Your message dated Wed, 01 Feb 2017 12:19:06 +0000 with message-id <[email protected]> and subject line Bug#853835: fixed in seaview 1:4.6.1.2-2 has caused the Debian Bug report #853835, regarding seaview: Wrong results in connection with multi-processing phyml 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.) -- 853835: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=853835 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: seaview Severity: grave Justification: renders package unusable Hi, when using phyml on multiprocessor machines it might happen that a greater number of bootstraps than specified by seaview is done by phyml. Phyml "decides" itself how many bootstrap steps it takes depending from the amount of processors can be used. I have described the issue in Debian bug #853738[1] and fixed the bug in a way which allows the user to call seaview like: PHYMLCPUS=8 seaview *.fna when intending to do for instance 1000 bootstrap steps. This works since 1000%8=0. However, for other numbers of CPUs for instance when calling PHYMLCPUS=16 seaview *.fna phyml would do (1000 / 16 + 1) * 16 = 1008 bootstrap processes. From phyml perspective this does not matter but the effect in seaview is that if 1000 bootstraps are considered 100% some values might end up beeing 101% which is nonsense. So seaview need to parse the phyml output for changed numbers of bootstraps to adjust the base of the calculations that are based on the effective number of bootstraps. Kind regards Andreas. -- System Information: Debian Release: 8.7 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages seaview depends on: ii libc6 2.19-18+deb8u7 pn libfltk-images1.3 <none> pn libfltk1.3 <none> ii libgcc1 1:4.9.2-10 ii libstdc++6 4.9.2-10 ii libx11-6 2:1.6.2-3 ii zlib1g 1:1.2.8.dfsg-2+b1 Versions of packages seaview recommends: pn clustalo <none> pn muscle <none> pn phyml <none> seaview suggests no packages.
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--- Begin Message ---Source: seaview Source-Version: 1:4.6.1.2-2 We believe that the bug you reported is fixed in the latest version of seaview, 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. Andreas Tille <[email protected]> (supplier of updated seaview 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: Wed, 01 Feb 2017 12:54:56 +0100 Source: seaview Binary: seaview Architecture: source amd64 Version: 1:4.6.1.2-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: seaview - Multiplatform interface for sequence alignment and phylogeny Closes: 853835 Changes: seaview (1:4.6.1.2-2) unstable; urgency=medium . * Enable reading number of bootstraps from phyml runs Closes: #853835 Checksums-Sha1: 72c62a7b370102ca0d0be6f6ddb9e0e8ec097669 2041 seaview_4.6.1.2-2.dsc 8e2dd9e9dd5533e68f4d86ac4c7a6aded6ecbf85 15948 seaview_4.6.1.2-2.debian.tar.xz 242ae4b6aeec1dfa82d8768c37722fb9f857c715 899890 seaview-dbgsym_4.6.1.2-2_amd64.deb bce3532aa0f063d997f6b4217b178b68893665c3 6587 seaview_4.6.1.2-2_amd64.buildinfo daf51edba2e096f7036aaafffb26f68782dc65a1 339182 seaview_4.6.1.2-2_amd64.deb Checksums-Sha256: e8c36f2e70e3b6b31174319a2a05ad3e4bf602511705068fe1883a67ed9a6973 2041 seaview_4.6.1.2-2.dsc d536af0c0dd1c3d180974facc80f5e59e9feb868d1cf450036a90b21c69e5425 15948 seaview_4.6.1.2-2.debian.tar.xz 7bf2a076e4c71b9de95ce50f363ef1e0421da1c2a9d10b6b958feceba49d9b87 899890 seaview-dbgsym_4.6.1.2-2_amd64.deb c91e06d6f09466b3bd3cae0664e15087c56523a00dabda1308c95a8628e3f5b0 6587 seaview_4.6.1.2-2_amd64.buildinfo 0fc689a053abe887517ed1f362aa54fa679c3213f8574569c293687cdd902a42 339182 seaview_4.6.1.2-2_amd64.deb Files: 9e2dbc0b8f6b71cf14b73efb1407e3d0 2041 science optional seaview_4.6.1.2-2.dsc 9ddc60ff6222992701ff63ff994e6989 15948 science optional seaview_4.6.1.2-2.debian.tar.xz 31223d1702cb6e6f83f5130fcb839b63 899890 debug extra seaview-dbgsym_4.6.1.2-2_amd64.deb 6bc589317ad8bf4a88230b12370d8b79 6587 science optional seaview_4.6.1.2-2_amd64.buildinfo 9f51d9e55f9f648b3cbf8a8cdbdf07a4 339182 science optional seaview_4.6.1.2-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJYkc2KAAoJEFeKBJTRxkbR6nYP/28GkcAUB7grVJCAz6ahDZd8 3v3WfDif1fDNm/7enY/vljMbnAZ3jz/yflA/N+Kq9EZmH1YJfCMCNHt10+vqMCcD tyMdiN472rivUB9aNKHSrIVXLyKxmn9Ng170vLP1v6GYUxKO8tf+G5qX1G1kGo28 Wx8YgvlqFSjLViRsbAVC1fdgbC3MVlU8Mo4qvrxq3Cz5Mu6sPdJQfepN64bCUbae 85clXIzjRL1xHgmdDHc5FbyAjpwVruWtzwAVd6O2zQP6NvdGVffDQsB/b1FDEb6I hMM2fzoElhlSsxHekb06mM3457sAo4ABuj8Z2nfcNfIBSj3qmnEQfCrqg7KnWPz8 j2ADKjheSV0tTUeTiQhJgkgppdOTspzXILbY4IXXY5nj7MtxFfbK5Ldtnso261CX H/f0bjU3P0QJfu0CcJ6nLOVuywmCDXtuL4n8DRF9yqKU2r32orFuXw3y5HkzhKE2 gHCgPdtdmkxhaqTvFpOGEAg/cprL80zAsykYmGI1l+uaNpkSXPk7M/eEPxhENo/l RIPIIizgqpGf5fvJghapVdi25rtmwUy8aUFIMsiOxJwIbj3ISpPzL8XKb2BC1zoV C1yLTrfZ0ke47Mn7H/4Fxx9tsHwJJuAFnZoN/vcVAxxaCiC0UGEMlAmpD9DWbxMq nmIL1dnnVdjj4yjjrLeI =rrRN -----END PGP SIGNATURE-----
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