Your message dated Tue, 11 Feb 2014 10:04:25 +0000 with message-id <e1wdacx-0006it...@franck.debian.org> and subject line Bug#737913: fixed in dnaclust 3-2 has caused the Debian Bug report #737913, regarding exonerate and dnaclust: error when trying to install together 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.) -- 737913: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=737913 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: dnaclust,exonerate Version: dnaclust/3-1 Version: exonerate/2.2.0-6 Severity: serious User: trei...@debian.org Usertags: edos-file-overwrite Date: 2014-02-06 Architecture: amd64 Distribution: sid Hi, automatic installation tests of packages that share a file and at the same time do not conflict by their package dependency relationships has detected the following problem: Selecting previously unselected package libboost-program-options1.54.0:amd64. (Reading database ... 10921 files and directories currently installed.) Preparing to unpack .../libboost-program-options1.54.0_1.54.0-4+b1_amd64.deb ... Unpacking libboost-program-options1.54.0:amd64 (1.54.0-4+b1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../libffi6_3.0.13-12_amd64.deb ... Unpacking libffi6:amd64 (3.0.13-12) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../libglib2.0-0_2.36.4-1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.36.4-1) ... Selecting previously unselected package dnaclust. Preparing to unpack .../dnaclust_3-1_amd64.deb ... Unpacking dnaclust (3-1) ... Selecting previously unselected package exonerate. Preparing to unpack .../exonerate_2.2.0-6_amd64.deb ... Unpacking exonerate (2.2.0-6) ... dpkg: error processing archive /var/cache/apt/archives/exonerate_2.2.0-6_amd64.deb (--unpack): trying to overwrite '/usr/bin/fastasort', which is also in package dnaclust 3-1 dpkg-deb: error: subprocess paste was killed by signal (Broken pipe) Processing triggers for man-db (2.6.6-1) ... Errors were encountered while processing: /var/cache/apt/archives/exonerate_2.2.0-6_amd64.deb E: Sub-process /usr/bin/dpkg returned an error code (1) This is a serious bug as it makes installation fail, and violates sections 7.6.1 and 10.1 of the policy. An optimal solution would consist in only one of the packages installing that file, and renaming or removing the file in the other package. Depending on the circumstances you might also consider Replace relations or file diversions. If the conflicting situation cannot be resolved then, as a last resort, the two packages have to declare a mutual Conflict. Please take into account that Replaces, Conflicts and diversions should only be used when packages provide different implementations for the same functionality. Here is a list of files that are known to be shared by both packages (according to the Contents file for sid/amd64, which may be slightly out of sync): /usr/bin/fastasort This bug has been filed against both packages. If you, the maintainers of the two packages in question, have agreed on which of the packages will resolve the problem please reassign the bug to that package. You may then also register in the BTS that the other package is affected by the bug. -Ralf. PS: for more information about the detection of file overwrite errors of this kind see http://edos.debian.net/file-overwrites/.
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--- Begin Message ---Source: dnaclust Source-Version: 3-2 We believe that the bug you reported is fixed in the latest version of dnaclust, 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 737...@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 dnaclust 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: Tue, 11 Feb 2014 10:02:25 +0100 Source: dnaclust Binary: dnaclust Architecture: source amd64 Version: 3-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: dnaclust - tool for clustering millions of short DNA sequences Closes: 737913 Changes: dnaclust (3-2) unstable; urgency=medium . * Move /usr/bin/fastasor to /usr/lib/dnaclust/fastasor to avoid name space conflict with exonerate. Closes: #737913 Checksums-Sha1: 0f84892dbd2a5c3000fb1dcbc975ef58496165d4 1942 dnaclust_3-2.dsc a7333439ca41c07289d65c9026c27f91cfcdf04b 6656 dnaclust_3-2.debian.tar.xz 5436e7fc93df4cc54f97d3dc64a26237d55c21df 86190 dnaclust_3-2_amd64.deb Checksums-Sha256: c392945a5f4f1542bb44dd8c6cab1816ab954482abbce53efa82c52573b861c8 1942 dnaclust_3-2.dsc 4d3d5ed5dc835e9e899d49a1dacf0efae5a41c9c21f49e586d0c461fc09ce466 6656 dnaclust_3-2.debian.tar.xz 3efd6d754bdcd1c2e2dc6a021a587af79568ab7b03e926e96ec8376e76d4635d 86190 dnaclust_3-2_amd64.deb Files: 21178ca48a1f812ae689a57062ca7ea0 1942 science optional dnaclust_3-2.dsc 14f30ea0bf4ed47468a365c78623cf4f 6656 science optional dnaclust_3-2.debian.tar.xz 5652300601d2687b33eafb015dbe66dc 86190 science optional dnaclust_3-2_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJS+e03AAoJEFeKBJTRxkbRaioP/jDnKgmR86RKdATiO59qLh28 xkUt1c1RnQYo7ZG3pY/eBA4NIqifGutTR41p3tleth2GrEzfUd3rCoWZMQJQkpFi Tumbf5MzU0WWIVPqhakrfEGkyYnMUdbZobHaaijCC7ySwOAa00IRrpciCVaPGEzS tnLkd7stFiI2+3jTdaW8AL7cF1UevfXEKzbbiMuSN8jFWpNwKmmbpkka9ccDdMvr d5v3c0rwz82grjqypeC+aHFKcz5SYwhqKcDUGGO5r1+E5KH6t6L9ShVJXOeoin+Q Ope1v/3YSnk5sY8bvCq3ojdRzUluGv62Mx+h7cx/u/fELSxDWRNUl0yyG358+EyX q77J2vqCURC/jZb92+GnBHQ+E+gKbYbA2BgMmuSVrc0OQ8Zs8kZFHvKlbk8lpU40 jGjXPaGe3Ii8CDGFprniqnvhDSoCV8mfCU0XqRVnjueYPJ942bivbzKxGYokr3Z8 u+AaQwFaeNck1Yb2/LR0WPWU0MF8z93HzFTSVLFJte5ur+jS25yQ2gVRiQWLSafc J7jlt2anF5AgdFO7i/6+XNwnaKD74VoQCZsUG8ig0OMG0NIecjQSJqiEKuR4+3Hs VWvpHOxOB9Vd0AzoZ45RBGsG7t5S5zcKC4gUqzwRp6mm9YybnKlcGHuGOMayjLfT GbtJfrNLEJ4oFgrVpK5f =SJkQ -----END PGP SIGNATURE-----
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