Installation of cyvcf
Hi,
I am installing cyvcf on my new Mac, but ran into trouble I have not experienced before. Cython v0.20.1 is used here. Do you have any idea why I get this error?
best, Sigve
python setup.py build running build running build_py creating build creating build/lib.macosx-10.9-intel-2.7 creating build/lib.macosx-10.9-intel-2.7/cyvcf copying cyvcf/init.py -> build/lib.macosx-10.9-intel-2.7/cyvcf copying cyvcf/filters.py -> build/lib.macosx-10.9-intel-2.7/cyvcf copying cyvcf/utils.py -> build/lib.macosx-10.9-intel-2.7/cyvcf copying cyvcf/version.py -> build/lib.macosx-10.9-intel-2.7/cyvcf running build_ext cythoning cyvcf/parser.pyx to cyvcf/parser.c warning: cyvcf/parser.pyx:352:37: cdef variable 'gt_bases' declared after it is used
Error compiling Cython file:
... raise StopIteration
#CHROM
cdef bytes chrom = row[0]
if self._prepend_chr:
chrom = 'chr' + chrom
^
cyvcf/parser.pyx:1172:26: Cannot convert 'str' to 'bytes' implicitly. This is not portable.
Error compiling Cython file:
... cdef list row = line.split('\t')
#CHROM
cdef bytes chrom = row[0]
if other._prepend_chr:
chrom = 'chr' + chrom
^
cyvcf/parser.pyx:1232:26: Cannot convert 'str' to 'bytes' implicitly. This is not portable.