmp/usr/bin/apbs
+usr/bin/apbs

Added: unstable/apbs/debian/apbs.manpages
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/apbs.manpages?rev=3552&op=file
==============================================================================
--- unstable/apbs/debian/apbs.manpages (added)
+++ unstable/apbs/debian/apbs.manpages Sun Apr 29 21:11:37 2012
@@ -1,0 +1,1 @@
+debian/apbs.1

Modified: unstable/apbs/debian/changelog
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/changelog?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/changelog (original)
+++ unstable/apbs/debian/changelog Sun Apr 29 21:11:37 2012
@@ -1,6 +1,27 @@
 apbs (1.3.0-2) UNRELEASED; urgency=low
 
+  [ Michael Banck ]
   * 
+
+  [ Daniel Leidert ]
+  * debian/apbs.install: Adjusted.
+  * debian/apbs.manpages: Added to fix binary-without-manpage.
+  * debian/compat: Increased dh level to 7.
+  * debian/control: Used wrap-and-sort.
+    (Standards-Version): Bumped to recent 3.9.3.
+    (Build-Depends): Removed unused cdbs. Added autotools-dev version
+    requirements. Lowered required debhelper version.
+    (Vcs-Browser): Fixed.
+  * debian/copyright: Updated. Removed BSD license file reference to fix
+    copyright-refers-to-deprecated-bsd-license-file.
+  * debian/rules: Run autotools_dev template. Added override target for
+    dh_install.
+  * debian/upstream: Added.
+  * debian/README.source: Dropped obsolete file.
+  * debian/patches/*.patch: Updated for quilt.
+  * debian/patches/04_remove_install-exec-am_rule.patch: Dropped. Moved
+    patch content to 07_destdir.patch.
+  * debian/patches/series: Adjusted.
 
  -- Michael Banck <mbanck at debian.org>  Sun, 11 Mar 2012 19:43:19 +0100
 

Modified: unstable/apbs/debian/compat
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/compat?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/compat (original)
+++ unstable/apbs/debian/compat Sun Apr 29 21:11:37 2012
@@ -1,1 +1,1 @@
-5
+7

Modified: unstable/apbs/debian/control
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/control?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/control (original)
+++ unstable/apbs/debian/control Sun Apr 29 21:11:37 2012
@@ -3,19 +3,29 @@
 Priority: optional
 Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
 Uploaders: Michael Banck <mbanck at debian.org>,
- Daniel Leidert (dale) <daniel.leidert at wgdd.de>
-Build-Depends: cdbs, debhelper (>= 8), dh-autoreconf, autoconf, automake,
- autotools-dev, bc, gfortran, libarpack2-dev, libblas-dev, libmaloc-dev,
- mpi-default-dev (>= 0.3), python-minimal, python-setuptools
-Standards-Version: 3.8.3
+           Daniel Leidert (dale) <daniel.leidert at wgdd.de>
+Build-Depends: autoconf,
+               automake,
+               autotools-dev (>> 20100122.1),
+               bc,
+               debhelper (>> 7.0.50~),
+               dh-autoreconf,
+               gfortran,
+               libarpack2-dev,
+               libblas-dev,
+               libmaloc-dev,
+               mpi-default-dev (>= 0.3),
+               python-minimal,
+               python-setuptools
+Standards-Version: 3.9.3
 Homepage: http://apbs.sourceforge.net
-Vcs-Browser: http://svn.debian.org/wsvn/debichem/
+Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/apbs/
 Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/apbs/
 DM-Upload-Allowed: yes
 
 Package: apbs
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Depends: ${misc:Depends}, ${shlibs: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

Modified: unstable/apbs/debian/copyright
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/copyright?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/copyright (original)
+++ unstable/apbs/debian/copyright Sun Apr 29 21:11:37 2012
@@ -11,8 +11,9 @@
 
 Copyright Holder:
 
-   Copyright (C) 2002-2009 Washington University in St. Louis.
-   Portions Copyright (C) 2002-2009 Nathan A. Baker.
+   Copyright (C) 2010 Pacific Northwest National Laboratory.
+   Portions Copyright (C) 2002-2010 Washington University in St. Louis.
+   Portions Copyright (C) 2002-2010 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.
@@ -27,7 +28,7 @@
    Copyright (C) 2001 Zope Corporation and Contributors.
    Copyright (C) 1999 Stefan Schwarzer.
 
-License: BSD-C3 (/usr/share/common-licenses/BSD)
+License: BSD
 
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are met: 

Modified: unstable/apbs/debian/patches/03_skip_expensive_tests.patch
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/patches/03_skip_expensive_tests.patch?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/patches/03_skip_expensive_tests.patch (original)
+++ unstable/apbs/debian/patches/03_skip_expensive_tests.patch Sun Apr 29 21:11:37 2012
@@ -1,13 +1,10 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 03_skip_expensive_tests.dpatch by Michael Banck <mbanck at debian.org>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Skip tests which take a lot of memory and CPU.
+# 03_skip_expensive_tests.patch by Michael Banck <mbanck at debian.org>
+#
+# Skip tests which take a lot of memory and CPU.
 
