Your message dated Tue, 31 Jan 2017 15:18:28 +0000 with message-id <[email protected]> and subject line Bug#853738: fixed in phyml 3:3.2.0+dfsg-6 has caused the Debian Bug report #853738, regarding phyml: MPI version uses different number of bootstrap steps breaking applications like seaview 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.) -- 853738: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=853738 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: phyml Severity: grave Justification: renders package unusable Hi, for optimisation reasons the bootstrap parameter (-b) is not matched exactly in phyml but rather adjusted to an optimized usage of processors by the following algorithm: (nBootstrap / nProzessors + 1) * nProzessors (see src/mpi_boot.c line 26 and 27). While this is OK for manual inspection of the results it breaks applications like seaview which is using the number of given bootstrap processes as 100% for a quality measure. If this number increases unexpectedly the measure will become above 100% which is no sensible result. As a workaround it would be needed to either determine the number of processors to fullfill the relation nBootstrap % nProzessors = 0 which results in unchanged number of bootstrap steps or simply set nProcessors=1 (disable multiprocessing at all). 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 phyml depends on: ii libc6 2.19-18+deb8u7 phyml recommends no packages. phyml suggests no packages.
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--- Begin Message ---Source: phyml Source-Version: 3:3.2.0+dfsg-6 We believe that the bug you reported is fixed in the latest version of phyml, 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 phyml 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: Tue, 31 Jan 2017 15:16:45 +0100 Source: phyml Binary: phyml Architecture: source amd64 Version: 3:3.2.0+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: phyml - Phylogenetic estimation using Maximum Likelihood Closes: 853737 853738 Changes: phyml (3:3.2.0+dfsg-6) unstable; urgency=medium . * Also provide version without beagle library since it causes trouble on machines without according graphics hardware Closes: #853737 * Provide link /usr/bin/phyml-beagle * Enable to switch of MPI version via environment variable since there are circumstances when it leads to wrong results Closes: #853738 * Test single processor and MPI in autopkgtest Checksums-Sha1: a6d234974bcdd8d2e6dc479104f807957c05567e 2140 phyml_3.2.0+dfsg-6.dsc 695575b83e2a215b7580239ff5613c0c3924cf09 16756 phyml_3.2.0+dfsg-6.debian.tar.xz 6aec72d56d2c6ec1efa7876f20a47affee0c2a6b 53836 phyml-dbgsym_3.2.0+dfsg-6_amd64.deb cc4be2cc20e1c4f09aaada2e8cbc9d7226eba8a3 5869 phyml_3.2.0+dfsg-6_amd64.buildinfo e20f292642948ea85d39f4bf3eb9e708be2163cd 1302608 phyml_3.2.0+dfsg-6_amd64.deb Checksums-Sha256: cf4b1f9f097ac1376d15a9f561b4956bae6ec32023d2f6bcd6440a0d84ce0d16 2140 phyml_3.2.0+dfsg-6.dsc 000291b39dd94f9d0c3fc2211b36fc83b7c5354aed1f641749eee5a89db1e150 16756 phyml_3.2.0+dfsg-6.debian.tar.xz 9f8af5f3f72df5dc41a981c6aa503e9c7a5d59a086945e61cc3920d8d80ac163 53836 phyml-dbgsym_3.2.0+dfsg-6_amd64.deb 001c5cb74fd6fa5f533d3010e93b3a5bd7b40117863f7902cc02cf0428369bc8 5869 phyml_3.2.0+dfsg-6_amd64.buildinfo 018825c4a187f49a835b64a4b803aee0cbdd6c92053577e83d93c95cf8f2f792 1302608 phyml_3.2.0+dfsg-6_amd64.deb Files: 267555a66b2205df136edd365677ec47 2140 science optional phyml_3.2.0+dfsg-6.dsc b91ebc5f05468206a6fd8f79eb3fda06 16756 science optional phyml_3.2.0+dfsg-6.debian.tar.xz c03659463361a6aaecd6fb61022d72aa 53836 debug extra phyml-dbgsym_3.2.0+dfsg-6_amd64.deb d1d3382f0f5a27c3ba244cfa5b8a01af 5869 science optional phyml_3.2.0+dfsg-6_amd64.buildinfo 183096aab5c0370cf7eb57657b76eb93 1302608 science optional phyml_3.2.0+dfsg-6_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJYkKOcAAoJEFeKBJTRxkbRmd8P/Ra+ZWL3UB5sS23q5So1XAr8 APEOi+3pbVS9WfbiWx0GYwH0WmPl3yjAG22OmE8G6Cim+4c/22mTbCRxQlSNWytt QwvzBMnKMZ9M7PhIiUgTrc4Xm8GZxKV0an/rvztN3uqRlbxMgWmeEkRkD8ghRTxY N6DURtECLiY5ZjyAVNtOOjuBmnx6B+cy5VCvdXuD/UqeIzUn6dG9lNYBRShl9JWG q0ua9c8UgnKVUCziEA1WTeXfWn3OGtpvyxNpTODCtUzgvRAGlSSho4QkqgoEmFER aFj3NaDkFvkyhWSUZ8oqMkCzEJCiT8tam8JOo3yDjrdbFzzGTPhKuec3JwgrDAW4 /Q4aBzX/XlFjFFKrkK0GQrSij/0R+RZv8sN3kB0YCSqgb7wY/mEdt2S833PSv/nm O18lwrrCmKJrnwFFmbwZTZdDqXX0WioakKsQ0uDuxhmUhOCq7k1LiFptUGAUo6Eg ZxoBH14x7cNEU9XbSA3cYam2ad/0Rezv1YGyclDIK4I+4k05R5YcQ+4XNCEZIe+P byfDJBrfxoc6eAaERt/wYBesPgf8Ypys1LbWOpKrFIQs0GWJogtejswfYjOr3NEV +ME35BVvQGXtui9gV93iC5EFDOvo0RjG27rk2w6V5uOloq5OudKNjWpHN6jW9jrO dxLrhxEzmXoKPvmYN4ix =ggOn -----END PGP SIGNATURE-----
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