[Pyrex] (no subject)

[Greg Ewing]

Kevin Conway wrote:
>    I can run the build for RSeQC, but it eventually produces this error:
> 
> ...
> running build_ext
> pyrexc lib/bx/bitset.pyx --> lib/bx/bitset.c
> /home/####/to-be-installed/RSeQC-2.3.7/lib/bx/bitset.pyx:75:12: Syntax error in C variable declaration
> ...

I just had a look at RSeQC, and discovered a few things:

1) It actually uses Cython, not Pyrex. This is probably the
reason for the above error -- Cython adds quite a lot of
extensions to Pyrex syntax.

2) You *shouldn't* need to have either Pyrex or Cython
in order to install RSeQC, because the generated .c files
are included in the source distribution. However...

3) The setup.py doesn't seem to make adequate provision for
building without Cython. In particular, if you happen to
have Pyrex installed, it tries to use it anyway, thereby
clobbering the otherwise perfectly good .c files.

I managed to get RSeQC to build by making the following
changes to the setup.py:

a) Comment out the following lines:

# Use build_ext from Cython if found
try:
	import Cython.Distutils
	command_classes['build_ext'] = Cython.Distutils.build_ext
except:
	pass

b) Replace all occurrences of ".pyx" with ".c".

Then it seems to build okay using the existing .c files.

Remember to restore a fresh copy of the RSeQC source to
get back the .c files that were clobbered.

(When the dust has settled, you might also like to contact
the authors of RSeQC and point out that their setup.py
file is broken. A setup.py intended for end users should
never invoke Pyrex or Cython automatically, even if it
happens to be installed.)

-- 
Greg