R devel - Jun 2004 - Nested shared library calls in Linux

Hi,

I have an interface from R to the wxPython GUI toolkit which 
works under Windows:
http://bioinf.wehi.edu.au/folders/james/wxPython/

(as long as you build RSPython with a shared (not static) 
Python library).

But on Linux I get an error:
> library(RSPython)
> importPythonModule("wx")
Error in .PythonEval(cmd) : Error in Python call: 
/export/share/disk501/lab0605/wettenhall/usr/local/lib/
python2.2/site-packages/wx/_core.so: 
undefined symbol: PyExc_IOError

I am working within my home area at the moment:
~ 
= /home/users/lab0605/wettenhall/
= /export/share/disk501/lab0605/wettenhall/

By running strace, I found that the Python command "import wx" 
correctly loads 
~/usr/local/lib/python2.2/site-packages/wx/_core.so

but then when _core.so tries to load libwx_gtk_html-2.5.so.1 
(its first shared-library-dependency), it only looks 
in one place:
~/usr/local/lib/R/bin/
i.e. THE DIRECTORY CONTAINING THE R SHARED LIBRARY.
when in fact it should be looking in:
~/usr/local/lib/

Has LD_LIBRARY_PATH somehow been collapsed into just one 
directory???  I have tried checking it with Sys.getenv() 
just before running importPythonModule("wx"), and 
it seems to be OK:  ~/usr/local/lib/ is certainly included 
in $LD_LIBRARY_PATH. 

I have included ~/usr/local/lib in my PYTHONPATH and 
I can also modify the Python path within R, using:
importPythonModule("sys")
.PythonEval("path=['path1','path2',...]",.module="sys")
or .PythonEval("path.append ...",.module="sys")

I have registered the shared libraries with ldconfig.

One more complication is that libwx_gtk_html-2.5.so.1 is 
actually a symbolic link to libwx_gtk_html-2.5.so.1.0.0 
(in the same directory, ~/usr/local/lib).

I'm running Fedora Linux with R 1.9.0. I've installed Python 
2.2.3 from source in ~/usr/local/ and I've built RSPython 
0.5-3 with a shared Python library libpython2.2.so (which I 
built from the Python source).  R and wxPython are also 
installed from source, both in ~/usr/local/ and R is 
configured with --enable-shlib.

If it would be helpful, I could try to come up with a much 
simpler example of nested shared-library calls from R, but 
people may wish to suggest that this is not the real problem.

Regards,
James
> version
         _
platform i686-pc-linux-gnu
arch     i686
os       linux-gnu
system   i686, linux-gnu
status
major    1
minor    9.0
year     2004
month    04
day      12
language R

Duncan,

Thanks for your answer.

I just realised that I was probably a bit too quick to claim 
that ~/usr/local/lib/R/bin/ is the only place that the dynamic 
linker is looking for libwx_gtk_html-2.5.so.1  I don't have much 
experience at reading strace output.  I think it looks in the 
wrong place initially, but then in the correct place.

On Jun 2004, Duncan Temple Lang wrote:
> What should happen is that _core.so and all Python packages
> should be linked against libpython2.2.so or libpython2.2.a.
> We can tell whether this has happened via
> 
>   ldd  /export/share/disk501/lab0605/wettenhall/usr/local/lib/
python2.2/site-packages/wx/_core.so 

I haven't included all the ldd output from wxPython's _core.so 
but I can tell you that libpython2.2.so is not there.  Here's 
some of the output:
unix28 507 % ldd _core.so
        libwx_gtk_html-2.5.so.1 => 
/home/users/lab0605/wettenhall/usr/local/lib/libwx_gtk_html-2.5.so.1 
(0x00842000)
        libwx_gtk_adv-2.5.so.1 => 
/home/users/lab0605/wettenhall/usr/local/lib/libwx_gtk_adv-2.5.so.1 
(0x00d98000)
        libwx_gtk_core-2.5.so.1 => 
/home/users/lab0605/wettenhall/usr/local/lib/libwx_gtk_core-2.5.so.1 
(0x00111000)
        libwx_base_xml-2.5.so.1 => 
/home/users/lab0605/wettenhall/usr/local/lib/libwx_base_xml-2.5.so.1 
(0x003e5000)
        libwx_base_net-2.5.so.1 => 
/home/users/lab0605/wettenhall/usr/local/lib/libwx_base_net-2.5.so.1 
(0x0054b000)
        libwx_base-2.5.so.1 => 
/home/users/lab0605/wettenhall/usr/local/lib/libwx_base-2.5.so.1 
(0x005e5000)
        libpthread.so.0 => /lib/tls/libpthread.so.0 (0x004e6000)
        libc.so.6 => /lib/tls/libc.so.6 (0x00a39000)
<snip>
> 
>   nm 
/export/share/disk501/lab0605/wettenhall/usr/local/lib/python2.2/site-packages/wx/_core.so
| grep PyExc_IOError
This returns:
unix28 510 % nm _core.so | grep PyExc_IOError
         U PyExc_IOError

i.e. the symbol is undefined in wxPython's _core.so

whereas it is defined in libpython2.2.so :
unix28 513 % nm libpython2.2.so | grep PyExc_IOError
000f65d8 B PyExc_IOError

(To be precise, it is declared but not initialized).

OK, so I guess I will experiment with trying to build wxPython 
and get it to link against libpython2.2.so.  

Or maybe for each wxPython .so file, I can just add a 
libpython2.2.so dependency with something like:
ld -o _core2.so _core.so libpython2.2.so
mv _core2.so _core.so

I'll play around with this sort of thing for a while...

Regards,
James