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Installation of cyvcf

Open sigven opened this issue 12 years ago • 0 comments

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.

sigven avatar Mar 04 '14 14:03 sigven