Date: Friday, June 26, 2015 @ 07:08:12
Author: foutrelis
Revision: 135888
Fix build with GCC 5.1 and Swig 3
Added:
python-openbabel/trunk/openbabel-gcc5.patch
python-openbabel/trunk/openbabel-swig3.patch
Modified:
python-openbabel/trunk/PKGBUILD
-----------------------+
PKGBUILD | 20 +++-
openbabel-gcc5.patch | 12 ++
openbabel-swig3.patch | 199 ++++++++++++++++++++++++++++++++++++++++++++++++
3 files changed, 226 insertions(+), 5 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2015-06-26 04:41:13 UTC (rev 135887)
+++ PKGBUILD 2015-06-26 05:08:12 UTC (rev 135888)
@@ -12,13 +12,23 @@
license=('GPL')
depends=('gcc-libs' "openbabel=${pkgver}" 'eigen2')
makedepends=('swig' 'cmake' 'python-setuptools' 'python2-setuptools')
-source=("http://downloads.sourceforge.net/openbabel/openbabel-$pkgver.tar.gz";)
-sha256sums=('4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188')
+source=("http://downloads.sourceforge.net/openbabel/openbabel-$pkgver.tar.gz";
+ openbabel-gcc5.patch
+ openbabel-swig3.patch)
+sha256sums=('4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188'
+ '0b022f4adeb16c8531e13871f6c6d256c8939defb5be0fe32d0a28711f2d933e'
+ '6c8fb33199d4b4fa03128278110275502266b915ca9c43ef0dc87f24a0cadf06')
+prepare() {
+ patch -d openbabel-$pkgver -Np1 < openbabel-gcc5.patch
+ patch -d openbabel-$pkgver -Np1 < openbabel-swig3.patch
+
+ cp -r openbabel-$pkgver python2-openbabel-$pkgver
+}
+
build() {
- cp -r openbabel-$pkgver python2-openbabel-$pkgver
- cd $srcdir/openbabel-$pkgver
-
+ cd "$srcdir/openbabel-$pkgver"
+
# Create babelconfig.h
cmake .
Added: openbabel-gcc5.patch
===================================================================
--- openbabel-gcc5.patch (rev 0)
+++ openbabel-gcc5.patch 2015-06-26 05:08:12 UTC (rev 135888)
@@ -0,0 +1,12 @@
+diff -upr openbabel-2.3.2.orig/include/openbabel/shared_ptr.h
openbabel-2.3.2/include/openbabel/shared_ptr.h
+--- openbabel-2.3.2.orig/include/openbabel/shared_ptr.h 2011-10-12
23:24:02.000000000 +0300
++++ openbabel-2.3.2/include/openbabel/shared_ptr.h 2015-06-26
08:00:31.909272930 +0300
+@@ -21,7 +21,7 @@ GNU General Public License for more deta
+ #define shared_ptr boost::shared_ptr
+ #else
+ #include <memory>
+- #if __GNUC__ == 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of
Konstantin Tokarev
++ #if __GNUC__ >= 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of
Konstantin Tokarev
+ #include <tr1/memory>
+ #endif
+ using std::tr1::shared_ptr;
Added: openbabel-swig3.patch
===================================================================
--- openbabel-swig3.patch (rev 0)
+++ openbabel-swig3.patch 2015-06-26 05:08:12 UTC (rev 135888)
@@ -0,0 +1,199 @@
+From 673dd2e864ba8a51e83d20cbdcabf3772f9df9d7 Mon Sep 17 00:00:00 2001
+From: David Hall <da...@acpharis.com>
+Date: Thu, 12 Feb 2015 08:50:23 -0500
+Subject: [PATCH] Swig3 patch from Fedora
+
+---
+ scripts/openbabel-perl.i | 20 ++++++++++----------
+ scripts/openbabel-python.i | 34 +++++++++++++++++-----------------
+ scripts/openbabel-ruby.i | 18 +++++++++---------
+ 3 files changed, 36 insertions(+), 36 deletions(-)
+
+diff --git a/scripts/openbabel-perl.i b/scripts/openbabel-perl.i
+index f3b35ed..4047859 100644
+--- a/scripts/openbabel-perl.i
++++ b/scripts/openbabel-perl.i
+@@ -179,7 +179,7 @@ CAST_GENERICDATA_TO(VirtualBond)
+
+ %import <openbabel/math/spacegroup.h>
+
+-# CloneData should be used instead of the following method
++%# CloneData should be used instead of the following method
+ %ignore OpenBabel::OBBase::SetData;
+ %rename(_local) OpenBabel::local;
+ %include <openbabel/base.h>
+@@ -224,7 +224,7 @@ namespace std { class stringbuf {}; }
+ %ignore OpenBabel::OBForceField::DiverseConfGen;
+ #endif
+
+-# Ignore shadowed methods
++%# Ignore shadowed methods
+ %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const
double *const, double *);
+ %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const
double, double *);
+ %include <openbabel/forcefield.h>
+@@ -234,20 +234,20 @@ namespace std { class stringbuf {}; }
+
+ %warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded
operators
+ %include <openbabel/bitvec.h>
+-# Ignore shadowed method
++%# Ignore shadowed method
+ %ignore OpenBabel::OBRotor::GetRotAtoms() const;
+ %warnfilter(314); // 'next' is a Perl keyword
+ %include <openbabel/rotor.h>
+ %ignore OpenBabel::Swab;
+ %include <openbabel/rotamer.h>
+
+-# The following %ignores avoid warning messages due to shadowed classes.
