Re: Help to run test suite for python-pysam needed (does not find libhts) (Was: 01/01: Reenable check to ask for help on Debian Python list)
Hi Charles,
On Sat, Sep 27, 2014 at 06:37:27PM +0900, Charles Plessy wrote:
>
> I had to disable the patch use_external_htslib.patch: setting HTSLIB_MODE to
> "external" in setup.py makes that script crash. It looks like the "external"
> mode was superseded by passing HTSLIB_LIBRARY_DIR HTSLIB_INCLUDE_DIR
> environment variables.
I noticed this as well when I checked status in Git some days ago.
> Then, trying to build the binary package I reproduced the problem of missing
> the faidx_fetch_nseq symbol. When uploading libhts1 version 1.1 I actually
> noticed that the symbol was dropped (thanks to the libhts1.symbols file), but
> hoped that the reason why the upstream authors did not bump the soname of their
> library after that backwards-incompatible change was that they knew it was not
> problematic. As it turns out, pysam needed it… This said, given that the the
> HTSlib 1.0 was only out for a few weeks, I think that the best is to move
> forward by updating pysam to the HTSlib 1.1. This is done easily with
> s/faidx_fetch_nseq/faidx_nseq/.
>
> Then, the package builds but some tests fail after trying to access a remote
> file.
OK, we need to skip thoise tests (or even better ask upstream for an
option to exclude tests needing online connection).
> I note that upstream committed changes to the test suite no later than
> yesterday. Maybe the best is to wait and see a week or two ? Or to ask
> him about his plans for the next pysam release ?
I'd really like to get this out as fast as possible. I have some
packages depending from python-pysam which I really want to let migrate
as soon as possible.
Kind regards
Andreas.
--
http://fam-tille.de
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