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[OpenBabel-scripting] Ruby-Open Babel not Still Not Working (detailed)
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From: richard a. <ric...@ya...> - 2006-10-14 20:47:56
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I upgraded to SWIG 1.3.29, as Geoff suggested. After
compiling the swig wrapper, I still get a segfault on
loading the Ruby module.
Before submitting a bug report to SWIG, I wanted to
make sure I was doing this correctly. So here is my
process in detail. I'm using Open Babel 2.0.2, Ruby
1.8.5, and Mandriva Linux 2007 amd64.
(1) ./configure, make, and (as root) make install OB
(2) cd into OPENBABEL/scripts
(3) edit openbabel.i: comment out line 27 (Swig can't
find std_list.i for Ruby - it works for Python,
though). Change line 5 to %module openbabel_wrap
(don't want to risk a collision w/ installed openbabel
library)
(4) generate the SWIG wrapper:
swig -ruby -c++ -I../src openbabel.i
This generates lots of warnings that don't appear when
the argument is -python instead of -ruby (maybe this
is the problem):
../src/math/vector3.h:114: Warning(389): operator[]
ignored (consider using %extend)
../src/math/vector3.h:123: Warning(362): operator=
ignored
../src/math/vector3.h:130: Warning(378): operator!=
ignored
../src/math/vector3.h:180: Warning(365): operator+=
ignored
../src/math/vector3.h:187: Warning(366): operator-=
ignored
../src/math/vector3.h:194: Warning(365): operator+=
ignored
../src/math/vector3.h:201: Warning(366): operator-=
ignored
../src/math/vector3.h:208: Warning(367): operator*=
ignored
../src/math/vector3.h:215: Warning(368): operator/=
ignored
../src/math/vector3.h:217: Warning(367): operator*=
ignored
../src/bitvec.h:121: Warning(362): operator= ignored
../src/bitvec.h:122: Warning(371): operator&= ignored
../src/bitvec.h:123: Warning(372): operator|= ignored
../src/bitvec.h:128: Warning(372): operator|= ignored
../src/bitvec.h:129: Warning(370): operator^= ignored
../src/bitvec.h:130: Warning(366): operator-= ignored
../src/bitvec.h:131: Warning(365): operator+= ignored
../src/bitvec.h:136: Warning(389): operator[] ignored
(consider using %extend)
../src/generic.h:152: Warning(362): operator= ignored
../src/generic.h:170: Warning(362): operator= ignored
../src/generic.h:279: Warning(362): operator= ignored
../src/generic.h:310: Warning(362): operator= ignored
../src/generic.h:364: Warning(362): operator= ignored
../src/generic.h:399: Warning(362): operator= ignored
../src/generic.h:437: Warning(362): operator= ignored
../src/generic.h:483: Warning(362): operator= ignored
../src/generic.h:531: Warning(362): operator= ignored
../src/generic.h:567: Warning(362): operator= ignored
../src/generic.h:598: Warning(362): operator= ignored
../src/mol.h:87: Warning(362): operator= ignored
../src/mol.h:233: Warning(362): operator= ignored
../src/mol.h:785: Warning(362): operator= ignored
../src/mol.h:786: Warning(365): operator+= ignored
../src/ring.h:62: Warning(362): operator= ignored
../src/parsmart.h:207: Warning(362): operator= ignored
../src/oberror.h:162: Warning(401): Nothing known
about base class 'std::stringbuf'. Ignored.
../src/obconversion.h:175: Warning(401): Nothing known
about base class 'std::binary_function<char const
*,char const *,bool >'. Ignored.