- at 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 @@
+--- a/examples/Makefile.am
++++ b/examples/Makefile.am
+@@ -34,13 +34,13 @@
  test:
  	rm -f TESTRESULTS.log
  	touch TESTRESULTS.log

Propchange: unstable/apbs/debian/patches/03_skip_expensive_tests.patch
            ('svn:executable' removed)

Modified: unstable/apbs/debian/patches/06_quicktest.patch
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/patches/06_quicktest.patch?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/patches/06_quicktest.patch (original)
+++ unstable/apbs/debian/patches/06_quicktest.patch Sun Apr 29 21:11:37 2012
@@ -1,29 +1,10 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 06_quicktest.dpatch by Michael Banck <mbanck at 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
+# 06_quicktest.patch by Michael Banck <mbanck at debian.org>
+#
+# Add a `quicktest' target which only runs a couple of small tests
 
- at DPATCH@
---- apbs-1.0.0.orig/examples/Makefile.am
-+++ apbs-1.0.0/examples/Makefile.am
+--- a/examples/Makefile.am
++++ b/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
  

Propchange: unstable/apbs/debian/patches/06_quicktest.patch
            ('svn:executable' removed)

Modified: unstable/apbs/debian/patches/07_destdir.patch
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/patches/07_destdir.patch?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/patches/07_destdir.patch (original)
+++ unstable/apbs/debian/patches/07_destdir.patch Sun Apr 29 21:11:37 2012
@@ -1,5 +1,7 @@
---- ./contrib/opal/ZSI/Makefile.am.orig	2012-03-10 18:01:43.827478005 +0100
-+++ ./contrib/opal/ZSI/Makefile.am	2012-03-10 18:02:56.427475647 +0100
+# Add support for $(DESTDIR)
+
+--- a/contrib/opal/ZSI/Makefile.am
++++ b/contrib/opal/ZSI/Makefile.am
 @@ -15,6 +15,6 @@
  export PYTHONPATH:=	${SITEPKGS}
  
@@ -9,3 +11,58 @@
 +	-mkdir -p $(DESTDIR)${SITEPKGS}
 +	${py_path} setup.py install --root=$(DESTDIR)/ --prefix=${prefix}
  	
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -28,10 +28,10 @@
+ 	-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
++	mkdir -p $(DESTDIR)/${prefix}/share
++	-cp -rf examples $(DESTDIR)/${prefix}/share
++	-cp -rf doc $(DESTDIR)/${prefix}/share
++	-cp -rf tools $(DESTDIR)/${prefix}/share
+ 
+ test:
+ 	cd examples; make test
+--- a/bin/Makefile.am
++++ b/bin/Makefile.am
+@@ -12,7 +12,7 @@
+ 
+ build_libraries = @apbs_build_libraries@
+ 
+-bindir = ${prefix}/bin
++bindir = $(DESTDIR)/${prefix}/bin
+ bin_PROGRAMS     = apbs
+ apbs_SOURCES     = main.c 
+ apbs_LDADD       = ${build_libraries}
+@@ -27,19 +27,19 @@
+ rm.apbs: Makefile
+ 	-rm -f apbs
+ 
+-libdir = ${prefix}/lib
++libdir = $(DESTDIR)/${prefix}/lib
+ lib_LTLIBRARIES = libapbsmainroutines.la
+ libapbsmainroutines_la_SOURCES = routines.c
+ libapbsmainroutines_la_LDFLAGS = -version-info ${APBS_VERSION}
+ 
+-INCLUDES = @inc_list@
++
+ AM_CFLAGS= @wall_pedantic@
+ AM_LDFLAGS       = @LDFLAGS@ @FFLAGS@
+  
+-includedir = ${prefix}/include/apbs
++includedir = $(DESTDIR)/${prefix}/include/apbs
+ include_HEADERS = routines.h
+ 	
+ install-data-local:
+-	-cp -p ${top_apbsdir}/bin/ApbsClient.py ${prefix}/bin
+-	-chmod 755 ${prefix}/bin/ApbsClient.py
+-	-rm -f ${prefix}/bin/wsdl2py 
+\ No newline at end of file
++	-cp -p ${top_apbsdir}/bin/ApbsClient.py $(DESTDIR)/${prefix}/bin
++	-chmod 755 $(DESTDIR)/${prefix}/bin/ApbsClient.py
++	-rm -f $(DESTDIR)/${prefix}/bin/wsdl2py

