combining TIFF and CSV file with metadata

[Thorondor]

Code: Select all

[root@bqichipdb1 ~]# ldd /usr/lib64/python2.4/lib-dynload/pyexpat.so
        libexpat.so.0 => /lib64/libexpat.so.0 (0x00002b794e34b000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b794e56d000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b794e788000)
        /lib64/ld-linux-x86-64.so.2 (0x0000003b20600000)
[root@bqichipdb1 ~]# rpm -qf /lib64/libexpat.so.0
expat-1.95.8-8.3.el5_5.3
[root@bqichipdb1 ~]# md5sum /lib64/libexpat.so.0
1b630688344f04a4e9448d832f0edb9c  /lib64/libexpat.so.0


hmm, I don't see a difference.

[cxallan]

Something else is definitely causing the expat library differences then can you try this:

Code: Select all

$ python -v
...
>>> import xml.parsers.expat
...


and paste the output here.

[Thorondor]

sure

Code: Select all

[omero@bqichipdb1 root]$ python -V
Python 2.4.3
[omero@bqichipdb1 root]$ python
Python 2.4.3 (#1, Feb 22 2012, 16:05:45)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import xml.parsers.expat
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib64/python2.4/xml/parsers/expat.py", line 4, in ?
    from pyexpat import *
ImportError: /usr/lib64/python2.4/lib-dynload/pyexpat.so: undefined symbol: XML_StopParser


[cxallan]

Lower case "-v".

[Thorondor]

oh, sry for that:

Code: Select all

python -v
# installing zipimport hook
import zipimport # builtin
# installed zipimport hook
# /usr/lib64/python2.4/site.pyc matches /usr/lib64/python2.4/site.py
import site # precompiled from /usr/lib64/python2.4/site.pyc
# /usr/lib64/python2.4/os.pyc matches /usr/lib64/python2.4/os.py
import os # precompiled from /usr/lib64/python2.4/os.pyc
import posix # builtin
# /usr/lib64/python2.4/posixpath.pyc matches /usr/lib64/python2.4/posixpath.py
import posixpath # precompiled from /usr/lib64/python2.4/posixpath.pyc
# /usr/lib64/python2.4/stat.pyc matches /usr/lib64/python2.4/stat.py
import stat # precompiled from /usr/lib64/python2.4/stat.pyc
import errno # builtin
# /usr/lib64/python2.4/UserDict.pyc matches /usr/lib64/python2.4/UserDict.py
import UserDict # precompiled from /usr/lib64/python2.4/UserDict.pyc
# /usr/lib64/python2.4/copy_reg.pyc matches /usr/lib64/python2.4/copy_reg.py
import copy_reg # precompiled from /usr/lib64/python2.4/copy_reg.pyc
# /usr/lib64/python2.4/types.pyc matches /usr/lib64/python2.4/types.py
import types # precompiled from /usr/lib64/python2.4/types.pyc
import japanese # directory /usr/lib64/python2.4/site-packages/japanese
# /usr/lib64/python2.4/site-packages/japanese/__init__.pyc matches /usr/lib64/python2.4/site-packages/japanese/__init__.py
import japanese # precompiled from /usr/lib64/python2.4/site-packages/japanese/__init__.pyc
import japanese.aliases # directory /usr/lib64/python2.4/site-packages/japanese/aliases
# /usr/lib64/python2.4/site-packages/japanese/aliases/__init__.pyc matches /usr/lib64/python2.4/site-packages/japanese/aliases/__init__.py
import japanese.aliases # precompiled from /usr/lib64/python2.4/site-packages/japanese/aliases/__init__.pyc
import encodings # directory /usr/lib64/python2.4/encodings
# /usr/lib64/python2.4/encodings/__init__.pyc matches /usr/lib64/python2.4/encodings/__init__.py
import encodings # precompiled from /usr/lib64/python2.4/encodings/__init__.pyc
# /usr/lib64/python2.4/codecs.pyc matches /usr/lib64/python2.4/codecs.py
import codecs # precompiled from /usr/lib64/python2.4/codecs.pyc
import _codecs # builtin
# /usr/lib64/python2.4/encodings/aliases.pyc matches /usr/lib64/python2.4/encodings/aliases.py
import encodings.aliases # precompiled from /usr/lib64/python2.4/encodings/aliases.pyc
# /usr/lib64/python2.4/warnings.pyc matches /usr/lib64/python2.4/warnings.py
import warnings # precompiled from /usr/lib64/python2.4/warnings.pyc
# /usr/lib64/python2.4/linecache.pyc matches /usr/lib64/python2.4/linecache.py
import linecache # precompiled from /usr/lib64/python2.4/linecache.pyc
# /usr/lib64/python2.4/encodings/utf_8.pyc matches /usr/lib64/python2.4/encodings/utf_8.py
import encodings.utf_8 # precompiled from /usr/lib64/python2.4/encodings/utf_8.pyc
Python 2.4.3 (#1, Feb 22 2012, 16:05:45)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
dlopen("/usr/lib64/python2.4/lib-dynload/readline.so", 2);
import readline # dynamically loaded from /usr/lib64/python2.4/lib-dynload/readline.so


