Hi Andreas, I can confirm that this problem doesn't show up in an up-to-date sid. Cython has a new version there as compared to todays testing, but installing this new version in testing didn't resolve the problem.
Anyway, the other question was about the missing symbol faidx_fetch_nseq in htslib-1.1. Well, the function is declared in one of the htslibs headers, but no function body is defined in the whole of the library source code, i.e. within its source tree I get: grep -r faidx_fetch_nseq * debian/libhts1.symbols:#MISSING: 1.1# faidx_fetch_nseq@Base 1.0 htslib/faidx.h: int faidx_fetch_nseq(const faidx_t *fai); According to this commit in the htslib repo [1] the function name has been replaced by "faidx_nseq" but it was not deleted from the header. Hope that helps, Gert [1] https://github.com/samtools/htslib/commit/5a0ee032c4e94f5b2814c6f389278b404f439713 On Thu, 2014-09-25 at 19:43 +0200, Andreas Tille wrote: > Hi Gert, > > On Thu, Sep 25, 2014 at 06:13:19PM +0200, Gert Wollny wrote: > > I got this: > > > > Traceback (most recent call last): > > File "tests/pysam_test.py", line 15, in <module> > > from TestUtils import checkBinaryEqual > > ImportError: No module named TestUtils > > > > and I saw that you had this too before [1], but the answer was missing. > > How did you solve this? Would the solution need a package from sid? > > I confirm that this problem existed but is now present any more in an up > to date sid chroot. I do not remember that I have done any means to > work around this. > > Kind regards > > Andreas. > > > [1]http://web.archiveorange.com/archive/v/WK9riEUrSSGTqb90VM4v > > > > > > On Thu, 2014-09-25 at 16:22 +0200, Andreas Tille wrote: > > > Ups, sorry, done. Andreas. > > > > > > On Thu, Sep 25, 2014 at 03:32:49PM +0200, Gert Wollny wrote: > > > > Hi Andreas, > > > > > > > > > > > > I tried to have a look, but ... > > > > > > > > > > > > On Thu, 2014-09-25 at 14:48 +0200, Andreas Tille wrote: > > > > > [1] git://git.debian.org/git/debian-med/python-pysam.git > > > > > > > > > Could you "git push --all --tags", because git doesn't have the > > > > upstream/0.8.0 version tagged. > > > > > > > > best > > > > Gert > > > > > > > > > > > > > > > > > > > > > >
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