[igraph] R igraph 0.6 crashing on assortativity.nominal

[Marcel Salathé]

Hi

I run into problems with assortativity calculations. When using 
assortativity.nominal on a directed graph, it crashes (segfault).

Here's an example code that reproduces the behavior on my system (R version 
2.12.2 (2011-02-25), Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit), igraph 
0.6 downloaded today):

library(igraph)
toy = graph.formula(1-+2, 1-+3, 2-+1, 2-+3, 2-+4, 3-+2, 4-+5, 5-+2)
V(toy)$prop = c(-1,-1,0,1,1)
assortativity.nominal(toy,types=V(toy)$prop)

It seems to calculate and return a value but then crashes immediately. Because 
of the segfault, I'm not sure I trust the result though....

Here's the output:

> assortativity.nominal(toy,types=V(toy)$prop)
[1] 0.06666667

 *** caught segfault ***
address 0x0, cause 'unknown'

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
[1] 0.06666667

 *** caught segfault ***
address 0x0, cause 'unknown'

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

 *** caught segfault ***
address 0x0, cause 'unknown'

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 
Selection:



Thanks
Marcel



On Mar 28, 2011, at 3:01 PM, Gábor Csárdi wrote:

> This is not very surprising, if you compile it for x86_64, then it
> works only on x86_64. Compile it for i386 as well, and place it in
> another R package directory. Another option is to create a fat binary,
> that contains both the x86_64 and the i386 versions. I don't know how
> to do that, but most probably it is covered in the R OS X guide.
> 
> Best,
> Gabor
> 
> On Mon, Mar 28, 2011 at 1:13 PM, Marcel Salathé
> <address@hidden> wrote:
>> Compiling works now. However, library can only be loaded in 64-bit version 
>> of R (Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)).
>> 
>> On regular 32 bit version (Platform: i386-apple-darwin9.8.0/i386 (32-bit)), 
>> I get
>> 
>> Error: package 'igraph' is not installed for 'arch=i386'
>> 
>> Thanks,
>> Marcel
>> 
>> PS: I'm using R 2.12.2
>> 
>> 
>> 
>> 
>> On Mar 28, 2011, at 12:02 PM, Gábor Csárdi wrote:
>> 
>>> Oh, this is the R package, sorry, I just noticed the 'R' in the
>>> subject. This is a bug in the nightly bug service, the package
>>> contains some extra files that should not be there. I have uploaded a
>>> new nightly build that should fix this problem. Let me know if it does
>>> not.
>>> 
>>> Best,
>>> Gabor
>>> 
>>> On Mon, Mar 28, 2011 at 10:22 AM, Marcel Salathé
>>> <address@hidden> wrote:
>>>> Hi Gabor
>>>> 
>>>> I've just ran into the exact same problem as Przemyslaw.
>>>> 
>>>> I'm on Mac OS X 10.6.6, and I've been trying to install 
>>>> igraph_nightly_0.6-2410-20110324.tar.gz which I downloaded an hour ago 
>>>> from http://code.google.com/p/igraph/downloads/list
>>>> 
>>>> The error I get is
>>>> dnaupd.c:450: error: conflicting types for ‘igraphdnaupd_’
>>>> igraph_arpack_internal.h:147: error: previous declaration of 
>>>> ‘igraphdnaupd_’ was here
>>>> make: *** [dnaupd.o] Error 1
>>>> ERROR: compilation failed for package ‘igraph’
>>>> 
>>>> 
>>>> Best,
>>>> Marcel
>>>> 
>>>> 
>>>> On Mar 25, 2011, at 7:21 PM, Gábor Csárdi wrote:
>>>> 
>>>>> Przemyslaw,
>>>>> 
>>>>> then please tell us about your platform and configuration because it
>>>>> works fine for me.
>>>>> 
>>>>> Best,
>>>>> Gabor
>>>>> 
>>>>> On Fri, Mar 25, 2011 at 7:02 PM, Przemek Grabowicz
>>>>> <address@hidden> wrote:
>>>>>>  Hi Gabor,
>>>>>> 
>>>>>> In the newest development version from code.google.com this problem is 
>>>>>> still
>>>>>> present.
>>>>>> 
>>>>>> 
>>>>>> Przemyslaw Grabowicz.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> On 03/25/2011 01:45 PM, Gábor Csárdi wrote:
>>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> I can't recall the exact reason, but this has been fixed.
>>>>>>> 
>>>>>>> Best,
>>>>>>> Gabor
>>>>>>> 
>>>>>>> On Fri, Mar 25, 2011 at 11:23 AM, Przemek Grabowicz
>>>>>>> <address@hidden>  wrote:
>>>>>> 
>>>>>> _______________________________________________
>>>>>> igraph-help mailing list
>>>>>> address@hidden
>>>>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> --
>>>>> Gabor Csardi <address@hidden>     MTA KFKI RMKI
>>>>> 
>>>>> _______________________________________________
>>>>> igraph-help mailing list
>>>>> address@hidden
>>>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>> 
>>>> 
>>>> _______________________________________________
>>>> igraph-help mailing list
>>>> address@hidden
>>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> Gabor Csardi <address@hidden>     MTA KFKI RMKI
>> 
>> 
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>> 
> 
> 
> 
> -- 
> Gabor Csardi <address@hidden>     MTA KFKI RMKI