Incompatible library version

Users Mailing List Archive
1

Hello,

Has anyone ever seen this error before?

ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/lxml/etree.so, 2): Library not loaded: /opt/local/lib/libxml2.2.dylib
Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/lxml/etree.so
Reason: Incompatible library version: etree.so requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0

I was trying to upgrade my AIMBAT package, which uses Obspy. I installed Obspy using Macports, per the instructions on Github.

Thanks for the help.

Greg

2

Hi Greg,
looks like the problem is not directly related to Obspy, but due to libxml2 and py-lxml.
Usually, such problems surface and get fixed pretty fast by the Macports maintainers.
Have you installed the up-to-date versions of these packages?

Could you provide me the command which triggers the problem, so I can have a look at this and reproduce this?

Thanks!
~petr

3

Hi Greg,
from what I see on my system there should be no problem any more (see below):

otool -L /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/lxml/etree.so
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/lxml/etree.so:
  /opt/local/lib/libxslt.1.dylib (compatibility version 3.0.0, current version 3.28.0)
  /opt/local/lib/libexslt.0.dylib (compatibility version 9.0.0, current version 9.17.0)
  /opt/local/lib/libxml2.2.dylib (compatibility version 12.0.0, current version 12.1.0)
  /opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)

You probably should be able to solve the problem by updating your `libxml2` library.

Just do a selfupdate to Macports:
  sudo port -v selfupdate

Then update `libxml2`:
  sudo port -v upgrade libxml2

Or upgrade `py27-obspy`, which should trigger the update of all dependencies as well:
  sudo port -v upgrade py27-obspy

Hope that helps!
~petr

4

Hi Greg,
I had a similar error on my mac os 10.9.4

You can find several libxml2.2.dylib files on disk and check the versions using otool:

otool -L /sw/lib/libxml2.2.dylib
/sw/lib/libxml2.2.dylib:
/sw/lib/libxml2.2.dylib (compatibility version 12.0.0, current version 12.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
/sw/lib/liblzma.5.dylib (compatibility version 6.0.0, current version 6.5.0)
/sw/lib/libiconv.2.dylib (compatibility version 8.0.0, current version 8.1.0)

otool -L /usr/lib/libxml2.2.dylib
/usr/lib/libxml2.2.dylib:
/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 51.1.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)

So maybe you just need to set your LIBRARY and/or LD_LIBRARY_PATH to point to
the right version.
That fixed it for me.

5

Does anyone have experience using swig to compile a c-routine
so that it can be imported into a python script ?

In particular, this is for mac os 10.9 and python 2.7

The examples shown in the swig docs are for older versions of mac os
and the gcc flags for linking don't really make sense (to me).

It would be extremely useful to be able to bring an obspy.core.Trace
object into C where data[] and stats could be accessed directly from trace.

Has anyone tried this ?

Cheers,
-Mike

6

Hi Mike,

I have no experience using swig, but did you have a look at Cython and scipy.weave?
I am not sure what exactly you need, but both of the named modules are capable of importing c/c++ libraries. I am for instance using scipy.weave with C GSL libs without any issues.

Cheers,
Martin

7

I covered some of this briefly in the 2010 USArray Data Processing short course. I think it is buried in IRIS web site but you can get a cleaner copy at by clicking on the following link:
password is swig2010 That exercise wraps one of the algorithms in seismic unix. Gary pavlis