[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

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 mode was superseded by passing HTSLIB_LIBRARY_DIR  HTSLIB_INCLUDE_DIR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


Reply to: