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samhelpers helper does not compile #9

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
$ hg tip
changeset:   842:70dd90cbef02
tag:         tip
user:        Kevin B. Jacobs <jacobs@bioinformed.com>
date:        Wed Jul 21 21:18:31 2010 -0400
summary:     Add trimming for unaligned portions of reads.  This is needed 
because many

$ pip freeze
Cython==0.12.1
Pyrex==0.9.9
numpy==1.4.1
wsgiref==0.1.2

$ python --version
Python 2.6.2

$ python setup.py build
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler 
options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler 
options
running build_src
build_src
building extension "glu.lib._illumina" sources
building extension "glu.lib.genolib.bitarrayc" sources
building extension "glu.lib.genolib._genoarray" sources
building extension "glu.modules.struct._admix" sources
building extension "glu.modules.ld.pqueue" sources
building extension "glu.modules.seq.samhelpers" sources
pyrexc:> build/src.linux-x86_64-2.6/glu/modules/seq/samhelpers.c
/home/james/glu/src/glu-genetics/glu/modules/seq/samhelpers.pyx:18:12: Syntax 
error in C variable declaration
error: 1 errors while compiling 'glu/modules/seq/samhelpers.pyx' with Pyrex

Original issue reported on code.google.com by cas...@gmail.com on 23 Jul 2010 at 1:27

GoogleCodeExporter commented 9 years ago 
The pyx files are intended to work with Cython, not Pyrex.  Sorry about the 
complexity of building GLU.

Original comment by bioinformed@gmail.com on 5 Aug 2010 at 5:56