Author: plessy Date: 2011-05-13 03:58:22 +0000 (Fri, 13 May 2011) New Revision: 6829
Added: trunk/packages/embassy-phylip/tags/3.69+20100721-3/ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/changelog trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/control trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/copyright trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/embassy-phylip.lintian-overrides Removed: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/changelog trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/control trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/copyright trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/embassy-phylip.lintian-overrides Log: [svn-buildpackage] Tagging embassy-phylip 3.69+20100721-3 Deleted: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/changelog =================================================================== --- trunk/packages/embassy-phylip/trunk/debian/changelog 2011-05-12 04:49:52 UTC (rev 6823) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/changelog 2011-05-13 03:58:22 UTC (rev 6829) @@ -1,45 +0,0 @@ -embassy-phylip (3.69+20100721-3) UNRELEASED; urgency=low - - * Set RPATH with “-Wl,--rpath” as GCC 4.6 does not accept “-R” anymore. - LP: #770835. - - -- Charles Plessy <[email protected]> Sun, 08 May 2011 21:05:07 +0900 - -embassy-phylip (3.69+20100721-2) unstable; urgency=low - - * Built on emboss-lib 6.3.1-6, pre-emptively depending on versions - lower than 6.3.2, because backwards compatibility is sometimes - broken (debian/control, debian/rules). - * Set an RPATH to /usr/lib/emboss/lib for using EMBOSS private - libraries (debian/rules, debian/embassy-phylip.lintian-overrides). - * Refreshed debian/copyright to test the latest DEP-5 format. - - -- Charles Plessy <[email protected]> Thu, 23 Sep 2010 14:07:26 +0900 - -embassy-phylip (3.69+20100721-1) unstable; urgency=low - - * New upstream release in which the version number was unchanged. - * Build-Depends on emboss 6.3.1 (debian/control, debian/rules). - * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed. - * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules). - * Incremented Standards-Version to reflect conformance with Policy 3.9.1 - (debian/control, no changes needed). - - -- Charles Plessy <[email protected]> Wed, 11 Aug 2010 19:46:37 +0900 - -embassy-phylip (3.69-1) unstable; urgency=low - - * New upstream release. - * debian/control: - - Corrected Vcs-Browser URL. - - Incremented Standards-Version to reflect conformance with Policy 3.8.4 - (no changes needed). - * Refreshed the manual pages (Debian-specific). - - -- Charles Plessy <[email protected]> Tue, 01 Jun 2010 21:43:33 +0900 - -embassy-phylip (3.68-1) unstable; urgency=low - - * Initial release (Closes: #493977) - - -- Charles Plessy <[email protected]> Sat, 08 Aug 2009 16:59:11 +0900 Copied: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/changelog (from rev 6828, trunk/packages/embassy-phylip/trunk/debian/changelog) =================================================================== --- trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/changelog (rev 0) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/changelog 2011-05-13 03:58:22 UTC (rev 6829) @@ -0,0 +1,49 @@ +embassy-phylip (3.69+20100721-3) unstable; urgency=low + + * Set RPATH with “-Wl,--rpath” as GCC 4.6 does not accept “-R” anymore. + (debian/rules) LP: #770835. + * Incremented Standards-Version to reflect conformance with Policy 3.9.2 + (debian/control, no changes needed). + * Updated debian/embassy-phylip.lintian-overrides for lintian 2.5. + * debian/copyright validated with config-edit. + + -- Charles Plessy <[email protected]> Thu, 12 May 2011 14:19:59 +0900 + +embassy-phylip (3.69+20100721-2) unstable; urgency=low + + * Built on emboss-lib 6.3.1-6, pre-emptively depending on versions + lower than 6.3.2, because backwards compatibility is sometimes + broken (debian/control, debian/rules). + * Set an RPATH to /usr/lib/emboss/lib for using EMBOSS private + libraries (debian/rules, debian/embassy-phylip.lintian-overrides). + * Refreshed debian/copyright to test the latest DEP-5 format. + + -- Charles Plessy <[email protected]> Thu, 23 Sep 2010 14:07:26 +0900 + +embassy-phylip (3.69+20100721-1) unstable; urgency=low + + * New upstream release in which the version number was unchanged. + * Build-Depends on emboss 6.3.1 (debian/control, debian/rules). + * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed. + * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules). + * Incremented Standards-Version to reflect conformance with Policy 3.9.1 + (debian/control, no changes needed). + + -- Charles Plessy <[email protected]> Wed, 11 Aug 2010 19:46:37 +0900 + +embassy-phylip (3.69-1) unstable; urgency=low + + * New upstream release. + * debian/control: + - Corrected Vcs-Browser URL. + - Incremented Standards-Version to reflect conformance with Policy 3.8.4 + (no changes needed). + * Refreshed the manual pages (Debian-specific). + + -- Charles Plessy <[email protected]> Tue, 01 Jun 2010 21:43:33 +0900 + +embassy-phylip (3.68-1) unstable; urgency=low + + * Initial release (Closes: #493977) + + -- Charles Plessy <[email protected]> Sat, 08 Aug 2009 16:59:11 +0900 Deleted: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/control =================================================================== --- trunk/packages/embassy-phylip/trunk/debian/control 2011-05-12 04:49:52 UTC (rev 6823) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/control 2011-05-13 03:58:22 UTC (rev 6829) @@ -1,40 +0,0 @@ -Source: embassy-phylip -Section: non-free/science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -DM-Upload-Allowed: yes -Uploaders: Charles Plessy <[email protected]> -Build-Depends: - cdbs, - debhelper (>= 7), - autotools-dev, - libxaw7-dev, - emboss-lib (>= 6.3.1-6~), - emboss-lib (<< 6.3.2~), - libgd2-xpm-dev, - libmysqlclient-dev, - libpq-dev -Standards-Version: 3.9.1 -Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#PHYLIPNEW -Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-phylip/trunk/?rev=0&sc=0 -Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-phylip/trunk - -Package: embassy-phylip -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (>= 6.3.1-6~), emboss-lib (<< 6.3.2~) -Description: EMBOSS conversions of the programs in the phylip package - This package is the adaptation of the PHYLIP package in which its - programs can operate with the biological sequence formats and databases - of the European Molecular Biology Open Software Suite (EMBOSS). The - software packages adapted for EMBOSS are called EMBASSY. - . - PHYLIP (the PHYLogeny Inference Package) is a package of programs for - inferring phylogenies (evolutionary trees). Methods that are available - in the package include parsimony, distance matrix, and likelihood - methods, including bootstrapping and consensus trees. Data types that - can be handled include molecular sequences, gene frequencies, - restriction sites and fragments, distance matrices, and discrete - characters. - . - The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them - from the original programs and avoid namespace conflict. Copied: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/control (from rev 6828, trunk/packages/embassy-phylip/trunk/debian/control) =================================================================== --- trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/control (rev 0) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/control 2011-05-13 03:58:22 UTC (rev 6829) @@ -0,0 +1,40 @@ +Source: embassy-phylip +Section: non-free/science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +DM-Upload-Allowed: yes +Uploaders: Charles Plessy <[email protected]> +Build-Depends: + cdbs, + debhelper (>= 7), + autotools-dev, + libxaw7-dev, + emboss-lib (>= 6.3.1-6~), + emboss-lib (<< 6.3.2~), + libgd2-xpm-dev, + libmysqlclient-dev, + libpq-dev +Standards-Version: 3.9.2 +Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#PHYLIPNEW +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-phylip/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-phylip/trunk + +Package: embassy-phylip +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (>= 6.3.1-6~), emboss-lib (<< 6.3.2~) +Description: EMBOSS conversions of the programs in the phylip package + This package is the adaptation of the PHYLIP package in which its + programs can operate with the biological sequence formats and databases + of the European Molecular Biology Open Software Suite (EMBOSS). The + software packages adapted for EMBOSS are called EMBASSY. + . + PHYLIP (the PHYLogeny Inference Package) is a package of programs for + inferring phylogenies (evolutionary trees). Methods that are available + in the package include parsimony, distance matrix, and likelihood + methods, including bootstrapping and consensus trees. Data types that + can be handled include molecular sequences, gene frequencies, + restriction sites and fragments, distance matrices, and discrete + characters. + . + The EMBASSY PHYLIP programs all have the prefix "f" to distinguish them + from the original programs and avoid namespace conflict. Deleted: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/copyright =================================================================== --- trunk/packages/embassy-phylip/trunk/debian/copyright 2011-05-12 04:49:52 UTC (rev 6823) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/copyright 2011-05-13 03:58:22 UTC (rev 6829) @@ -1,46 +0,0 @@ -Format: DEP-5 -Source: ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-(.*).tar.gz -Disclaimer: This package is not part of the Debian operating system. - . - The embassy-phylip source and binary Debian packages are part of the - “non-free” area in the Debian archive. The packages in this area are not part - of the Debian system, although they have been configured for use with Debian. - We nevertheless support the use of the seaview source and binary Debian - packages and provide infrastructure for non-free packages (such as our bug - tracking system and mailing lists). The licence of PHYLIPNEW does not forbid - Debian from using autobuilders to create binary packages. -Copyright: Copyright 1993-2004 by the University of Washington. -License: - Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. - Permission is granted to copy and use this program provided no fee is - charged for it and provided that this copyright notice is not removed. -Comment: It was confirmed on the EMBOSS User mailing list that the COPYING file - (GNU GPL) is there by error and the Phylip copyright file applies on all the - package. http://lists.open-bio.org/pipermail/emboss/2009-August/003713.html - -Files: doc/*, emboss-doc/* -Copyright: 1986-2002 by the University of Washington. -License: - Written by Joseph Felsenstein. Permission is granted to copy this document - provided that no fee is charged for it and that this copyright notice is not - removed. - -Files: debian/* -Copyright: 2009, Charles Plessy <[email protected]> -License: BOLA-1.0 - This work is provided 'as-is', without any express or implied warranty. In no - event will the authors be held liable for any damages arising from the use of - this work. - . - To all effects and purposes, this work is to be considered Public Domain. - . - . - However, if you want to be "buena onda", you should: - . - 1. Not take credit for it, and give proper recognition to the authors. - 2. Share your modifications, so everybody benefits from them. - 3. Do something nice for the authors. - 4. Help someone who needs it. - 5. Don't waste. Anything, but specially energy that comes from natural - non-renewable resources. - 6. Be tolerant. Everything that's good in nature comes from cooperation. Copied: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/copyright (from rev 6828, trunk/packages/embassy-phylip/trunk/debian/copyright) =================================================================== --- trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/copyright (rev 0) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/copyright 2011-05-13 03:58:22 UTC (rev 6829) @@ -0,0 +1,48 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.69.tar.gz +Disclaimer : This package is not part of the Debian operating system. + . + The embassy-phylip source and binary Debian packages are part of the + “non-free” area in the Debian archive. The packages in this area are not part + of the Debian system, although they have been configured for use with Debian. + We nevertheless support the use of the seaview source and binary Debian + packages and provide infrastructure for non-free packages (such as our bug + tracking system and mailing lists). The licence of PHYLIPNEW does not forbid + Debian from using autobuilders to create binary packages. +Comment: It was confirmed on the EMBOSS User mailing list that the COPYING file + (GNU GPL) is there by error and the Phylip copyright file applies on all the + package. http://lists.open-bio.org/pipermail/emboss/2009-August/003713.html + +Files: * +Copyright: © 1993-2004 by the University of Washington. +License: Phylip + Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe. + Permission is granted to copy and use this program provided no fee is + charged for it and provided that this copyright notice is not removed. + +Files: doc/*, emboss-doc/* +Copyright: 1986-2002 by the University of Washington. +License: Phylip-doc + Written by Joseph Felsenstein. Permission is granted to copy this document + provided that no fee is charged for it and that this copyright notice is not + removed. + +Files: debian/* +Copyright: 2009–2011 Charles Plessy <[email protected]> +License: BOLA-1.0 + This work is provided 'as-is', without any express or implied warranty. In no + event will the authors be held liable for any damages arising from the use of + this work. + . + To all effects and purposes, this work is to be considered Public Domain. + . + . + However, if you want to be "buena onda", you should: + . + 1. Not take credit for it, and give proper recognition to the authors. + 2. Share your modifications, so everybody benefits from them. + 3. Do something nice for the authors. + 4. Help someone who needs it. + 5. Don't waste. Anything, but specially energy that comes from natural + non-renewable resources. + 6. Be tolerant. Everything that's good in nature comes from cooperation. Deleted: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/embassy-phylip.lintian-overrides =================================================================== --- trunk/packages/embassy-phylip/trunk/debian/embassy-phylip.lintian-overrides 2011-05-12 04:49:52 UTC (rev 6823) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/embassy-phylip.lintian-overrides 2011-05-13 03:58:22 UTC (rev 6829) @@ -1,42 +0,0 @@ -# The embassy packages use privately some of the EMBOSS libraries. They have -# the same upstream authors and are released together. -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fclique /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fconsense /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fcontml /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fcontrast /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdiscboot /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnacomp /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnadist /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnainvar /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnaml /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnamlk /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnamove /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnapars /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdnapenny /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdollop /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdolmove /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdolpenny /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdrawgram /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fdrawtree /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/ffactor /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/ffitch /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/ffreqboot /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fgendist /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fkitsch /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fmix /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fmove /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fneighbor /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fpars /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fpenny /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fproml /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fpromlk /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fprotdist /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fprotpars /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/frestboot /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/frestdist /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/frestml /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fretree /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fseqboot /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/fseqbootall /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/ftreedist /usr/lib/emboss/lib -embassy-phylip: binary-or-shlib-defines-rpath ./usr/bin/ftreedistpair /usr/lib/emboss/lib Copied: trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/embassy-phylip.lintian-overrides (from rev 6828, trunk/packages/embassy-phylip/trunk/debian/embassy-phylip.lintian-overrides) =================================================================== --- trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/embassy-phylip.lintian-overrides (rev 0) +++ trunk/packages/embassy-phylip/tags/3.69+20100721-3/debian/embassy-phylip.lintian-overrides 2011-05-13 03:58:22 UTC (rev 6829) @@ -0,0 +1,3 @@ +# The embassy packages use privately some of the EMBOSS libraries. They have +# the same upstream authors and are released together. +embassy-phylip: binary-or-shlib-defines-rpath * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
