Your message dated Sun, 20 Mar 2016 06:34:09 +0000 with message-id <[email protected]> and subject line Bug#818584: fixed in spades 3.7.1+dfsg-2 has caused the Debian Bug report #818584, regarding ImportError: No module named pyyaml2 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.) -- 818584: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=818584 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: spades Version: 3.7.1+dfsg-1 Severity: important Control: block 818575 by -1 Tests for the circlator package in progress failed while runnining spades: ~~~ 0:00:47.008 92M / 484M INFO General (path_extend_launch.hpp : 247) Traversing tandem repeats 0:00:47.008 92M / 484M INFO PathExtendIO (pe_io.hpp : 190) Writing contigs to /tmp/adt-run.gG5zgN/build.2PK/circlator-1.2.0/test/test-dir/OUT/03.assemble.tmp.spades.107.c0mblm8f//K107/scaffolds 0:00:47.061 92M / 484M INFO General (launch.hpp : 114) SPAdes finished 0:00:47.068 84M / 484M INFO General (main.cpp : 169) Assembling time: 0 hours 0 minutes 47 seconds ===== Assembling finished. ===== Mismatch correction started. == Processing of contigs No module named pyyaml2 Traceback (most recent call last): File "/usr/lib/spades/bin/spades.py", line 844, in main ext_python_modules_home, log, assembled, result_corrected_filename) File "/usr/share/spades/spades_pipeline/corrector_logic.py", line 43, in run_corrector import pyyaml2 as pyyaml ImportError: No module named pyyaml2 == Error == exception caught: <type 'exceptions.ImportError'> In case you have troubles running SPAdes, you can write to [email protected] Please provide us with params.txt and spades.log files from the output directory. ~~~ Although spades declares a dependency on python-yaml, either the import statement needs to be patched to say "import yaml" (if the interface is the same), or this other python yaml library may need to be packaged.
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--- Begin Message ---Source: spades Source-Version: 3.7.1+dfsg-2 We believe that the bug you reported is fixed in the latest version of spades, 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. Sascha Steinbiss <[email protected]> (supplier of updated spades 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: SHA256 Format: 1.8 Date: Fri, 18 Mar 2016 14:25:06 +0000 Source: spades Binary: spades Architecture: source Version: 3.7.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Sascha Steinbiss <[email protected]> Description: spades - genome assembler for single-cell and isolates data sets Closes: 818584 Changes: spades (3.7.1+dfsg-2) unstable; urgency=medium . [ Sascha Steinbiss ] * Use asciidoctor instead of ronn for reproducible man pages * enable full hardening * add override for pedantic Lintian msg * use correct YAML module Closes: #818584 . [ Afif Elghraoui ] * Replace patch with a sed command to fix python-yaml imports Checksums-Sha1: bcce6ac1157b317e04e48f58e6e62084af64ee26 2199 spades_3.7.1+dfsg-2.dsc c5f3d8edcf2a29870d3eba4435cbc9bfe478b154 17748 spades_3.7.1+dfsg-2.debian.tar.xz Checksums-Sha256: 8146543007463e1b21366c688fc25dd2f44d1d6695db28faac9c3a8ccee18821 2199 spades_3.7.1+dfsg-2.dsc d6c4ec5b6bea3a5a89c1ab1fe3e086eacd14fcbff492a8d96d47dc04b921170c 17748 spades_3.7.1+dfsg-2.debian.tar.xz Files: 8c6d0dfd6415a7340374e3bc129660c1 2199 science optional spades_3.7.1+dfsg-2.dsc bc0e709ab3a370c1037ad5dce2ce9371 17748 science optional spades_3.7.1+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJW7kDuAAoJEM6uatOv6Cb72vwP/0xnBsb2hlPkVfZp/Msi6UDh NC8gVCK1IkYPvtoETH86vPRRHJy0n6/xq63ugVPJifiUOZt1EpxujewN+vvThweX MaFsRCjmUTtxs+AoWmT+uQppPvpOZlC7fLOQAiB3kXEPutSps61hQNgN3vpQbLNr jfb/fAB4gOl4ABUCOhoFxn4gwXe2NsW7GUVIYgsd8isrj1etDcfGzx2B1t7MTNIT 3VcyDp3nMC25JGFwuU/Jp0TCd2iPV7RDL5+9w3hG3khr9H+f5tWfwu77tMEdR+BL 1NLyQ8y7AMlZ3uwQicCpVRAJcCryR1lxUhoJGnkBM7UG01yONrCeH5tqO3IJXhn4 FfvPkQb4fEz3uwoUHGmV3zG+189STJQ1DTnP7l2Pd0v/YYdnL6ITc3+csxNHe5xG g/HwQnQs3x+Ld0P2v5e7HPVY26XUCRZntnv48t+SX4lsRyeZKcKUdr4bXowKfvBB j6bM2ChBSl96UGGVJP5glFZ47ciqSguGfJY2Tt5a5EV9PKYD7/IaUuMGgSMceIdH PyHiXF78xwD/6VOnOvP9T21Ut5j7VEWfUDK5HreoSkk1jlunquqcr5m/gFW+EWSh APju94QPXrHRYi3BuEEO6uCwCb1Qw68lmtN+ebkiXT5rGDejRJmooKnU15R0OJsv HVjd83wdwwxAIIJKuKJB =ItxR -----END PGP SIGNATURE-----
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