[med-svn] r7168 - in trunk/packages/phyml/tags: . 2:20110526-1/debian
Charles Plessy
plessy at alioth.debian.org
Sun Jun 26 04:28:44 UTC 2011
Author: plessy
Date: 2011-06-26 04:28:43 +0000 (Sun, 26 Jun 2011)
New Revision: 7168
Added:
trunk/packages/phyml/tags/2:20110526-1/
trunk/packages/phyml/tags/2:20110526-1/debian/changelog
trunk/packages/phyml/tags/2:20110526-1/debian/compat
trunk/packages/phyml/tags/2:20110526-1/debian/control
trunk/packages/phyml/tags/2:20110526-1/debian/copyright
trunk/packages/phyml/tags/2:20110526-1/debian/phyml.1
trunk/packages/phyml/tags/2:20110526-1/debian/rules
Removed:
trunk/packages/phyml/tags/2:20110526-1/debian/changelog
trunk/packages/phyml/tags/2:20110526-1/debian/compat
trunk/packages/phyml/tags/2:20110526-1/debian/control
trunk/packages/phyml/tags/2:20110526-1/debian/copyright
trunk/packages/phyml/tags/2:20110526-1/debian/phyml.1
trunk/packages/phyml/tags/2:20110526-1/debian/rules
Log:
[svn-buildpackage] Tagging phyml 2:20110526-1
Deleted: trunk/packages/phyml/tags/2:20110526-1/debian/changelog
===================================================================
--- trunk/packages/phyml/trunk/debian/changelog 2011-06-25 21:18:40 UTC (rev 7162)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/changelog 2011-06-26 04:28:43 UTC (rev 7168)
@@ -1,59 +0,0 @@
-phyml (2:20100720-1) unstable; urgency=low
-
- * New upstream version
- * Fixed watch file
- * Standard-Version: 3.9.1 (no changes needed)
- * Source format 3.0 (quilt)
- * Wrote man page
-
- -- Andreas Tille <tille at debian.org> Mon, 14 Feb 2011 15:04:52 +0100
-
-phyml (2:20100123-1) unstable; urgency=low
-
- * New upstream release.
-
- [ Nelson A. de Oliveira ]
- * Fix watch file.
- * Increment the epoch number to fix a typo in the version number.
-
- [ Charles Plessy ]
- * Checked conformance with Policy 3.8.4 and incremented Standards-Version
- in debian/control to reflect this (no changes needed).
- * Moved the bibliographic reference from debian/reference to
- debian/upstream-metadata.yaml.
- * Adapted debian/rules to the new location of the auto(conf|make) files.
-
- -- Charles Plessy <plessy at debian.org> Sun, 07 Mar 2010 19:55:08 +0900
-
-phyml (1:200900706-2) unstable; urgency=low
-
- * Disable parallel building, that was incorrectly supported and
- induced build failures by race condition (Closes: #536967).
-
- -- Charles Plessy <plessy at debian.org> Wed, 15 Jul 2009 09:35:40 +0900
-
-phyml (1:200900706-1) unstable; urgency=low
-
- * New upstream release.
- * Suppressed unneeded Lintian overrides, and use ‘dh clean’ in debian/rules.
- * Checked conformance with Policy 3.8.2 and incremented Standards-Version
- in debian/control to reflect this (no changes needed).
- * Experimentation on the format of debian/copyright.
-
- -- Charles Plessy <plessy at debian.org> Sat, 11 Jul 2009 14:25:23 +0900
-
-phyml (1:20090501-1) unstable; urgency=low
-
- * New upstream release clarifying the license of the documentation and
- switching to a versionning system that can be sorted by numerical order.
- * Added debian/source.lintian-overrides to indicate that the
- configure-generated files are deleted at cleaning time.
- * Using ‘dh binary-arch’ to simplify debian/rules.
-
- -- Charles Plessy <plessy at debian.org> Sat, 16 May 2009 14:55:14 +0900
-
-phyml (30042009-1) unstable; urgency=low
-
- * Initial release (Closes: #517165)
-
- -- Charles Plessy <plessy at debian.org> Fri, 01 May 2009 08:53:44 +0900
Copied: trunk/packages/phyml/tags/2:20110526-1/debian/changelog (from rev 7167, trunk/packages/phyml/trunk/debian/changelog)
===================================================================
--- trunk/packages/phyml/tags/2:20110526-1/debian/changelog (rev 0)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/changelog 2011-06-26 04:28:43 UTC (rev 7168)
@@ -0,0 +1,72 @@
+phyml (2:20110526-1) unstable; urgency=low
+
+ * New upstream version.
+ * debian/control:
+ - Corrected VCS URLs.
+ - Using debhelper 8 (debian/compat).
+ - Enhances bioperl-run (that has a PhyML wrapper).
+ - Standards-Version incremented to reflect compliance with Policy 3.9.2.
+ * Added build-arch and build-indep targets to debian/rules.
+ * Build and distribute PhyTime (debian/rules, debian/control).
+
+ -- Charles Plessy <plessy at debian.org> Sun, 26 Jun 2011 12:14:54 +0900
+
+phyml (2:20100720-1) unstable; urgency=low
+
+ * New upstream version
+ * Fixed watch file
+ * Standard-Version: 3.9.1 (no changes needed)
+ * Source format 3.0 (quilt)
+ * Wrote man page
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Feb 2011 15:04:52 +0100
+
+phyml (2:20100123-1) unstable; urgency=low
+
+ * New upstream release.
+
+ [ Nelson A. de Oliveira ]
+ * Fix watch file.
