Monthly Archives: March 2013

Using valgrind to debug R programs

Posted on March 14, 2013 by Thomas Cokelaer

If you want to debug your R program because of a segmentation fault or memory leak, you can use valgrind as follows in a shell: R -d "valgrind –leak-check=full –show-reachable=yes" -f your_script.RR -d "valgrind –leak-check=full –show-reachable=yes" -f your_script.R

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ipython error

Posted on March 13, 2013 by Thomas Cokelaer

If you get this kind of error when starting ipython: /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/kernmagic/__init__.py in activate(ip, *args) 14 continue 15 magic_name = name[len(’magic_’):] —> 16 ip.shell.define_magic(magic_name, getattr(mymagics, name)) 17 18 def activate_aliases(ip, *args):   AttributeError: ‘TerminalInteractiveShell’ object has no attribute ‘shell’/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/kernmagic/__init__.py in activate(ip, … Continue reading →

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Accessing Life Science Web Services from Python

Posted on March 11, 2013 by Thomas Cokelaer

In a previous post, I started to discuss about Web Services in Life Science and what a maze it is to navigate between them. Some Web Services provides Python code to access to their databases but not all of them. … Continue reading →

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