[R] problem loading rgdal with Rapache, problem solved due to libexpat with apache.

[Mike Marchywka]

Well, I'm not sure it is really an rgdal "problem" as much as 
having a stale so and I didn;t want to go wreck the thing to capture
the exact error message, the point was that apache build seems to have
come with incompatible expat so.  In the apache/lib dir, I apparently had a much
different libs, now named xxx, than that which was in /lib64. If I dump
the symbols with objdump the one rgdal complained about, IIRC XML_StopParser
does not appear in either output but they do grep differently
as shown below ( 

-rw-r--r-- 1 root root 605314 May  1 07:09 libexpat.a
-rwxr-xr-x 1 root root    805 May  1 07:09 libexpat.la
lrwxrwxrwx 1 root root     17 May  1 07:09 libexpat.so -> libexpat.so.0.5.0
lrwxrwxrwx 1 root root     17 May  1 07:09 libexpat.so.0 -> libexpat.so.0.5.0
-rwxr-xr-x 1 root root 143144 Jul  6 16:29 libexpat.so.0.5.0
-rwxr-xr-x 1 root root 398422 Jul  6 16:27 libexpat.soxxx.0.5.0

[marchywka at 351915-www1 lib]$ grep XML_StopParser libexpat*
Binary file libexpat.so matches
Binary file libexpat.so.0 matches
Binary file libexpat.so.0.5.0 matches
[marchywka at 351915-www1 lib]$ 



libexpat.so.0.5.0:
    linux-vdso.so.1 =>  (0x00002b4a1fdd2000)
    libc.so.6 => /lib64/libc.so.6 (0x00000035aca00000)
    /lib64/ld-linux-x86-64.so.2 (0x00000035ac600000)
libexpat.soxxx.0.5.0:
    linux-vdso.so.1 =>  (0x00007fff8bdfc000)
    libc.so.6 => /lib64/libc.so.6 (0x00002b143b19e000)
    /lib64/ld-linux-x86-64.so.2 (0x00000035ac600000)







> To: r-help at r-project.org
> Subject: Re: [R] problem loading rgdal with Rapache, problem solved due to libexpat with apache.
>
> You should provide at least the output of sessionInfo() and the messages
> issued by rgdal on load. rgdal has recently been updated to try to address
> issues of interference between applications, and it would help very much to
> know your intentions, platform, and the versions of the software you are
> using.
>
> Roger
>
>
> Mike Marchywka wrote:
> >
> > Has anyone had problems with Rapache that don't show up on command line
> > execution of R? I just ran into this loading rgdal in Rapache page and
> > having
> > a problem with loading shared object. The final complaint was that
> > Stop_XMLParser
> > was undefined- this was surprising since grep -l showed it in expat lib
> > and it worked
> > fine from command line. Finally, I noted the search path had apache/lib
> > ahead
> > of the other places where expat exists.  The libexpat there although
> > apparently having
> > same versio, so.0.5.0 did not grep for this symbol. Anyway, copying one
> > into
> > the other fixed the problem and the page works fine but curious is anyone
> > has thoughts on what could have caused this. Sorry I don't have
> > specific output but i thought you may remember if you ran into
> > it and it is not worth trying to replicate. Thanks.
> >
> >
> >
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
> -----
> Roger Bivand
> Department of Economics
> NHH Norwegian School of Economics
> Helleveien 30
> N-5045 Bergen, Norway
>
> --
> View this message in context: http://r.789695.n4.nabble.com/problem-loading-rgdal-with-Rapache-problem-solved-due-to-libexpat-with-apache-tp3650119p3652639.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.