../src/obconversion.h:175: Warning(401): Maybe you
forgot to instantiate 'std::binary_function<char const
*,char const *,bool >' using %template.
openbabel.i:33: Warning(801): Wrong class name
(corrected to `VectorInt')
openbabel.i:33: Warning(801): Wrong class name
(corrected to `VectorInt')
openbabel.i:34: Warning(801): Wrong class name
(corrected to `VvInt')
openbabel.i:34: Warning(801): Wrong class name
(corrected to `VvInt')
openbabel.i:35: Warning(801): Wrong class name
(corrected to `VectorDouble')
openbabel.i:35: Warning(801): Wrong class name
(corrected to `VectorDouble')
openbabel.i:36: Warning(801): Wrong class name
(corrected to `VVector3')
openbabel.i:36: Warning(801): Wrong class name
(corrected to `VVector3')
openbabel.i:38: Warning(801): Wrong class name
(corrected to `VectorMol')
openbabel.i:38: Warning(801): Wrong class name
(corrected to `VectorMol')
openbabel.i:39: Warning(801): Wrong class name
(corrected to `VectorBond')
openbabel.i:39: Warning(801): Wrong class name
(corrected to `VectorBond')
openbabel.i:40: Warning(801): Wrong class name
(corrected to `VectorResidue')
openbabel.i:40: Warning(801): Wrong class name
(corrected to `VectorResidue')
openbabel.i:41: Warning(801): Wrong class name
(corrected to `VectorRing')
openbabel.i:41: Warning(801): Wrong class name
(corrected to `VectorRing')
../src/math/vector3.h:57: Warning(801): Wrong class
name (corrected to `Vector3')
../src/math/vector3.h:57: Warning(801): Wrong class
name (corrected to `Vector3')
../src/math/vector3.h:126: Warning(503): Can't wrap
'operator <<' unless renamed to a valid identifier.
../src/math/vector3.h:129: Warning(503): Can't wrap
'operator ==' unless renamed to a valid identifier.
../src/math/vector3.h:137: Warning(503): Can't wrap
'operator +' unless renamed to a valid identifier.
../src/math/vector3.h:142: Warning(503): Can't wrap
'operator -' unless renamed to a valid identifier.
../src/math/vector3.h:147: Warning(503): Can't wrap
'operator -' unless renamed to a valid identifier.
../src/math/vector3.h:152: Warning(503): Can't wrap
'operator *' unless renamed to a valid identifier.
../src/math/vector3.h:157: Warning(503): Can't wrap
'operator *' unless renamed to a valid identifier.
../src/math/vector3.h:162: Warning(503): Can't wrap
'operator /' unless renamed to a valid identifier.
../src/math/vector3.h:171: Warning(503): Can't wrap
'operator *' unless renamed to a valid identifier.
../src/math/vector3.h:225: Warning(503): Can't wrap
'OpenBabel::dot' unless renamed to a valid identifier.
../src/math/vector3.h:228: Warning(503): Can't wrap
'OpenBabel::cross' unless renamed to a valid
identifier.
../src/math/vector3.h:231: Warning(503): Can't wrap
'OpenBabel::vectorAngle' unless renamed to a valid
identifier.
../src/math/vector3.h:235: Warning(503): Can't wrap
'OpenBabel::CalcTorsionAngle' unless renamed to a
valid identifier.
../src/oberror.h:162: Warning(801): Wrong class name
(corrected to `ObLogBuf')
(5) create a new directory called "ruby"
(6) move openbabel_wrap.cxx, generated from SWIG, into
the ruby directory
(7) cd into ruby directory
(8) save the following as "extconf.rb":
require 'mkmf'
dir_config('openbabel')
dir_config('openbabel-2.0')
have_library('openbabel')
create_makefile('openbabel_wrap')
(9) create the makefile:
ruby extconf.rb
--with-openbabel-include='/usr/local/include/openbabel-2.0/openbabel'
--with-openbabel-2.0-include='/usr/local/include/openbabel-2.0'
this produces:
checking for main() in -lopenbabel... yes
creating Makefile
and creates "Makefile"
(10) add the following to line 10 of
openbabel_wrap.cxx:
#include <math.h>
(11) make. This generates the following messages:
g++ -I. -I. -I/usr/lib/ruby/1.8/x86_64-linux-gnu -I.