+ * Increment the epoch number to fix a typo in the version number.
+
+ [ Charles Plessy ]
+ * Checked conformance with Policy 3.8.4 and incremented Standards-Version
+ in debian/control to reflect this (no changes needed).
+ * Moved the bibliographic reference from debian/reference to
+ debian/upstream-metadata.yaml.
+ * Adapted debian/rules to the new location of the auto(conf|make) files.
+
+ -- Charles Plessy <plessy at debian.org> Sun, 07 Mar 2010 19:55:08 +0900
+
+phyml (1:200900706-2) unstable; urgency=low
+
+ * Disable parallel building, that was incorrectly supported and
+ induced build failures by race condition (Closes: #536967).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 15 Jul 2009 09:35:40 +0900
+
+phyml (1:200900706-1) unstable; urgency=low
+
+ * New upstream release.
+ * Suppressed unneeded Lintian overrides, and use ‘dh clean’ in debian/rules.
+ * Checked conformance with Policy 3.8.2 and incremented Standards-Version
+ in debian/control to reflect this (no changes needed).
+ * Experimentation on the format of debian/copyright.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 11 Jul 2009 14:25:23 +0900
+
+phyml (1:20090501-1) unstable; urgency=low
+
+ * New upstream release clarifying the license of the documentation and
+ switching to a versionning system that can be sorted by numerical order.
+ * Added debian/source.lintian-overrides to indicate that the
+ configure-generated files are deleted at cleaning time.
+ * Using ‘dh binary-arch’ to simplify debian/rules.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 16 May 2009 14:55:14 +0900
+
+phyml (30042009-1) unstable; urgency=low
+
+ * Initial release (Closes: #517165)
+
+ -- Charles Plessy <plessy at debian.org> Fri, 01 May 2009 08:53:44 +0900
Deleted: trunk/packages/phyml/tags/2:20110526-1/debian/compat
===================================================================
--- trunk/packages/phyml/trunk/debian/compat 2011-06-25 21:18:40 UTC (rev 7162)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/compat 2011-06-26 04:28:43 UTC (rev 7168)
@@ -1 +0,0 @@
-7
Copied: trunk/packages/phyml/tags/2:20110526-1/debian/compat (from rev 7164, trunk/packages/phyml/trunk/debian/compat)
===================================================================
--- trunk/packages/phyml/tags/2:20110526-1/debian/compat (rev 0)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/compat 2011-06-26 04:28:43 UTC (rev 7168)
@@ -0,0 +1 @@
+8
Deleted: trunk/packages/phyml/tags/2:20110526-1/debian/control
===================================================================
--- trunk/packages/phyml/trunk/debian/control 2011-06-25 21:18:40 UTC (rev 7162)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/control 2011-06-26 04:28:43 UTC (rev 7168)
@@ -1,36 +0,0 @@
-Source: phyml
-Section: 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>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7), automake, autoconf
-Standards-Version: 3.9.1
-Homepage: http://www.atgc-montpellier.fr/phyml
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phyml/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/phyml/trunk/
-
-Package: phyml
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Phylogenetic estimation using Maximum Likelihood
- PhyML is a software that estimates maximum likelihood phylogenies from
- alignments of nucleotide or amino acid sequences. It provides a wide
- range of options that were designed to facilitate standard phylogenetic
- analyses. The main strengths of PhyML lies in the large number of
- substitution models coupled to various options to search the space of
- phylogenetic tree topologies, going from very fast and efficient methods
- to slower but generally more accurate approaches. It also implements
- two methods to evaluate branch supports in a sound statistical framework
- (the non-parametric bootstrap and the approximate likelihood ratio test).
- .
- PhyML was designed to process moderate to large data sets. In theory,
- alignments with up to 4,000 sequences 2,000,000 character-long can
- be analyzed. In practice however, the amount of memory required to process
- a data set is proportional of the product of the number of sequences by their
- length. Hence, a large number of sequences can only be processed provided
- that they are short. Also, PhyML can handle long sequences provided that
- they are not numerous. With most standard personal computers, the “comfort
- zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
- character long.
Copied: trunk/packages/phyml/tags/2:20110526-1/debian/control (from rev 7167, trunk/packages/phyml/trunk/debian/control)
===================================================================
--- trunk/packages/phyml/tags/2:20110526-1/debian/control (rev 0)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/control 2011-06-26 04:28:43 UTC (rev 7168)
@@ -0,0 +1,39 @@
+Source: phyml
+Section: 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>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 8), automake, autoconf
+Standards-Version: 3.9.2
+Homepage: http://www.atgc-montpellier.fr/phyml
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phyml/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phyml/trunk/
+
+Package: phyml
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Enhances: bioperl-run
+Description: Phylogenetic estimation using Maximum Likelihood
+ PhyML is a software that estimates maximum likelihood phylogenies from
+ alignments of nucleotide or amino acid sequences. It provides a wide
+ range of options that were designed to facilitate standard phylogenetic
+ analyses. The main strengths of PhyML lies in the large number of
+ substitution models coupled to various options to search the space of
+ phylogenetic tree topologies, going from very fast and efficient methods
+ to slower but generally more accurate approaches. It also implements
+ two methods to evaluate branch supports in a sound statistical framework
+ (the non-parametric bootstrap and the approximate likelihood ratio test).
+ .
+ PhyML was designed to process moderate to large data sets. In theory,
+ alignments with up to 4,000 sequences 2,000,000 character-long can
+ be analyzed. In practice however, the amount of memory required to process
+ a data set is proportional of the product of the number of sequences by their
+ length. Hence, a large number of sequences can only be processed provided
+ that they are short. Also, PhyML can handle long sequences provided that
+ they are not numerous. With most standard personal computers, the “comfort
+ zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
+ character long.
