Access violation exception when reading/writing xml formats

8 messages

Access violation exception when reading/writing xml formats

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I was working on the next release of OBDotNet when I discovered that read or writing any xml format triggers an access violation exception. After debugging into the C++ code I was able to identify the call to xmlFreeTextReader as the source of the exception. I've spent the last 3 days trying to figure out a work around but I'm stumped. Any thoughts?

-Matt

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Noel O'Boyle

Re: Access violation exception when reading/writing xml formats

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Are you working off the svn 22x branch?

2009/11/4 Matt Sprague <[hidden email]>:

> I was working on the next release of OBDotNet when I discovered that read
> or writing any xml format triggers an access violation exception. After
> debugging into the C++ code I was able to identify the call to
> xmlFreeTextReader as the source of the exception. I've spent the last 3 days
> trying to figure out a work around but I'm stumped. Any thoughts?
>
> -Matt
>
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Noel O'Boyle

Re: Access violation exception when reading/writing xml formats

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2009/11/4 Matt Sprague <[hidden email]>:
> On Wed, Nov 4, 2009 at 7:11 AM, Noel O'Boyle <[hidden email]> wrote:
> Are you working off the svn 22x branch?
>
> Yes, is there a another branch I should switch to?

No - that's fine. Just checking.

> Also, just to clarify,
> this is only a problem in with the bindings it works fine in C++.

Ok - that's useful to know.

That's pretty weird though. The XML formats are always problematic
though as everything goes through libxml and it seems to be a bit
messy. Could it be that it is picking up on the wrong libxml2 or
whatever? Or that there is some conflict there? Chris is the resident
expert on all things XML/Windows, but if it cannot be reproduced in
C++ it'll be next to impossible for him to debug.

I have a mixture of different OBs on my computer so I can't easily
check whether XML read/writing works from Python, but I will do so as
soon as possible.

- Noel

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Chris Morley

Re: Access violation exception when reading/writing xml formats

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In reply to this post by Matt Sprague

Matt Sprague wrote:
> I was working on the next release of OBDotNet when I discovered that
> read or writing any xml format triggers an access violation exception.
> After debugging into the C++ code I was able to identify the call to
> xmlFreeTextReader as the source of the exception. I've spent the last 3
> days trying to figure out a work around but I'm stumped. Any thoughts?

I find libxml2 difficult and cumbersome to work with. Its interface is
C, not a C++, in style and sometimes, but not always, you have to
delete the memory used by strings it has given you and other objects.
I have to confess I never really sorted this out properly and the code
was left working in C++ but possibly with memory leaks. I'm sorry if
it has turned out to be more than this and has wasted your time.

I'll try to look at it again, but, in the meantime, it looks as if it
could benefit addition of the second line here

xmlFreeTextReader(_reader);
_reader = NULL;

This would ensure it wasn't deleted twice, which might be the
immediate cause of the error.

Chris

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Matt Sprague

Re: Access violation exception when reading/writing xml formats

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In reply to this post by Noel O'Boyle

Noel, did you ever get a chance to check whether or not this exception happens in the python bindings? I downloaded the libxml2 source and built the dll with MinGW using the posix threading library (pthreadgc2.dll) and that seems to work fine on my machine. Maybe be it's a bug in the VC runtime?

-Matt

On Thu, Nov 5, 2009 at 4:41 AM, Noel O'Boyle <[hidden email]> wrote:

2009/11/4 Matt Sprague <[hidden email]>:

> On Wed, Nov 4, 2009 at 7:11 AM, Noel O'Boyle <[hidden email]> wrote:
> Are you working off the svn 22x branch?
>
> Yes, is there a another branch I should switch to?

No - that's fine. Just checking.

> Also, just to clarify,
> this is only a problem in with the bindings it works fine in C++.

Ok - that's useful to know.

That's pretty weird though. The XML formats are always problematic
though as everything goes through libxml and it seems to be a bit
messy. Could it be that it is picking up on the wrong libxml2 or
whatever? Or that there is some conflict there? Chris is the resident
expert on all things XML/Windows, but if it cannot be reproduced in
C++ it'll be next to impossible for him to debug.

