[med-svn] r6829 - in trunk/packages/embassy-phylip/tags: . 3.69+20100721-3/debian
Charles Plessy
plessy at alioth.debian.org
Fri May 13 03:58:28 UTC 2011
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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> Tue, 01 Jun 2010 21:43:33 +0900
-
-embassy-phylip (3.68-1) unstable; urgency=low
-
- * Initial release (Closes: #493977)
-
- -- Charles Plessy <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> 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 <plessy at debian.org> Tue, 01 Jun 2010 21:43:33 +0900
+
+embassy-phylip (3.68-1) unstable; urgency=low
+
+ * Initial release (Closes: #493977)
+
+ -- Charles Plessy <plessy at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-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 <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+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 <plessy at debian.org>
-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 <plessy at debian.org>
+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 *
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