+ .
+ This pakcage also includes PhyTime.
Deleted: trunk/packages/phyml/tags/2:20110526-1/debian/copyright
===================================================================
--- trunk/packages/phyml/trunk/debian/copyright 2011-06-25 21:18:40 UTC (rev 7162)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/copyright 2011-06-26 04:28:43 UTC (rev 7168)
@@ -1,85 +0,0 @@
-Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-
-Name : PhyML
-Source : http://phyml.googlecode.com/files/phyml_20090706.tar.gz
-Contact :
- Stephane Guindon <guindon at stat.auckland.ac.nz>
- Department of Statistics. University of Auckland. New Zealand
- Universite Montpellier II - CNRS UMR 5506. LIRMM. Montpellier France.
-
- Olivier Gascuel <gascuel at lirmm.fr>
- Universite Montpellier II - CNRS UMR 5506. LIRMM. Montpellier France.
-
- Jean-Francois Dufayard <jeanfrancois.dufayard at gmail.com>
- Universite Montpellier II - CNRS UMR 5506. LIRMM. Montpellier France.
-
-Copyright : Stephane Guindon <guindon at stat.auckland.ac.nz>
- Olivier Gascuel <gascuel at lirmm.fr>
- Jean-Francois Dufayard <jeanfrancois.dufayard at gmail.com>
- Wim Hodrijk <wim at santafe.edu>
- Franck Lethiec <lethiec at lirmm.fr>
-Licence : GPL-2+
-
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License along
- with this program; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-On the Debian operating system, a copy of the GNU GPL version 2 can be found in
-‘/usr/share/common-licenses/GPL-2’.
-
-Files: src/depcomp
-Copyright: © 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
-Licence: GPL-2+, plus special exemption
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2, or (at your option)
- any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
- 02110-1301, USA.
-
- As a special exception to the GNU General Public License, if you
- distribute this file as part of a program that contains a
- configuration script generated by Autoconf, you may include it under
- the same distribution terms that you use for the rest of that program.
-
-Files: /src/missing
-Copyright: © 1996, 1997 Free Software Foundation, Inc.
- © Franc,ois Pinard <pinard at iro.umontreal.ca>, 1996.
-License: GPL-2+
- (see above)
-
-Files: src/install-sh
-Copyright: © 1991 by the Massachusetts Institute of Technology
-License: MIT
- Permission to use, copy, modify, distribute, and sell this software and its
- documentation for any purpose is hereby granted without fee, provided that
- the above copyright notice appear in all copies and that both that
- copyright notice and this permission notice appear in supporting
- documentation, and that the name of M.I.T. not be used in advertising or
- publicity pertaining to distribution of the software without specific,
- written prior permission. M.I.T. makes no representations about the
- suitability of this software for any purpose. It is provided "as is"
- without express or implied warranty.
-
-Files: debian/*
-Copyright: © 2009 Charles Plessy <plessy at debian>
-License: same as PhyML.
- See above.
Copied: trunk/packages/phyml/tags/2:20110526-1/debian/copyright (from rev 7163, trunk/packages/phyml/trunk/debian/copyright)
===================================================================
--- trunk/packages/phyml/tags/2:20110526-1/debian/copyright (rev 0)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/copyright 2011-06-26 04:28:43 UTC (rev 7168)
@@ -0,0 +1,192 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://googlecode.debian.net/p/phyml/phyml-20110526.tar.gz
+
+Files: *
+Copyright: Stephane Guindon <guindon at stat.auckland.ac.nz>
+ Olivier Gascuel <gascuel at lirmm.fr>
+ Jean-Francois Dufayard <jeanfrancois.dufayard at gmail.com>
+ Wim Hodrijk <wim at santafe.edu>
+ Franck Lethiec <lethiec at lirmm.fr>
+Licence: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+Comment: On the Debian operating system, a copy of the GNU GPL version 2
+ can be found in ‘/usr/share/common-licenses/GPL-2’.
+
+Files: doc/phyml_manual.ps
+Copyright: © 1999 - 2008 by PhyML Development Team
+ © 1996 Craig Barratt, Michael C. Grant, and David Carlisle.
+ © 1997, 2009 American Mathematical Society (<http://www.ams.org>)
+License: mixture
+ In my understanding, the text (GPL-2+) is only aggregated with the
+ font (OFL-1.1) and the PostScript code (psfrag). CP, 2011-06-26.
+
+License: psfrag
+ All rights are reserved.
+ .
+ This system is distributed in the hope that it will be
+ useful, but WITHOUT ANY WARRANTY; without even the
+ implied warranty of MERCHANTABILITY or FITNESS FOR A
+ PARTICULAR PURPOSE. Don't come complaining to us if you
+ modify this file and it doesn't work! If this file is
+ modified by anyone but the authors, those changes and
+ their authors must be explicitly stated HERE.
+Comment: see the following URLs:
+ ftp://ftp.riken.jp/pub/tex-archive/macros/latex/contrib/psfrag/psfrag.dtx
+ http://www.ctan.org/tex-archive/macros/latex/contrib/psfrag
+ .
+ Psfrag seems to have been accepted in main, so I suppose that the absence of
+ explicit authorisation of redistributing the work has been clarified…
+ .
+ texlive-latex-recommended: /usr/share/texmf-texlive/tex/latex/psfrag/psfrag.sty
+
+License: OFL-1.1
+ SIL OPEN FONT LICENSE
+ .