+-# This does not imply a loss of functionality as (in this case)
+-# the shadowed class is identical (from the point of view of SWIG) to
+-# the shadowing class.
+-# This is because C++ references (&) are transformed by SWIG back into
+-# pointers, so that OBAtomIter(OBMol &) would be treated the same as
+-# OBAtomIter(OBMol *).
++%# The following %ignores avoid warning messages due to shadowed classes.
++%# This does not imply a loss of functionality as (in this case)
++%# the shadowed class is identical (from the point of view of SWIG) to
++%# the shadowing class.
++%# This is because C++ references (&) are transformed by SWIG back into
++%# pointers, so that OBAtomIter(OBMol &) would be treated the same as
++%# OBAtomIter(OBMol *).
+
+ %ignore OBAtomAtomIter(OBAtom &);
+ %ignore OBAtomBondIter(OBAtom &);
+diff --git a/scripts/openbabel-python.i b/scripts/openbabel-python.i
+index dd1d263..90741f6 100644
+--- a/scripts/openbabel-python.i
++++ b/scripts/openbabel-python.i
+@@ -229,7 +229,7 @@ CAST_GENERICDATA_TO(SquarePlanarStereo)
+ %include <openbabel/math/transform3d.h>
+ %include <openbabel/math/spacegroup.h>
+
+-# CloneData should be used instead of the following method
++%# CloneData should be used instead of the following method
+ %ignore OpenBabel::OBBase::SetData;
+ %include <openbabel/base.h>
+
+@@ -291,7 +291,7 @@ OBMol.BeginResidues = OBMol.EndResidues =
OBMol.BeginResidue = OBMol.EndResidue
+ %ignore OpenBabel::OBDescriptor::LessThan;
+ %include <openbabel/descriptor.h>
+
+-# Ignore shadowed methods
++%# Ignore shadowed methods
+ %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const
double *const, double *);
+ %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const
double, double *);
+ %include <openbabel/forcefield.h>
+@@ -312,7 +312,7 @@ OBMol.BeginResidues = OBMol.EndResidues =
OBMol.BeginResidue = OBMol.EndResidue
+
+ %warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded
operators
+ %include <openbabel/bitvec.h>
+-# Ignore shadowed method
++%# Ignore shadowed method
+ %ignore OpenBabel::OBRotor::GetRotAtoms() const;
+ %include <openbabel/rotor.h>
+ %ignore OpenBabel::Swab;
+@@ -323,13 +323,13 @@ OBMol.BeginResidues = OBMol.EndResidues =
OBMol.BeginResidue = OBMol.EndResidue
+ %include <openbabel/math/align.h>
+ #endif
+
+-# The following %ignores avoid warning messages due to shadowed classes.
+-# This does not imply a loss of functionality as (in this case)
+-# the shadowed class is identical (from the point of view of SWIG) to
+-# the shadowing class.
+-# This is because C++ references (&) are transformed by SWIG back into
+-# pointers, so that OBAtomIter(OBMol &) would be treated the same as
+-# OBAtomIter(OBMol *).
++%# The following %ignores avoid warning messages due to shadowed classes.
++%# This does not imply a loss of functionality as (in this case)
++%# the shadowed class is identical (from the point of view of SWIG) to
++%# the shadowing class.
