From duncan@rice.research.bell-labs.com  Fri Nov 12 16:48:01 1999
From: duncan@rice.research.bell-labs.com (Duncan Temple Lang)
Date: Fri, 12 Nov 1999 11:48:01 -0500
Subject: Compilation of R under Mandrake Linux 6.1 (helios)
Message-ID: <199911121649.RAA12920@stat.math.ethz.ch>


> Cc: Duncan Temple Lang <duncan@rice.research.bell-labs.com>,
>         R-devel@stat.math.ethz.ch
> 
> rossini@biostat.washington.edu (A.J. Rossini) writes:
> 
> > (ob-reason for posting to R-devel:
> > 	Has anyone ever seen the error message:
> > 	"Abort."
> > 	with R?  Thomas hadn't either, and suggested running under
> > 	gdb, which I hope to, late this afternoon -- it's occuring
> > 	during a library call, in particular, the R/OMEGAHAT/CORBA
> > 	package, Duncan :-(...). 
> 
> I think that happens when the program calls abort(), which seems to
> happen (potentially) two times in memory.c and thrice in saveload.c.
> For the Windows version, there are three cases in regex.c.
> 
> Both cases in memory.c happen if one bumps into an object with an
> invalid typeof field during garbage collection. The ones in saveload.c
> all seem to be in the HDF5 code (where it would seem to be a bit of an
> overkill!). The ones in regex seem to be related to inconsistencies in
> the compiled regexp code. My guess would be that there's a memory
> corruption going on, triggering one of the traps in memory.c.
> 

It is going to be tricky to diagnose an abort() call without the
actual R command that caused it. My guess would be that there is an
exception being thrown in the Orbacus libraries and that is
propogating its way to abort.


Tony.
>> Sure, but they are two slightly different things.  R/GNOME/CORBA is
>> more for standard desktop integration, a bit away from the user; GNOME
>> is pretty useful/stable these days.  R/OMEGAHAT/CORBA still seems to
>> need some work, but theoretically will be quite interesting for
>> user-land stuff. 

Well the code for integrating R with Gnumeric is not "stable" either.
In fact I am not sure how much, if any, exists at this point. So
comparing the stability Gnome and the R/CORBA mechanism is
irrelevant. Even if there was that connection at the C level, more
would be needed to actual map data from R to CORBA and vice-versa.
This is what the dynamic CORBA facility in R does via "remote references".

Additionally, the R-S/CORBA interfaces are pretty solid here. A few
bug reports to omega-remote@omegahat.org (with perhaps a little more
information than above ;-)) will probably get them fixed pretty
rapidly.






> 
> -- 
>    O__  ---- Peter Dalgaard             Blegdamsvej 3  
>   c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
>  (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
> ~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907
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-- 
_______________________________________________________________

Duncan Temple Lang                duncan@research.bell-labs.com
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Compilation of R under Mandrake Linux 6.1 (helios)
Duncan Temple Lang