+ Version 1.1 - 26 February 2007
+ .
+ PREAMBLE
+ .
+ The goals of the Open Font License (OFL) are to stimulate worldwide
+ development of collaborative font projects, to support the font creation
+ efforts of academic and linguistic communities, and to provide a free and
+ open framework in which fonts may be shared and improved in partnership
+ with others.
+ .
+ The OFL allows the licensed fonts to be used, studied, modified and
+ redistributed freely as long as they are not sold by themselves. The
+ fonts, including any derivative works, can be bundled, embedded,
+ redistributed and/or sold with any software provided that any reserved
+ names are not used by derivative works. The fonts and derivatives,
+ however, cannot be released under any other type of license. The
+ requirement for fonts to remain under this license does not apply
+ to any document created using the fonts or their derivatives.
+ .
+ DEFINITIONS
+ .
+ "Font Software" refers to the set of files released by the Copyright
+ Holder(s) under this license and clearly marked as such. This may
+ include source files, build scripts and documentation.
+ .
+ "Reserved Font Name" refers to any names specified as such after the
+ copyright statement(s).
+ .
+ "Original Version" refers to the collection of Font Software components as
+ distributed by the Copyright Holder(s).
+ .
+ "Modified Version" refers to any derivative made by adding to, deleting,
+ or substituting — in part or in whole — any of the components of the
+ Original Version, by changing formats or by porting the Font Software to a
+ new environment.
+ .
+ "Author" refers to any designer, engineer, programmer, technical
+ writer or other person who contributed to the Font Software.
+ .
+ PERMISSION & CONDITIONS
+ .
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of the Font Software, to use, study, copy, merge, embed, modify,
+ redistribute, and sell modified and unmodified copies of the Font
+ Software, subject to the following conditions:
+ .
+ 1) Neither the Font Software nor any of its individual components,
+ in Original or Modified Versions, may be sold by itself.
+ .
+ 2) Original or Modified Versions of the Font Software may be bundled,
+ redistributed and/or sold with any software, provided that each copy
+ contains the above copyright notice and this license. These can be
+ included either as stand-alone text files, human-readable headers or
+ in the appropriate machine-readable metadata fields within text or
+ binary files as long as those fields can be easily viewed by the user.
+ .
+ 3) No Modified Version of the Font Software may use the Reserved Font
+ Name(s) unless explicit written permission is granted by the corresponding
+ Copyright Holder. This restriction only applies to the primary font name as
+ presented to the users.
+ .
+ 4) The name(s) of the Copyright Holder(s) or the Author(s) of the Font
+ Software shall not be used to promote, endorse or advertise any
+ Modified Version, except to acknowledge the contribution(s) of the
+ Copyright Holder(s) and the Author(s) or with their explicit written
+ permission.
+ .
+ 5) The Font Software, modified or unmodified, in part or in whole,
+ must be distributed entirely under this license, and must not be
+ distributed under any other license. The requirement for fonts to
+ remain under this license does not apply to any document created
+ using the Font Software.
+ .
+ TERMINATION
+ .
+ This license becomes null and void if any of the above conditions are
+ not met.
+ .
+ DISCLAIMER
+ .
+ THE FONT SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
+ OF COPYRIGHT, PATENT, TRADEMARK, OR OTHER RIGHT. IN NO EVENT SHALL THE
+ COPYRIGHT HOLDER BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ INCLUDING ANY GENERAL, SPECIAL, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL
+ DAMAGES, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF THE USE OR INABILITY TO USE THE FONT SOFTWARE OR FROM
+ OTHER DEALINGS IN THE FONT SOFTWARE.
+
+Files: src/depcomp
+Copyright: © 1999, 2000, 2003, 2004, 2005 Free Software Foundation, Inc.
+Licence: GPL-2+ with Autoconf exception
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2, or (at your option)
+ any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+ 02110-1301, USA.
+ .
+ As a special exception to the GNU General Public License, if you
+ distribute this file as part of a program that contains a
+ configuration script generated by Autoconf, you may include it under
+ the same distribution terms that you use for the rest of that program.
+
+Files: /src/missing
+Copyright: © 1996, 1997 Free Software Foundation, Inc.
+ © Franc,ois Pinard <pinard at iro.umontreal.ca>, 1996.
+License: GPL-2+
+ (see above)
+
+Files: src/install-sh
+Copyright: © 1991 by the Massachusetts Institute of Technology
+License: install-sh
+ Permission to use, copy, modify, distribute, and sell this software and its
+ documentation for any purpose is hereby granted without fee, provided that
+ the above copyright notice appear in all copies and that both that
+ copyright notice and this permission notice appear in supporting
+ documentation, and that the name of M.I.T. not be used in advertising or
+ publicity pertaining to distribution of the software without specific,
+ written prior permission. M.I.T. makes no representations about the
+ suitability of this software for any purpose. It is provided "as is"
+ without express or implied warranty.
+
+Files: debian/*
+Copyright: © 2009 Charles Plessy <plessy at debian>
+License: same-as-phyml
+ See above.
Deleted: trunk/packages/phyml/tags/2:20110526-1/debian/phyml.1
===================================================================
--- trunk/packages/phyml/trunk/debian/phyml.1 2011-06-25 21:18:40 UTC (rev 7162)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/phyml.1 2011-06-26 04:28:43 UTC (rev 7168)
@@ -1,247 +0,0 @@
-.TH PhyML "1" "3.0" "phyml " "User Commands"
-.SH NAME
-phyml \- Phylogenetic estimation using Maximum Likelihood
-.SH SYNOPSIS:
-.PP
-phyml [command args]
-
-.IP
-All the options below are optional (except '\-i' if you want to use the command\-line interface).
