Your message dated Fri, 10 Nov 2017 19:35:06 +0000 with message-id <[email protected]> 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 879867: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=879867 Debian Bug Tracking System Contact [email protected] 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
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--- 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Mattia Rizzolo <[email protected]> (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 [email protected]) -----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 <[email protected]> Changed-By: Mattia Rizzolo <[email protected]> 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. Checksums-Sha1: 07daab250dfac1bbfa50a0bd97c2115aa940e5fb 2565 python-pysam_0.12.0.1+ds-4.dsc 868c8b3e3f223bf9fdc52f118ceac6ac1e191299 9440 python-pysam_0.12.0.1+ds-4.debian.tar.xz 308e3d8b4dad56c127e38baa852baf3f2e0af529 6106 python-pysam_0.12.0.1+ds-4_source.buildinfo Checksums-Sha256: 12efda4c6815bbf2631d7ad5640c7beb92ba67747130b8999d8ddff1ac34a91e 2565 python-pysam_0.12.0.1+ds-4.dsc ad70316c7caa5def9e34c025e7bd92ed500a868956bf56f93f91c320d55a2fe5 9440 python-pysam_0.12.0.1+ds-4.debian.tar.xz 81a74c74d33bcf3b3906219250512ff7919077889d56f7076cd9013f0cd8387f 6106 python-pysam_0.12.0.1+ds-4_source.buildinfo Files: 054e64ec06ab9399fb5cc63be2ed1a7f 2565 python optional python-pysam_0.12.0.1+ds-4.dsc 580b406c3f974a6b94c7530133ac0c06 9440 python optional python-pysam_0.12.0.1+ds-4.debian.tar.xz c31a0f5a1a2fb71ad800472955f96037 6106 python optional python-pysam_0.12.0.1+ds-4_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEi3hoeGwz5cZMTQpICBa54Yx2K60FAloF+sYSHG1hdHRpYUBk ZWJpYW4ub3JnAAoJEAgWueGMdiutNs4P/0q3TvnPV0zZB3i1fAW5Xdwf/wDQ9gTA UQwEsIMyG7ZtTCHbF4qKdlXiyRxBXRo25AoEB6SamIoaUIlykUrnXBxeE4TDOzY0 WW1mlXBSof1anYPgFUMM+XymepjwhHMRSR2hR79kCcY2iTQ3u+Pr6xOaL9bFIf+2 e9TB7o2SWgNvAWLuxyOzekq/SbSnDMZS7JVyo7TIiBa+f0T9VLYFlyZsEqeTuqIh Jv/oAQtFQ7liXR4JDZygpFc4PyoXYbyjPfvW72Ink7CJabIUHutjfDyRDmhkKIpe sBmW8bkQch86wAAz/xzh06YaXZUTfjo9eKtJLiMNRFAXnTUMVH2yb6V9Lh9D3A2x iHyvAG5U2BRG3BIK7UzIeKlDlmUbCmRGp9SRjp4s5w7wf2rGI/CXN6oPP4oyFsuW lkIPz2fuqa8YY0P56VyENGhEGkhfkxeyGZMV3V0MxF4mhD8CG4jGswDwPn1L5Rpr +ysOBAZS/CxHb9IlWSC33wgpvu9XY8JfXlcXwG21vOrqbzoT13x8qwQZNmMoNgtB 4xYCAzx1JjB7GIlvlsUJfFM1xdZsgLfLLy7mH5lX+iIHkjY+7gUwKv6VCa8RyDP/ jFBPi029bU1yLwu9BQaX4kgZR7uVeuiPtiM6YeO9R+BBSl6yh44lu1rjk06XAYZc MGbfl7ToVPws =ScQ2 -----END PGP SIGNATURE-----
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