-I/usr/local/include/openbabel-2.0
-I/usr/local/include/openbabel-2.0/openbabel -fPIC
-O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
-Wall -fPIC -c openbabel_wrap.cxx
In file included from
/usr/local/include/openbabel-2.0/openbabel/obutil.h:23,
from openbabel_wrap.cxx:1648:
/usr/local/include/openbabel-2.0/openbabel/babelconfig.h:18:1:
warning: "EXTERN" redefined
In file included from
/usr/lib/ruby/1.8/x86_64-linux-gnu/ruby.h:28,
from openbabel_wrap.cxx:809:
/usr/lib/ruby/1.8/x86_64-linux-gnu/defines.h:203:1:
warning: this is the location of the previous
definition
openbabel_wrap.cxx: In function int
SWIG_AsPtr_std_string(VALUE, std::string**):
openbabel_wrap.cxx:2186: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorInt__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:2455: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorInt(int, VALUE*, VALUE):
openbabel_wrap.cxx:2509: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorInt___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:2568: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorInt_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:2604: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vvInt__SWIG_2(int, VALUE*, VALUE):
openbabel_wrap.cxx:2874: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vvInt__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:2918: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:2922: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vvInt(int, VALUE*, VALUE):
openbabel_wrap.cxx:2969: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:2978: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3014: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vvInt___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:3050: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3054: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vvInt_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:3082: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3086: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vvInt_push(int, VALUE*, VALUE):
openbabel_wrap.cxx:3149: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vvInt___setitem__(int, VALUE*, VALUE):
openbabel_wrap.cxx:3273: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorDouble__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:3429: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorDouble(int, VALUE*, VALUE):
openbabel_wrap.cxx:3483: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorDouble___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:3542: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorDouble_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:3578: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vVector3__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:3883: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3887: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vVector3(int, VALUE*, VALUE):
openbabel_wrap.cxx:3934: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3943: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vVector3___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:3993: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:3997: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vVector3_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:4025: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4029: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorMol__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:4343: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4347: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorMol(int, VALUE*, VALUE):
openbabel_wrap.cxx:4394: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4403: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorMol___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:4453: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4457: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorMol_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:4485: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4489: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorBond__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:4803: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4807: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorBond(int, VALUE*, VALUE):
openbabel_wrap.cxx:4854: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4863: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorBond___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:4913: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4917: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorBond_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:4945: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:4949: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorResidue__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:5263: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5267: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorResidue(int, VALUE*, VALUE):
openbabel_wrap.cxx:5314: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5323: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorResidue___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:5373: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5377: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorResidue_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:5405: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5409: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorRing__SWIG_3(int, VALUE*, VALUE):
openbabel_wrap.cxx:5723: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5727: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_new_vectorRing(int, VALUE*, VALUE):
openbabel_wrap.cxx:5774: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5783: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorRing___len__(int, VALUE*, VALUE):
openbabel_wrap.cxx:5833: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5837: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx: In function VALUE
_wrap_vectorRing_emptyq___(int, VALUE*, VALUE):
openbabel_wrap.cxx:5865: warning: dereferencing
type-punned pointer will break strict-aliasing rules
openbabel_wrap.cxx:5869: warning: dereferencing
type-punned pointer will break strict-aliasing rules
gcc -shared -L"/usr/lib64" -o openbabel_wrap.so
openbabel_wrap.o -lruby -lopenbabel -lpthread -ldl
-lcrypt -lm -lc
The following files are created:
openbabel_wrap.o
openbabel_wrap.so
(12) irb
(13) require 'openbabel_wrap'
produces:
irb(main):001:0> require 'openbabel_wrap'
(eval): [BUG] Segmentation fault
ruby 1.8.5 (2006-08-25) [x86_64-linux-gnu]
Aborted
As I mentioned before, if I remove the OBAtom, OBBond,
and OBMol definitions from Init_openbabel_wrap (last
function), the Ruby module is loaded without
segfaulting. I can also remove everything from the
respective stanzas except the first line and still I
get a segfault, so I'm guessing this is where the
error happens.
Would someone be willing to go through this series of
steps to verify that the problem is not related to my
system's configuration (my version of Ruby, my
platform, my compiler, etc.)
cheers,
Rich
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