-.PP
-
-Command options:
-
-.HP
-\fB-i\fR (or \fB\-\-input\fR) \fIseq_file_name\fR
-.IP
-\fIseq_file_name\fR is the name of the nucleotide or amino\-acid sequence file in PHYLIP format.
-.PP
-
-.HP
-\fB\-d\fR (or \fB\-\-datatype\fR) \fIdata_type\fR
-.IP
-\fIdata_type\fR is 'nt' for nucleotide (default), 'aa' for amino\-acid sequences, or 'generic',
-(use NEXUS file format and the 'symbols' parameter here).
-.PP
-
-.HP
-\fB\-q\fR (or \fB\-\-sequential\fR)
-.IP
-Changes interleaved format (default) to sequential format.
-.PP
-
-.HP
-\fB\-n\fR (or \fB\-\-multiple\fR) \fInb_data_sets\fR
-.IP
-\fInb_data_sets\fR is an integer corresponding to the number of data sets to analyse.
-.PP
-
-.HP
-\fB\-p\fR (or \fB\-\-pars\fR)
-.OP
-Use a minimum parsimony starting tree. This option is taken into account when the '\-u' option
-is absent and when tree topoLOGy modifications are to be done.
-
-.HP
-\fB\-b\fR (or \fB\-\-bootstrap\fR) \fIint\fR
-.IP
-\fIint > 0:\fR int is the number of bootstrap replicates.
-.IP
-\fIint = 0:\fR neither approximate likelihood ratio test nor bootstrap values are computed.
-.IP
-\fIint = \-1\fR: approximate likelihood ratio test returning aLRT statistics.
-.IP
-\fIint = \-2\fR: approximate likelihood ratio test returning Chi2\-based parametric branch supports.
-.IP
-\fIint = \-4\fR: (default) SH\-like branch supports alone.
-
-.HP
-\fB\-m\fR (or \fB\-\-model\fR) \fImodel\fR
-.IP
-model : substitution model name.
-\- \fINucleotide\fR\-based models : \fIHKY85\fR (default) | \fIJC69\fR | \fIK80\fR | \fIF81\fR | \fIF84\fR | \fITN93\fR | \fIGTR\fR | \fIcustom\fR
-(for the custom option, a string of six digits identifies the model. For instance, 000000)
-.IP
-corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
-012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.
-.IP
-\- \fIAmino\-acid\fR based models : \fILG\fR (default) | \fIWAG\fR | \fIJTT\fR | \fIMtREV\fR | \fIDayhoff\fR | \fIDCMut\fR | \fIRtREV\fR | \fICpREV\fR | \fIVT\fR
-\fIBlosum62\fR | \fIMtMam\fR | \fIMtArt\fR | \fIHIVw\fR |
-\fIHIVb\fR | \fIcustom\fR
-
-.HP
-\fB\-\-aa_rate_file\fR \fIfilename\fR
-.IP
-\fIfilename\fR is the name of the file that provides the amino acid substitution rate matrix in PAML format.
-It is compulsory to use this option when analysing amino acid sequences with the `custom' model.
-.PP
-
-.HP
-\fB\-f\fR \fIe\fR, \fIm\fR, or \fIfA,fC,fG,fT\fR
-.IP
-\fIe\fR : the character frequencies are determined as follows :
-.IP
-\- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting
-the occurence of the different bases in the alignment.
-.IP
-\- Amino\-acid sequences: (Empirical) the equilibrium amino\-acid frequencies are estimated by counting
-the occurence of the different amino\-acids in the alignment.
-.IP
-\fIm\fR : the character frequencies are determined as follows :
-.IP
-\- Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood
-.IP
-\- Amino\-acid sequences: (Model) the equilibrium amino\-acid frequencies are estimated using
-the frequencies defined by the substitution model.
-.IP
-\fI"fA,fC,fG,fT"\fR : only valid for nucleotide\-based models. fA, fC, fG and fT are floating numbers that
-correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between
-your values of nucleotide frequencies, only commas!)
-
-.HP
-\fB\-t\fR (or \fB\-\-ts\fR/tv) \fIts/tv_ratio\fR
-.IP
-\fIts/tv_ratio\fR : transition/transversion ratio. DNA sequences only.
-Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.
-
-.HP
-\fB\-v\fR (or \fB\-\-pinv\fR) \fIprop_invar\fR
-.IP
-\fIprop_invar\fR: proportion of invariable sites.
-Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate.
-
-.HP
-\fB\-c\fR (or \fB\-\-nclasses\fR) \fInb_subst_cat\fR
-.IP
-\fInb_subst_cat\fR : number of relative substitution rate categories. Default: \fInb_subst_cat=4\fR.
-Must be a positive integer.
-
-.HP
-\fB\-a\fR (or \fB\-\-alpha\fR) \fIgamma\fR
-.IP
-\fIgamma\fR : distribution of the gamma distribution shape parameter.
-Can be a fixed positive value or \fIe\fR to get the maximum likelihood estimate.
-
-.HP
-\fB\-s\fR (or \fB\-\-search\fR) \fImove\fR
-.IP
-Tree topoLOGy search operation option.
-Can be either \fINNI\fR (default, fast) or \fISPR\fR (a bit slower than NNI) or \fIBEST\fR (best of NNI and SPR search).
-
-.HP
-\fB\-u\fR (or \fB\-\-inputtree\fR) \fIuser_tree_file\fR
-.IP
-\fIuser_tree_file\fR : starting tree filename. The tree must be in Newick format.