I have a mixture of different OBs on my computer so I can't easily
check whether XML read/writing works from Python, but I will do so as
soon as possible.

- Noel

Noel O'Boyle

Re: Access violation exception when reading/writing xml formats

Reply Threaded

No I didn't. I saw that Geoff had attempted to fix this issue so I was
waiting to hear from you:
http://openbabel.svn.sourceforge.net/viewvc/openbabel?view=rev&revision=3455

This is on the trunk, but presumably you could cut 'n' paste onto the branch.

If you can check this out, I'll follow up with python.

- Noel

2009/11/30 Matt Sprague <[hidden email]>:

> Noel, did you ever get a chance to check whether or not this exception
> happens in the python bindings? I downloaded the libxml2 source and built
> the dll with MinGW using the posix threading library (pthreadgc2.dll) and
> that seems to work fine on my machine. Maybe be it's a bug in the VC
> runtime?
>
> -Matt
>
>
> On Thu, Nov 5, 2009 at 4:41 AM, Noel O'Boyle <[hidden email]> wrote:
>>
>> 2009/11/4 Matt Sprague <[hidden email]>:
>> > On Wed, Nov 4, 2009 at 7:11 AM, Noel O'Boyle <[hidden email]>
>> > wrote:
>> > Are you working off the svn 22x branch?
>> >
>> > Yes, is there a another branch I should switch to?
>>
>> No - that's fine. Just checking.
>>
>> > Also, just to clarify,
>> > this is only a problem in with the bindings it works fine in C++.
>>
>> Ok - that's useful to know.
>>
>> That's pretty weird though. The XML formats are always problematic
>> though as everything goes through libxml and it seems to be a bit
>> messy. Could it be that it is picking up on the wrong libxml2 or
>> whatever? Or that there is some conflict there? Chris is the resident
>> expert on all things XML/Windows, but if it cannot be reproduced in
>> C++ it'll be next to impossible for him to debug.
>>
>> I have a mixture of different OBs on my computer so I can't easily
>> check whether XML read/writing works from Python, but I will do so as
>> soon as possible.
>>
>> - Noel
>
>

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Matt Sprague

Re: Access violation exception when reading/writing xml formats

Reply Threaded

Nope, that didn't help. The program is crashing inside of the the call to xmlFreeTextReader. You can view the source here:

http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup

Whatever is happening occurs between the beginning of the function (line 2177)

and the call to xmlFreeParserInputBuffer(input) (line 2245). I thought I was closing in on the problem, but the version of libxml2 I built with MinGW works just fine. So now I'm really puzzled.

-Matt

Noel O'Boyle

Re: Access violation exception when reading/writing xml formats

Reply Threaded

Seems to work fine from Python. Using OpenBabel on the trunk, I have:

>>> mol = pybel.readstring("smi", "CC(=O)Cl")
>>> print mol.write("cml")
<molecule>
<atomArray>
<atom id="a1" elementType="C"/>
<atom id="a2" elementType="C"/>
<atom id="a3" elementType="O"/>
<atom id="a4" elementType="Cl"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a2 a3" order="2"/>
<bond atomRefs2="a2 a4" order="1"/>
</bondArray>
</molecule>

>>>

I am using the libxml2.dll that comes with OpenBabel 2.2.3, which I
can test with Cygwin's "which" as follows:
C:\> which libxml2.dll
/cygdrive/c/Program Files/OpenBabel-2.2.3/libxml2.dll

I haven't done any work enabling other scripting languages on the
trunk, so I can't easily test whether it works from C# there...

- Noel

2009/12/1 Matt Sprague <[hidden email]>:

> Nope, that didn't help. The program is crashing inside of the the call
> to xmlFreeTextReader. You can view the source here:
> http://svn.gnome.org/viewvc/libxml2/trunk/xmlreader.c?revision=3795&view=markup
> Whatever is happening occurs between the beginning of the function (line
> 2177)
> and the call to xmlFreeParserInputBuffer(input) (line 2245). I thought I was
> closing in on the problem, but the version of libxml2 I built with MinGW
> works just fine. So now I'm really puzzled.
>
> -Matt
>
>
>