Your message dated Fri, 10 Nov 2017 19:35:06 +0000
with message-id <e1edf50-000gii...@fasolo.debian.org>
and subject line Bug#879867: fixed in python-pysam 0.12.0.1+ds-4
has caused the Debian Bug report #879867,
regarding python3-pysam: import pysam throws ImportError undefined symbol:
hts_log
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
879867: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=879867
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: python3-pysam
Version: 0.12.0.1+ds-3
Severity: normal
Dear Maintainer,
Importing pysam on testing in either python2 or python3 fails with this
error.
python3 -c 'import pysam'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 5, in <module>
from pysam.libchtslib import *
File "pysam/libchtslib.pyx", line 1, in init pysam.libchtslib
ImportError:
/usr/lib/python3/dist-packages/pysam/libcbcftools.cpython-35m-x86_64-linux-gnu.so:
undefined symbol: hts_log
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=871314
htslib: new version break python-pysam
When I upgrade to libhts2 to 1.5-1 the import error goes away.
I suspect the 0.12 version of pysam needs libhts2 (>= 1.5) and bug
871314 needs to be closed so libhts2 will migrate to testing.
Diane
-- System Information:
Debian Release: buster/sid
APT prefers testing-debug
APT policy: (500, 'testing-debug'), (500, 'stable-debug'), (500, 'testing'),
(500, 'stable'), (110, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 4.13.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages python3-pysam depends on:
ii libc6 2.24-17
ii libhts2 1.4.1-5
ii python3 3.5.3-3
ii zlib1g 1:1.2.8.dfsg-5
python3-pysam recommends no packages.
python3-pysam suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: python-pysam
Source-Version: 0.12.0.1+ds-4
We believe that the bug you reported is fixed in the latest version of
python-pysam, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 879...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Mattia Rizzolo <mat...@debian.org> (supplier of updated python-pysam package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 10 Nov 2017 12:56:10 +0100
Source: python-pysam
Binary: python-pysam python3-pysam python-pysam-tests
Architecture: source
Version: 0.12.0.1+ds-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Mattia Rizzolo <mat...@debian.org>
Description:
python-pysam - interface for the SAM/BAM sequence alignment and mapping format
(
python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping
format (
python3-pysam - interface for the SAM/BAM sequence alignment and mapping
format (
Closes: 879867
Changes:
python-pysam (0.12.0.1+ds-4) unstable; urgency=medium
.
* Team upload.
* Revert "Skip tests on ppc64el to avoid build-dep on bcftools currently
uninstallable". It seems to be installable now, and anyway now that the
python3 transition is done we should fix it properly anyway.
* d/control:
+ Bump the libhts-dev buil-dep to 1.5-3, to make sure we gain appropriate
versioned symbols and therefore an appropriate versioned dependency on
libhts2. Closes: #879867
+ Bump Standards-Version to 4.1.1.
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