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DoaneAS / rseqc

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Cython failure; lib/bx/arrays/array_tree.pyx:9:8: 'bx.arrays.wiggle.pxd' not found While installing 2.3.3 #13

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Hi! I'm trying to upgrade to version 2.3.3 (from 2.3) on our cluster, and am 
getting the following error when I try to install to a custom location:
How do I fix this??? 
Thanks 

python setup.py install --root=/hox/g/uq/sw/x86_64/RSeQC/2.3.3
running install
running build
running build_py
running build_ext
skipping 'lib/bx/bitset.c' Cython extension (up-to-date)
skipping 'lib/bx/intervals/intersection.c' Cython extension (up-to-date)
skipping 'lib/bx/align/_core.c' Cython extension (up-to-date)
skipping 'lib/bx/seq/_nib.c' Cython extension (up-to-date)
skipping 'lib/bx/seq/_twobit.c' Cython extension (up-to-date)
skipping 'lib/bx/_seqmapping.c' Cython extension (up-to-date)
skipping 'lib/bx/misc/bgzf.c' Cython extension (up-to-date)
skipping 'lib/bx/intervals/cluster.c' Cython extension (up-to-date)
skipping 'lib/bx/pwm/_position_weight_matrix.c' Cython extension (up-to-date)
skipping 'lib/bx/motif/_pwm.c' Cython extension (up-to-date)
cythoning lib/bx/arrays/array_tree.pyx to lib/bx/arrays/array_tree.c

Error compiling Cython file:
------------------------------------------------------------
...

import numpy
from numpy import *
cimport numpy

cimport bx.arrays.wiggle
       ^
------------------------------------------------------------

lib/bx/arrays/array_tree.pyx:9:8: 'bx.arrays.wiggle.pxd' not found
building 'bx.arrays.array_tree' extension
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -O2 -fPIC 
-I/hox/g/uq/sw/x86_64/python/epd-7.2/lib/python2.7/site-packages/numpy/core/incl
ude -I/hox/g/uq/sw/x86_64/python/epd-7.2/include/python2.7 -c 
lib/bx/arrays/array_tree.c -o 
build/temp.linux-x86_64-2.7/lib/bx/arrays/array_tree.o
lib/bx/arrays/array_tree.c:1:2: error: #error Do not use this file, it is the 
result of a failed Cython compilation.
error: command 'gcc' failed with exit status 1

Original issue reported on code.google.com by gal...@gmail.com on 14 Sep 2012 at 5:11

GoogleCodeExporter commented 9 years ago 
Have tried installing 2.3.2 and 2.3.1, getting the same error. Have been 
running 2.3 for a while now, and did not have this issue.

Please help!

Original comment by gal...@gmail.com on 17 Sep 2012 at 7:03

GoogleCodeExporter commented 9 years ago 
Help still needed :(

Original comment by gal...@gmail.com on 25 Sep 2012 at 3:43

GoogleCodeExporter commented 9 years ago 
This was found to be an error of using the enthought python distribution.

Original comment by gal...@gmail.com on 27 Sep 2012 at 5:37

GoogleCodeExporter commented 9 years ago 
I am also having this error, using Python 2.7 compiled from source on CentOS 
5.8.  Since we are not using the enthought distribution, any idea what 
specifically was causing it?

Original comment by Branden....@gmail.com on 8 Oct 2012 at 8:02

GoogleCodeExporter commented 9 years ago 
installing 2.3.3 failed with this same error, installing 2.3.1 successfully.

Original comment by augix....@gmail.com on 7 Nov 2012 at 2:41

GoogleCodeExporter commented 9 years ago 
Same issue with 2.3.3 augix using Python 2.7.3. Also works fine with 2.3.1.

Original comment by rory.kir...@gmail.com on 7 Nov 2012 at 5:23

GoogleCodeExporter commented 9 years ago 
I am using the Enthought python distribution. Has there been any progress in 
figuring out how to install RSeQC in the Enthought distribution?

Original comment by blari...@mac.com on 1 Jan 2013 at 9:56

GoogleCodeExporter commented 9 years ago 
Just to update - this is not an Enthought problem. I tried it with the Python 
2.7.3 downloaded from the Python website as well and I got a similar error.

Original comment by blari...@mac.com on 3 Jan 2013 at 4:47

GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
[deleted comment]
GoogleCodeExporter commented 9 years ago 
Very odd thing.

I bumped into the same problem but weirdly installation worked the first time.
Turns out, this seems to be related to some python eggs i installed trying to 
get RSeQC running on my ion torrent files.

At some point i removed all my .egg directories from 
Python-2.7/lib/python2.7/site-packages and then RSeQC 2.3.4 installed fine.

It seems to bring its own version of one of the eggs i had installed.

FYI i had these eggs installed in python when RSeQC 2.3.4 was not installing:
bx_python-0.7.1-py2.7-linux-x86_64.egg  
pysam-0.7-py2.7-linux-x86_64.egg
Cython-0.17.4-py2.7-linux-x86_64.egg
distribute-0.6.34-py2.7.egg
numpy-1.6.2-py2.7-linux-x86_64.egg
pip-1.2.1-py2.7.egg

I removed them all so i dont know which one was responsible. (dont remove 
distribute-xxx !)

Hope that helps !

Original comment by karl.kas...@gmail.com on 10 Jan 2013 at 10:07