Re: python-cyvcf2 test failures (Was: python-pybedtools: fixing the failing tests)
Hello Liubov,
On 7/20/18 2:57 PM, Liubov Chuprikova wrote:
> ...
>
> On Sun, 8 Jul 2018 at 01:23 Steffen Möller <steffen_moeller@gmx.de
> <mailto:steffen_moeller@gmx.de>> wrote:
>
> - cyvcf2 is in a new version 0.9.0 now, but, well, tests fail.
>
>
> There was a new upstream version recently in which one of the tests
> (issue44) was supposed to be fixed, but hadn't yet [1]. I tried to dig
> into this and its other test failures, but they seem to be quite
> tricky for me. So I think, Steffen's claim for someone's help with
> cyvcf2 and its dependency htslib still remains on the table:
>
>
> It comes
> with its own version of htslib, which may well contribute to the
> situation since I had nothing better to do than to substitute it with
> the one the distribution ships. Is anybody close to upstream on this
> list to have a look?
>
>
> With regards,
> Liubov
>
> [1] https://github.com/brentp/cyvcf2/issues/89#issuecomment-406354822
I think we got as far. also with the help by upstream, that if we take
upstream's regular code base, everything compiles and installs as
expected. This leaves it to a failing assert in the htslib library. I
have finally compared the htslib of cyvcf2 with the original htslib 1.8
version and found that these two have diverged a bit. I came to the
conclusion that we should then not substitute that subdirectory with our
repository's htslib 1.8.
On a sidenote, because of incompatibilities with existing packages we
have htslib in experimental (the latest version of htslib is now 1.9).
The update was once performed only because of cyvcf2 if I recall
correctly. I had a look at 1.9 but need to learn about gcc symbol
files, first.
Concerning cyvcf2 I want to wait for a reply from upstream on
https://github.com/brentp/cyvcf2/issues/91 . Do you also think that it
would be fine to keep cyvcf2 statically linked against that local fork
of htslib?
Cheers,
Steffen
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