-
-.HP
-\fB\-o\fR \fIparams\fR
-.IP
-This option focuses on specific parameter optimisation.
-.IP
-\fIparams\fR=tlr : tree topoLOGy (t), branch length (l) and rate parameters (r) are optimised.
-.IP
-\fIparams\fR=tl : tree topoLOGy and branch length are optimised.
-.IP
-\fIparams\fR=lr : branch length and rate parameters are optimised.
-.IP
-\fIparams\fR=l : branch length are optimised.
-.IP
-\fIparams\fR=r : rate parameters are optimised.
-.IP
-\fIparams\fR=n : no parameter is optimised.
-
-.HP
-\fB\-\-rand_start\fR
-.IP
-This option sets the initial tree to random. It is only valid if SPR searches are to be performed.
-
-.HP
-\fB\-\-n_rand_starts\fR \fInum\fR
-.IP
-\fInum\fR is the number of initial random trees to be used.
-It is only valid if SPR searches are to be performed.
-
-.HP
-\fB\-\-r_seed\fR \fInum\fR
-.IP
-\fInum\fR is the seed used to initiate the random number generator.
-Must be an integer.
-
-.HP
-\fB\-\-print_site_lnl\fR
-.IP
-Print the likelihood for each site in file *_phyml_lk.txt.
-.PP
-
-.HP
-\fB\-\-print_trace\fR
-.IP
-Print each phyLOGeny explored during the tree search process
-in file *_phyml_trace.txt.
-
-.HP
-\fB\-\-run_id\fR \fIID_string\fR
-.IP
-Append the string \fIID_string\fR at the end of each PhyML output file.
-This option may be useful when running simulations involving PhyML.
-.PP
-
-.HP
-\fB\-\-quiet\fR
-.IP
-No interactive question (for running in batch mode) and quiet output.
-.PP
-
-.HP
-\fB\-\-no_memory_check\fR
-.IP
-No interactive question for memory usage (for running in batch mode). Normal ouput otherwise.
-.PP
-
-.HP
-\fB\-\-alias_subpatt\fR
-.IP
-Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations.
-See Kosakovsky Pond SL, Muse SV, Sytematic Biology (2004) for an example.
-.PP
-
-.HP
-\fB\-\-boot_progress_display\fR \fInum\fR (default=20)
-.IP
-\fInum\fR is the frequency at which the bootstrap progress bar will be updated.
-Must be an integer.
-
-.SH PHYLIP\-LIKE INTERFACE
-.PP
-You can also use PhyML with no argument, in this case change the value of
-a parameter by typing its corresponding character as shown on screen.
-
-.SH EXAMPLES
-.PP
-DNA interleaved sequence file, default parameters :
-.IP
-\fBphyml \-i seqs1\fR
-.PP
-AA interleaved sequence file, default parameters :
-.IP
-\fBphyml \-i seqs2 \-d aa\fR
-.TP
-AA sequential sequence file, with customization :
-.IP
-\fBphyml \-i seqs3 \-q \-d aa \-m JTT \-c 4 \-a e\fR
-
-.SH "SEE ALSO"
-.PP
-A simple, fast, and accurate algorithm to estimate large phyLOGenies by maximum likelihood
-.PP
-Stephane Guindon and Olivier Gascuel,
-Systematic BioLOGy 52(5):696\-704, 2003.
-.PP
-Please cite this paper if you use this software in your publications.
-
-.SH AUTHOR
-\fBPhyML\fP was written by Stephane Guindon and Olivier Gascuel
-and others
-.PP
-This manual page was written by Andreas Tille <tille at debian.org>,
-for the Debian project (but may be used by others).
Copied: trunk/packages/phyml/tags/2:20110526-1/debian/phyml.1 (from rev 7165, trunk/packages/phyml/trunk/debian/phyml.1)
===================================================================
--- trunk/packages/phyml/tags/2:20110526-1/debian/phyml.1 (rev 0)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/phyml.1 2011-06-26 04:28:43 UTC (rev 7168)
@@ -0,0 +1,247 @@
+.TH PhyML "1" "3.0" "phyml " "User Commands"
+.SH NAME
+phyml \- Phylogenetic estimation using Maximum Likelihood
+.SH SYNOPSIS:
+.PP
+phyml [command args]
+
+.IP
+All the options below are optional (except '\-i' if you want to use the command\-line interface).
+.PP
+
+Command options:
+
+.HP
+\fB-i\fR (or \fB\-\-input\fR) \fIseq_file_name\fR
+.IP
+\fIseq_file_name\fR is the name of the nucleotide or amino\-acid sequence file in PHYLIP format.
+.PP
+
+.HP
+\fB\-d\fR (or \fB\-\-datatype\fR) \fIdata_type\fR
+.IP
+\fIdata_type\fR is 'nt' for nucleotide (default), 'aa' for amino\-acid sequences, or 'generic',
+(use NEXUS file format and the 'symbols' parameter here).
+.PP
+
+.HP
+\fB\-q\fR (or \fB\-\-sequential\fR)
+.IP
+Changes interleaved format (default) to sequential format.
+.PP
+
+.HP
+\fB\-n\fR (or \fB\-\-multiple\fR) \fInb_data_sets\fR
+.IP
+\fInb_data_sets\fR is an integer corresponding to the number of data sets to analyse.
+.PP
+
+.HP
+\fB\-p\fR (or \fB\-\-pars\fR)
+.OP
+Use a minimum parsimony starting tree. This option is taken into account when the '\-u' option
+is absent and when tree topoLOGy modifications are to be done.