[cxallan]

I need you to do the whole thing with a Python interpreter started with "-v", that includes the import of "xml.parsers.expat". I'm trying to figure out what module is causing the extra expat library load.

[Thorondor]

ah ok.
so then after the the code I already posted:

Code: Select all

>>> import xml.parsers.expat
import xml # directory /usr/lib64/python2.4/xml
# /usr/lib64/python2.4/xml/__init__.pyc matches /usr/lib64/python2.4/xml/__init__.py
import xml # precompiled from /usr/lib64/python2.4/xml/__init__.pyc
import xml.parsers # directory /usr/lib64/python2.4/xml/parsers
# /usr/lib64/python2.4/xml/parsers/__init__.pyc matches /usr/lib64/python2.4/xml/parsers/__init__.py
import xml.parsers # precompiled from /usr/lib64/python2.4/xml/parsers/__init__.pyc
# /usr/lib64/python2.4/xml/parsers/expat.pyc matches /usr/lib64/python2.4/xml/parsers/expat.py
import xml.parsers.expat # precompiled from /usr/lib64/python2.4/xml/parsers/expat.pyc
dlopen("/usr/lib64/python2.4/lib-dynload/pyexpat.so", 2);
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib64/python2.4/xml/parsers/expat.py", line 4, in ?
    from pyexpat import *
ImportError: /usr/lib64/python2.4/lib-dynload/pyexpat.so: undefined symbol: XML_StopParser



I get this.

[cxallan]

Okay, so based on what you posted earlier about your /lib64/libexpat.so.0 I'd say that something has overwritten that. What I'm not sure. Can you run the following:

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$ md5sum /lib64/libexpat.so.0
27decdf31adedd772fe306c225c81d89  /lib64/libexpat.so.0
$ ls -al /lib64/libexpat.so.0
lrwxrwxrwx 1 root root 17 Oct 27  2010 /lib64/libexpat.so.0 -> libexpat.so.0.5.0


The fact that you have the same packages but the md5sum of your /lib64/libexpat.so.0 is different implies another package has overwritten the library.

[Thorondor]

Code: Select all

[omero@bqichipdb1 root]$ md5sum /lib64/libexpat.so.0
1b630688344f04a4e9448d832f0edb9c  /lib64/libexpat.so.0
[omero@bqichipdb1 root]$ ls -al /lib64/libexpat.so.0
lrwxrwxrwx 1 root root 17 Apr 27 13:49 /lib64/libexpat.so.0 -> libexpat.so.0.5.0


seems so. So I reinstall libexpat?

[cxallan]

Certainly worth a try. Just be forewarned that if other people are relying on a newer version of expat in that location you reinstalling it will break their usage.