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prody / ProDy

A Python Package for Protein Dynamics Analysis
http://prody.csb.pitt.edu
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TypeError: object of type '_sre.SRE_Pattern' has no len() #165

Closed xijunw closed 11 years ago

xijunw commented 11 years ago

I just built and installed Prody-1.4.6 on my Linuxmint 13 MATE 64-bit desktop (3.2.0-23-generic) following the instruction on the website. the fisrt-time runing of $ prody fetch 2k39 gave me the following error:

Traceback (most recent call last): File "/usr/local/bin/prody", line 26, in apps = imp.load_module('prody.apps', apps) File "/usr/local/lib/python2.7/dist-packages/prody/apps/init.py", line 55, in from .evol_apps import evol_main, evol_parser, EVOL_APPS File "/usr/local/lib/python2.7/dist-packages/prody/apps/evol_apps/init.py", line 31, in from ..apptools import File "/usr/local/lib/python2.7/dist-packages/prody/apps/apptools.py", line 30, in from prody.utilities import wrapText File "/usr/local/lib/python2.7/dist-packages/prody/init.py", line 92, in from . import atomic File "/usr/local/lib/python2.7/dist-packages/prody/atomic/init.py", line 174, in from .select import * File "/usr/local/lib/python2.7/dist-packages/prody/atomic/select.py", line 739, in PP_SCHARS = pp.Regex(RE_SCHARS) File "/usr/lib/python2.7/dist-packages/pyparsing.py", line 1750, in init if len(pattern) == 0: TypeError: object of type '_sre.SRE_Pattern' has no len()

I have Python-2.7.3 and numpy-1.6.1, matplotlib-1.1.1 installed in my box. Anything else information needed?

Xijun Wang Concordia University Montreal, Canada

abakan-zz commented 11 years ago

No, you have what's needed. 'pyparsing' version may not be right. Can you execute the following:

python -c "import pyparsing; print(pyparsing.__version__)

I have pyparsing v1.5.6. You may upgrade that to prevent this problem.

Alternatively, I may suggest you Anaconda which comes with all scientific Python packages you might need. That's what I am using. You can get it from: https://store.continuum.io/cshop/anaconda/

Could you let me know pyparsnig version, and whether the upgrade resolvesd your problem?

xijunw commented 11 years ago

Hi, abakan,

Your suggestion works like a charm, upgrading pyparsing solved my problem.

My pyparsing version was 1.5.2, highest version available in Linuxmint13 repository. Then I manually downloaded and upgraded it to 2.0.1, and the error disappeared.

Also, thanks for your suggestion about Anaconda. I will try it later since it looks like a huge and powerful guy.

Regards, Xijun

abakan-zz commented 11 years ago

Thanks for the update and reporting the problem! I will add a pyparsing version check into the code.