Modified: unstable/apbs/debian/patches/08_distclean.patch
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/patches/08_distclean.patch?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/patches/08_distclean.patch (original)
+++ unstable/apbs/debian/patches/08_distclean.patch Sun Apr 29 21:11:37 2012
@@ -1,6 +1,6 @@
---- apbs-1.3.0.orig/contrib/opal/ZSI/Makefile.am
-+++ apbs-1.3.0/contrib/opal/ZSI/Makefile.am
-@@ -18,3 +18,9 @@ install-data-local:
+--- a/contrib/opal/ZSI/Makefile.am
++++ b/contrib/opal/ZSI/Makefile.am
+@@ -18,3 +18,9 @@
  	-mkdir -p $(DESTDIR)${SITEPKGS}
  	${py_path} setup.py install --root=$(DESTDIR)/ --prefix=${prefix}
  	
@@ -10,8 +10,8 @@
 +
 +clean-local:
 +	${py_path} setup.py clean
---- ./configure.ac.orig	2012-03-11 15:24:25.795778441 +0100
-+++ ./configure.ac	2012-03-11 15:25:01.895780837 +0100
+--- a/configure.ac
++++ b/configure.ac
 @@ -702,12 +702,6 @@
    [MAXMEM=$withval],
    [MAXMEM="-1"])
@@ -33,8 +33,8 @@
  
  ])
  AC_OUTPUT
---- ./examples/Makefile.am.orig	2012-03-11 17:47:40.515780211 +0100
-+++ ./examples/Makefile.am	2012-03-11 17:48:24.339779294 +0100
+--- a/examples/Makefile.am
++++ b/examples/Makefile.am
 @@ -16,7 +16,24 @@
  
  #SUBDIRS = actin-dimer alkanes born FKBP hca-bind ion-pmf ion-protein ionize pka-lig point-pmf protein-rna smpbe solv opal

Modified: unstable/apbs/debian/patches/09_acinclude_fix.patch
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/patches/09_acinclude_fix.patch?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/patches/09_acinclude_fix.patch (original)
+++ unstable/apbs/debian/patches/09_acinclude_fix.patch Sun Apr 29 21:11:37 2012
@@ -1,5 +1,5 @@
---- ./acinclude.m4.orig	2012-03-11 16:16:01.095781744 +0100
-+++ ./acinclude.m4	2012-03-11 16:16:11.723781286 +0100
+--- a/acinclude.m4
++++ b/acinclude.m4
 @@ -54,14 +54,11 @@
  AC_LANG_C
  ac_save_LIBS="$LIBS"

Modified: unstable/apbs/debian/patches/series
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/patches/series?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/patches/series (original)
+++ unstable/apbs/debian/patches/series Sun Apr 29 21:11:37 2012
@@ -1,5 +1,4 @@
 03_skip_expensive_tests.patch
-04_remove_install-exec-am_rule.patch
 06_quicktest.patch
 07_destdir.patch
 08_distclean.patch

Modified: unstable/apbs/debian/rules
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/rules?rev=3552&op=diff
==============================================================================
--- unstable/apbs/debian/rules (original)
+++ unstable/apbs/debian/rules Sun Apr 29 21:11:37 2012
@@ -7,7 +7,7 @@
 export F77=/usr/bin/mpif77.$(ARCH_DEFAULT_MPI_IMPL)
 
 %:
-	dh $@ --with autoreconf
+	dh $@ --with autotools_dev,autoreconf
 
 override_dh_auto_clean:
 	-(cd examples; $(MAKE) distclean)
@@ -29,4 +29,7 @@
 override_dh_auto_test:
 	-$(MAKE) -C $(CURDIR)/examples/ quicktest APBS=$(CURDIR)/bin/apbs APBSBIN=$(CURDIR)/bin/apbs
 
+override_dh_install:
+	dh_install --sourcedir=$(CURDIR)/debian/tmp --list-missing
+
 .NOTPARALLEL:

Added: unstable/apbs/debian/upstream
URL: http://svn.debian.org/wsvn/debichem/unstable/apbs/debian/upstream?rev=3552&op=file
==============================================================================
--- unstable/apbs/debian/upstream (added)
+++ unstable/apbs/debian/upstream Sun Apr 29 21:11:37 2012
@@ -1,0 +1,12 @@
+Name: APBS
+Reference:
+ - Author: Nathan A. Baker, David Sept, Simpson Joseph, Michael J. Holst, J. Andrew McCammon
+   Title: "Electrostatics of nanosystems: application to microtubules and the ribosome"
+   Journal: Proc. Natl. Acad. Sci.
+   Year: 2001
+   Volume: 98
+   Number: 18
+   Pages: 10037-10041
+   eprint: http://www.pnas.org/content/98/18/10037.full.pdf
+   URL: http://www.pnas.org/content/98/18/10037.full
+   DOI: 10.1073/ypnas.181342398




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