+
+.HP
+\fB\-b\fR (or \fB\-\-bootstrap\fR) \fIint\fR
+.IP
+\fIint > 0:\fR int is the number of bootstrap replicates.
+.IP
+\fIint = 0:\fR neither approximate likelihood ratio test nor bootstrap values are computed.
+.IP
+\fIint = \-1\fR: approximate likelihood ratio test returning aLRT statistics.
+.IP
+\fIint = \-2\fR: approximate likelihood ratio test returning Chi2\-based parametric branch supports.
+.IP
+\fIint = \-4\fR: (default) SH\-like branch supports alone.
+
+.HP
+\fB\-m\fR (or \fB\-\-model\fR) \fImodel\fR
+.IP
+model : substitution model name.
+\- \fINucleotide\fR\-based models : \fIHKY85\fR (default) | \fIJC69\fR | \fIK80\fR | \fIF81\fR | \fIF84\fR | \fITN93\fR | \fIGTR\fR | \fIcustom\fR
+(for the custom option, a string of six digits identifies the model. For instance, 000000)
+.IP
+corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
+012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.
+.IP
+\- \fIAmino\-acid\fR based models : \fILG\fR (default) | \fIWAG\fR | \fIJTT\fR | \fIMtREV\fR | \fIDayhoff\fR | \fIDCMut\fR | \fIRtREV\fR | \fICpREV\fR | \fIVT\fR
+\fIBlosum62\fR | \fIMtMam\fR | \fIMtArt\fR | \fIHIVw\fR |
+\fIHIVb\fR | \fIcustom\fR
+
+.HP
+\fB\-\-aa_rate_file\fR \fIfilename\fR
+.IP
+\fIfilename\fR is the name of the file that provides the amino acid substitution rate matrix in PAML format.
+It is compulsory to use this option when analysing amino acid sequences with the `custom' model.
+.PP
+
+.HP
+\fB\-f\fR \fIe\fR, \fIm\fR, or \fIfA,fC,fG,fT\fR
+.IP
+\fIe\fR : the character frequencies are determined as follows :
+.IP
+\- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting
+the occurence of the different bases in the alignment.
+.IP
+\- Amino\-acid sequences: (Empirical) the equilibrium amino\-acid frequencies are estimated by counting
+the occurence of the different amino\-acids in the alignment.
+.IP
+\fIm\fR : the character frequencies are determined as follows :
+.IP
+\- Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood
+.IP
+\- Amino\-acid sequences: (Model) the equilibrium amino\-acid frequencies are estimated using
+the frequencies defined by the substitution model.
+.IP
+\fI"fA,fC,fG,fT"\fR : only valid for nucleotide\-based models. fA, fC, fG and fT are floating numbers that
+correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between
+your values of nucleotide frequencies, only commas!)
+
+.HP
+\fB\-t\fR (or \fB\-\-ts\fR/tv) \fIts/tv_ratio\fR
+.IP
+\fIts/tv_ratio\fR : transition/transversion ratio. DNA sequences only.
+Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.
+
+.HP
+\fB\-v\fR (or \fB\-\-pinv\fR) \fIprop_invar\fR
+.IP
+\fIprop_invar\fR: proportion of invariable sites.
+Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate.
+
+.HP
+\fB\-c\fR (or \fB\-\-nclasses\fR) \fInb_subst_cat\fR
+.IP
+\fInb_subst_cat\fR : number of relative substitution rate categories. Default: \fInb_subst_cat=4\fR.
+Must be a positive integer.
+
+.HP
+\fB\-a\fR (or \fB\-\-alpha\fR) \fIgamma\fR
+.IP
+\fIgamma\fR : distribution of the gamma distribution shape parameter.
+Can be a fixed positive value or \fIe\fR to get the maximum likelihood estimate.
+
+.HP
+\fB\-s\fR (or \fB\-\-search\fR) \fImove\fR
+.IP
+Tree topoLOGy search operation option.
+Can be either \fINNI\fR (default, fast) or \fISPR\fR (a bit slower than NNI) or \fIBEST\fR (best of NNI and SPR search).
+
+.HP
+\fB\-u\fR (or \fB\-\-inputtree\fR) \fIuser_tree_file\fR
+.IP
+\fIuser_tree_file\fR : starting tree filename. The tree must be in Newick format.
+
+.HP
+\fB\-o\fR \fIparams\fR
+.IP
+This option focuses on specific parameter optimisation.
+.IP
+\fIparams\fR=tlr : tree topoLOGy (t), branch length (l) and rate parameters (r) are optimised.
+.IP
+\fIparams\fR=tl : tree topoLOGy and branch length are optimised.
+.IP
+\fIparams\fR=lr : branch length and rate parameters are optimised.
+.IP
+\fIparams\fR=l : branch length are optimised.
+.IP
+\fIparams\fR=r : rate parameters are optimised.
+.IP
+\fIparams\fR=n : no parameter is optimised.
+
+.HP
+\fB\-\-rand_start\fR
+.IP
+This option sets the initial tree to random. It is only valid if SPR searches are to be performed.
+
+.HP
+\fB\-\-n_rand_starts\fR \fInum\fR
+.IP
+\fInum\fR is the number of initial random trees to be used.
+It is only valid if SPR searches are to be performed.
+
+.HP
+\fB\-\-r_seed\fR \fInum\fR
+.IP
+\fInum\fR is the seed used to initiate the random number generator.
+Must be an integer.
+
+.HP
+\fB\-\-print_site_lnl\fR
+.IP
+Print the likelihood for each site in file *_phyml_lk.txt.
