Your message dated Fri, 13 May 2022 13:34:33 +0000 with message-id <[email protected]> and subject line Bug#1010788: fixed in spades 3.15.4+dfsg-2 has caused the Debian Bug report #1010788, regarding spades: Mismatch correction / --careful mode broken by Debian patch 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.) -- 1010788: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1010788 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: spades Version: 3.15.4+dfsg-1 Severity: normal Dear Maintainer, Using spades with the --careful flag triggers the following error: Traceback (most recent call last): File "/usr/libexec/spades/spades.py", line 683, in <module> main(sys.argv) File "/usr/libexec/spades/spades.py", line 621, in main cfg, dataset_data, command_line = parse_args(args, log) File "/usr/libexec/spades/spades.py", line 257, in parse_args options, cfg, dataset_data = options_parser.parse_args(log, bin_home, spades_home, File "/usr/share/spades/spades_pipeline/options_parser.py", line 1157, in parse_args add_to_cfg(cfg, log, bin_home, spades_home, options_storage.args) File "/usr/share/spades/spades_pipeline/options_parser.py", line 995, in add_to_cfg if which("bwa-spades"): NameError: name 'which' is not defined Reproducible with e.g.: f="$(mktemp XXXX.fq)" echo -e "@a\nA\n+\n!" > "$f" spades --careful --12 "$f" -o "/tmp" The code path related to that flag in options_parser.py has been patched in Debian to add the call to which(): https://salsa.debian.org/med-team/spades/-/blob/d3c54b2ae8f0ee29a639fe0246d670fcad54b45b/debian/patches/0003_accept-system-bwa.patch#L82-L95 When the patch was initially created in this commit: https://salsa.debian.org/med-team/spades/-/commit/ac1cfa145bf4066ca7f3af47db1aae6dd28ac5ab the call and definition of which() were both in spades.py but the call was later moved to options_parser.py while the definition was left behind unused. Rather than adding multiple definitions of which() in the patch, the single version in support.py could be imported wherever it needs to be used. -- System Information: Debian Release: bookworm/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.17.0-1-amd64 (SMP w/4 CPU threads; PREEMPT) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages spades depends on: ii bamtools 2.5.1+dfsg-10+b1 ii bwa 0.7.17-7 ii libc6 2.33-7 ii libgcc-s1 12.1.0-1 ii libgomp1 12.1.0-1 ii libnlopt0 2.7.1-4+b1 ii libssw0 1.1-13 ii libstdc++6 12.1.0-1 ii python3 3.10.4-1+b1 ii python3-distutils 3.9.12-1 ii python3-joblib 0.17.0-4 ii python3-yaml 5.4.1-1+b1 ii samtools 1.13-4 ii zlib1g 1:1.2.11.dfsg-4 spades recommends no packages. spades suggests no packages. -- no debconf information
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--- Begin Message ---Source: spades Source-Version: 3.15.4+dfsg-2 Done: Lance Lin <[email protected]> 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. Lance Lin <[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: SHA512 Format: 1.8 Date: Tue, 10 May 2022 20:15:40 +0700 Source: spades Architecture: source Version: 3.15.4+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Lance Lin <[email protected]> Closes: 1010788 Changes: spades (3.15.4+dfsg-2) unstable; urgency=medium . * Team upload. . [ Lance Lin ] * d/patches/0003_accept-system-bwa.patch - refactored 'which' Closes: #1010788 . [ Andreas Tille ] * Review copyright Checksums-Sha1: 663e611a1754cc7e10c53b87dcaddd875b095cc8 2386 spades_3.15.4+dfsg-2.dsc 35712b30fc13ce110f4cbdf07f520ed5c0bad509 28968 spades_3.15.4+dfsg-2.debian.tar.xz 5a73150776f81370ada75a1391de06367121a535 9361 spades_3.15.4+dfsg-2_amd64.buildinfo Checksums-Sha256: e8fd2386dff433abc5172c2594cf5e767ef830d58be6cc17996d2e60ec879b0a 2386 spades_3.15.4+dfsg-2.dsc 255bb5438cd1e70e4fab162d79812df8c5f183bdd1d9a2550c44d34ef0f63752 28968 spades_3.15.4+dfsg-2.debian.tar.xz 8ff6d7b9c24d54a37d8408b3bf3c64ddab53ea3b979a97c2281332ebad8305fc 9361 spades_3.15.4+dfsg-2_amd64.buildinfo Files: 4022ea0253866bf5f73526bc29f8d869 2386 science optional spades_3.15.4+dfsg-2.dsc f22e7979016cd11e96be848fedbc20b1 28968 science optional spades_3.15.4+dfsg-2.debian.tar.xz 3c2da0529297149f51311ed02be7db4d 9361 science optional spades_3.15.4+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmJ+W8ERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGMABAAjNUAyH1kmaW2EiFoY0SLxHS/+6wcgfDZ M3f7AnERVqaU0S0aNpnMs0j57xwwqTxl5VegPmcKmzaeShcXZZ+j6ogGYk1hU+BK L/0uDr2EhoukUVgW9P6yL3x1lr5taM1uqu0/CiyNdqqQsNOSHXrAQKwmYb/mHB6X 5z+s56YE6HH3rJu3vEPRI03o7BIyhBlM2oA7js4xk4sJsaHqQJATU293F9kkyO0Y Up4Xhi48zDcU6UkcQo34xNGn4OP85TZ6ZDp5INXYg2dl4OBOBrbKy3tl4hMncZMT YHIKwc1y0Tb9jbZaODL2CZwwKP1FpOOBODVqWbm9lxXdoExEEWzRZckVvKSm7YEO MyuEIhxY/foIAW8PkOm5kZ78x7Nt7DR6WqJAHPIEfYRF/7yW+gA6ae4mYwHWTb7r JDqtAlp2dggkurmxpGSAMcuKmXvnA9roX2Gbb1ZMhk0iarAVgjKY42eFbUN37ZDu dX4XO8hr5yzd2JhOyDG3rcjypDSTnvSniHUcYfLyptAAHo5b+NTc0RAEfLhtdC6X bYJnE5cF49yRmNEuwIUwHB7LWKmWiFC63Y/l07mtZTxs28aEcVjDkLBzs/9xJDew zyM7y+71qEiQkBrFCFXcN6cetdsihsUDOzLEtCFDe2eHyhGGgbokwZBlJXpYrQfU Ed0jvhj/N18= =rIaP -----END PGP SIGNATURE-----
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