Your message dated Sat, 28 Jul 2018 03:34:31 +0000 with message-id <e1fjfzz-0008ds...@fasolo.debian.org> and subject line Bug#904317: fixed in python-biopython 1.72+dfsg-1 has caused the Debian Bug report #904317, regarding python-biopython: FTBFS and test failure with Python3.7 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 ow...@bugs.debian.org immediately.) -- 904317: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=904317 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: python-biopython Version: 1.71+dfsg-1 X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: needs-update Dear maintainers, Currently the python3.7 transition¹ is going on, which means that python3.7 is added to the supported python3 versions. However, since python3-defaults added python3.7 support, your autopkgtest has been failing. I copied the first error below, there are quite a few very similar ones). Could you please investigate? It looks like the source isn't ready for Python3.7 yet, I suggest you pick this up with upstream and point upstream at PEP-479². I think the right action right now is to claim that the package doesn't support Python3.7 by adding the right X-Python3-Version³ to debian/control. Don't forget to check if the autopkgtest also needs updates to test with the right versions. Paul PS: it seems in unstable there is more regression as the test already fails in the python2.7 part and doesn't even test any python3 code. ¹ https://release.debian.org/transitions/html/python3.7.html ² https://docs.python.org/3.7/whatsnew/3.7.html#changes-in-python-behavior ³ https://www.debian.org/doc/packaging-manuals/python-policy/ch-module_packages.html#s-specifying_versions https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-biopython/657128/log.gz ====================================================================== ERROR: test_AlignIO ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/Bio/AlignIO/NexusIO.py", line 42, in NexusIterator n = Nexus.Nexus(handle) File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 623, in __init__ self.read(input) File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 657, in read commandlines = _get_command_lines(file_contents) File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 1898, in _get_command_lines lines = _kill_comments_and_break_lines(file_contents) File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 454, in _kill_comments_and_break_lines t2 = next(contents) StopIteration The above exception was the direct cause of the following exception: Traceback (most recent call last): File "run_tests.py", line 451, in runTest suite = loader.loadTestsFromName(name) File "/usr/lib/python3.7/unittest/loader.py", line 154, in loadTestsFromName module = __import__(module_name) File "/tmp/autopkgtest-lxc.rsofcney/downtmp/autopkgtest_tmp/Tests/test_AlignIO.py", line 237, in <module> alignments = list(AlignIO.parse(handle, t_format)) File "/usr/lib/python3/dist-packages/Bio/AlignIO/__init__.py", line 376, in parse for a in i: RuntimeError: generator raised StopIteration
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--- Begin Message ---Source: python-biopython Source-Version: 1.72+dfsg-1 We believe that the bug you reported is fixed in the latest version of python-biopython, 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 904...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated python-biopython 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: SHA256 Format: 1.8 Date: Sat, 28 Jul 2018 04:45:32 +0200 Source: python-biopython Binary: python-biopython python3-biopython python-biopython-doc python-biopython-sql python3-biopython-sql Architecture: source Version: 1.72+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: python-biopython - Python library for bioinformatics (implemented in Python 2) python-biopython-doc - Documentation for the Biopython library python-biopython-sql - Biopython support for the BioSQL database schema (Python 2) python3-biopython - Python library for bioinformatics (implemented in Python 3) python3-biopython-sql - Biopython support for the BioSQL database schema (Python 3) Closes: 904317 Changes: python-biopython (1.72+dfsg-1) unstable; urgency=medium . * New upstream version Closes: #904317 * Standards-Version: 4.1.5 * debian/rules: Respect DEB_BUILD_OPTIONS in dh_auto_test * Drop ancient Python version fields * Deactivate exclusion of samtools_tool test and see if it works Checksums-Sha1: a7c60fcd5637c461a7c47bbcc04126e4e05d5611 3070 python-biopython_1.72+dfsg-1.dsc 8976a4c1e922cc1d7e115548b4035daae948b157 8942228 python-biopython_1.72+dfsg.orig.tar.xz b85e4f59b0f724b8a8f9d213c296509e5f5a77ef 14016 python-biopython_1.72+dfsg-1.debian.tar.xz Checksums-Sha256: 839cad4269df52f34d3b92bc6544cce2024c702c803756f21c30f0c4fd748e88 3070 python-biopython_1.72+dfsg-1.dsc 380d296485cfcedade98b427b38ffbb08503e1ff6ed1c09e958b08032695fc8d 8942228 python-biopython_1.72+dfsg.orig.tar.xz 0bf190cec3f6891a768ce0ab81a60737351d150933770f869d16e01a57c3e8bd 14016 python-biopython_1.72+dfsg-1.debian.tar.xz Files: 257895752b0cf0e866f74d15ed16521f 3070 python optional python-biopython_1.72+dfsg-1.dsc d98fca1550d27b4fe774233f6ebc0592 8942228 python optional python-biopython_1.72+dfsg.orig.tar.xz bd023fecf1ec183471996e0ddf21dd22 14016 python optional python-biopython_1.72+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltb3aYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEeZQ/+PAgKu18FMBI+LleXjGWHnQ3Aj8/6NAT6 EsoyHjc6C11/biaTJ9A+DmEKhYP6L+a6sufy1u72O1v2QDsJOdDQm0sG4ZAjdNic HEWipL5d1gjyDPMlX6nR520OxjH8WDfzUCqmE9i0Ugn0Lqk3oC+MYWds4+eXLirG UGCySnrEWWWZK3WEWeQbXW6EuuocYTRSRQyuDva0lOtmNjq5TEluVgjfJfq2bbSm CbMLX+W3GglElfxAV9eVu8z0HcE0F6Ov/k7V2R6qx/jYsa1vxgvg87xV7A+trRCB 2Lf0eFZ3dyK8nQazRXilN7PSLbBMemzSo5Pv9PNMo+LytnsAB8rpWMN4dpd8OijE r6pePKvARaEAR9xkRbUjXa3ibWKeyIsPfBy+To/gd+EWTJnUeFvs77AzN9w9iCDi s7Br3QTCSJdO+gO9U8vlyBTU9XxoYoKqsX81OJD9RrUL16NEX6dxAvGJ54wNIvpD +zaRaQQtRRhg1TECBON5/afQOGXMXbKRjSnBZ6bHqeg9vMEVzK6jlrAdDLHciKtu U8GldP+/MwMVwKWji8h8icx+8gzIObKBgJCfoYZfgixKTKMG7HiQFubjUu8+3liU 1QxMIgv7nhUyr8Cp0UbtSjRQWsGFGl4CJc6V1jQmmzGZpr+eViV4YYoxefFHigMX B0r/0JFy5uQ= =REy8 -----END PGP SIGNATURE-----
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