++%# This is because C++ references (&) are transformed by SWIG back into
++%# pointers, so that OBAtomIter(OBMol &) would be treated the same as
++%# OBAtomIter(OBMol *).
+
+ %ignore OBAtomAtomIter(OBAtom &);
+ %ignore OBAtomBondIter(OBAtom &);
+@@ -348,9 +348,9 @@ OBMol.BeginResidues = OBMol.EndResidues =
OBMol.BeginResidue = OBMol.EndResidue
+ %ignore OBResidueIter(OBMol &);
+ %ignore OBResidueAtomIter(OBResidue &);
+
+-# These classes are renamed so that they can be replaced by Python
+-# classes of the same name which provide Pythonic iterators
+-# (see %pythoncode section below)
++%# These classes are renamed so that they can be replaced by Python
++%# classes of the same name which provide Pythonic iterators
++%# (see %pythoncode section below)
+
+ %rename(_OBAtomAtomIter) OpenBabel::OBAtomAtomIter;
+ %rename(_OBAtomBondIter) OpenBabel::OBAtomBondIter;
+@@ -369,8 +369,8 @@ OBMol.BeginResidues = OBMol.EndResidues =
OBMol.BeginResidue = OBMol.EndResidue
+
+ %include <openbabel/obiter.h>
+
+-# The following class, OBiter, is subclassed to provide Python iterators
+-# equivalent to the C++ iterators in obiter.h and the plugin iterators
++%# The following class, OBiter, is subclassed to provide Python iterators
++%# equivalent to the C++ iterators in obiter.h and the plugin iterators
+
+ %pythoncode %{
+ class OBIter(object):
+@@ -460,7 +460,7 @@ def double_array(mylist):
+ return c
+ %}
+
+-# Copy some of the global variables in cvar into the openbabel namespace
++%# Copy some of the global variables in cvar into the openbabel namespace
+
+ %pythoncode %{
+ obErrorLog = cvar.obErrorLog
+@@ -471,7 +471,7 @@ atomtyper = cvar.atomtyper
+ aromtyper = cvar.aromtyper
+ %}
+
+-# Functions to set the log file to std::cout and std::cerr
++%# Functions to set the log file to std::cout and std::cerr
+
+ %ignore OBForceField::SetLogFile(std::ostream *pos);
+ %extend OpenBabel::OBForceField {
+diff --git a/scripts/openbabel-ruby.i b/scripts/openbabel-ruby.i
+index c812383..40773d8 100644
+--- a/scripts/openbabel-ruby.i
++++ b/scripts/openbabel-ruby.i
+@@ -181,7 +181,7 @@ CAST_GENERICDATA_TO(VirtualBond)
+
+ %import <openbabel/math/spacegroup.h>
+
+-# CloneData should be used instead of the following method
++%# CloneData should be used instead of the following method
+ %ignore OpenBabel::OBBase::SetData;
+ %include <openbabel/base.h>
+ %include <openbabel/generic.h>
+@@ -217,7 +217,7 @@ namespace std { class stringbuf {}; }
+ %include <openbabel/fingerprint.h>
+ %include <openbabel/descriptor.h>
+
+-# Ignore shadowed methods
++%# Ignore shadowed methods
+ %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const
double *const, double *);
+ %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const
double, double *);
+ #ifdef HAVE_EIGEN
+@@ -241,13 +241,13 @@ namespace std { class stringbuf {}; }
+ %ignore OpenBabel::Swab;
+ %include <openbabel/rotamer.h>
+
+-# The following %ignores avoid warning messages due to shadowed classes.
+-# This does not imply a loss of functionality as (in this case)
+-# the shadowed class is identical (from the point of view of SWIG) to
+-# the shadowing class.
+-# This is because C++ references (&) are transformed by SWIG back into
+-# pointers, so that OBAtomIter(OBMol &) would be treated the same as
+-# OBAtomIter(OBMol *).
++%# The following %ignores avoid warning messages due to shadowed classes.
++%# This does not imply a loss of functionality as (in this case)
++%# the shadowed class is identical (from the point of view of SWIG) to
++%# the shadowing class.
++%# This is because C++ references (&) are transformed by SWIG back into
++%# pointers, so that OBAtomIter(OBMol &) would be treated the same as
++%# OBAtomIter(OBMol *).
+
+ %ignore OBAtomAtomIter(OBAtom &);
+ %ignore OBAtomBondIter(OBAtom &);