+.PP
+
+.HP
+\fB\-\-print_trace\fR
+.IP
+Print each phyLOGeny explored during the tree search process
+in file *_phyml_trace.txt.
+
+.HP
+\fB\-\-run_id\fR \fIID_string\fR
+.IP
+Append the string \fIID_string\fR at the end of each PhyML output file.
+This option may be useful when running simulations involving PhyML.
+.PP
+
+.HP
+\fB\-\-quiet\fR
+.IP
+No interactive question (for running in batch mode) and quiet output.
+.PP
+
+.HP
+\fB\-\-no_memory_check\fR
+.IP
+No interactive question for memory usage (for running in batch mode). Normal output otherwise.
+.PP
+
+.HP
+\fB\-\-alias_subpatt\fR
+.IP
+Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations.
+See Kosakovsky Pond SL, Muse SV, Sytematic Biology (2004) for an example.
+.PP
+
+.HP
+\fB\-\-boot_progress_display\fR \fInum\fR (default=20)
+.IP
+\fInum\fR is the frequency at which the bootstrap progress bar will be updated.
+Must be an integer.
+
+.SH PHYLIP\-LIKE INTERFACE
+.PP
+You can also use PhyML with no argument, in this case change the value of
+a parameter by typing its corresponding character as shown on screen.
+
+.SH EXAMPLES
+.PP
+DNA interleaved sequence file, default parameters :
+.IP
+\fBphyml \-i seqs1\fR
+.PP
+AA interleaved sequence file, default parameters :
+.IP
+\fBphyml \-i seqs2 \-d aa\fR
+.TP
+AA sequential sequence file, with customization :
+.IP
+\fBphyml \-i seqs3 \-q \-d aa \-m JTT \-c 4 \-a e\fR
+
+.SH "SEE ALSO"
+.PP
+A simple, fast, and accurate algorithm to estimate large phyLOGenies by maximum likelihood
+.PP
+Stephane Guindon and Olivier Gascuel,
+Systematic BioLOGy 52(5):696\-704, 2003.
+.PP
+Please cite this paper if you use this software in your publications.
+
+.SH AUTHOR
+\fBPhyML\fP was written by Stephane Guindon and Olivier Gascuel
+and others
+.PP
+This manual page was written by Andreas Tille <tille at debian.org>,
+for the Debian project (but may be used by others).
Deleted: trunk/packages/phyml/tags/2:20110526-1/debian/rules
===================================================================
--- trunk/packages/phyml/trunk/debian/rules 2011-06-25 21:18:40 UTC (rev 7162)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/rules 2011-06-26 04:28:43 UTC (rev 7168)
@@ -1,46 +0,0 @@
-#!/usr/bin/make -f
-# Sample debian/rules that uses debhelper.
-# This file is public domain software, originally written by Joey Hess.
-
-# Pasted from Policy 4.9.1 :(but disabled parallel building).
-CFLAGS = -Wall -g
-
-ifneq (,$(filter noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-ifeq (,$(filter nostrip,$(DEB_BUILD_OPTIONS)))
- INSTALL_PROGRAM += -s
-endif
-#ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
-# NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
-# MAKEFLAGS += -j$(NUMJOBS)
-#endif
-
-
-src/Makefile:
- aclocal ; autoconf -f ; automake -f ; ./configure --prefix=/usr
-
-build: src/Makefile build-stamp
-build-stamp:
- dh_testdir
- $(MAKE) CFLAGS="$(CFLAGS)"
- touch build-stamp
-
-clean:
- dh clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs
- $(MAKE) prefix=`pwd`/debian/`dh_listpackages`/usr install
-
-binary-indep: build install
-binary-arch: build install
- dh binary-arch
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
Copied: trunk/packages/phyml/tags/2:20110526-1/debian/rules (from rev 7167, trunk/packages/phyml/trunk/debian/rules)
===================================================================
--- trunk/packages/phyml/tags/2:20110526-1/debian/rules (rev 0)
+++ trunk/packages/phyml/tags/2:20110526-1/debian/rules 2011-06-26 04:28:43 UTC (rev 7168)
@@ -0,0 +1,53 @@
+#!/usr/bin/make -f
+# Sample debian/rules that uses debhelper.
+# This file is public domain software, originally written by Joey Hess.
+
+# Pasted from Policy 4.9.1 :(but disabled parallel building).
+CFLAGS = -Wall -g
+
+ifneq (,$(filter noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(filter nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+#ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
+# NUMJOBS = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
+# MAKEFLAGS += -j$(NUMJOBS)
+#endif
+
+build:
+ dh build
+
+clean:
+ dh clean
+
+binary-indep:
+ dh binary-indep
+binary-arch:
+ dh binary-arch
+
+override_dh_auto_configure:
+override_dh_auto_build:
+ dh_testdir
+ aclocal ; autoconf -f ; automake -f ; ./configure --prefix=/usr
+ $(MAKE) CFLAGS="$(CFLAGS)"
+ $(MAKE) prefix=`pwd`/debian/`dh_listpackages`/usr install
+ $(MAKE) distclean
+ aclocal ; autoconf -f ; automake -f ; ./configure --prefix=/usr --enable-phytime
+ $(MAKE) CFLAGS="$(CFLAGS)"
+ $(MAKE) prefix=`pwd`/debian/`dh_listpackages`/usr install
+ touch build-stamp
+override_dh_auto_install:
+
+override_dh_prep:
+ dh_prep -X debian/phyml
+
+binary: binary-indep binary-arch
+
+build-arch: build
+build-indep:
+
+.PHONY: build-arch build-indep clean binary-indep binary-arch binary
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