[med-svn] r7088 - in trunk/packages/bioperl-run/tags: . 1.6.9-1/debian 1.6.9-1/debian/patches
Charles Plessy
plessy at alioth.debian.org
Sat Jun 18 05:19:05 UTC 2011
Author: plessy
Date: 2011-06-18 05:19:05 +0000 (Sat, 18 Jun 2011)
New Revision: 7088
Added:
trunk/packages/bioperl-run/tags/1.6.9-1/
trunk/packages/bioperl-run/tags/1.6.9-1/debian/changelog
trunk/packages/bioperl-run/tags/1.6.9-1/debian/control
trunk/packages/bioperl-run/tags/1.6.9-1/debian/copyright
trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Some-spellchecking.patch
trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Use-system-s-Perl.patch
trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/install-scripts.patch
trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/series
trunk/packages/bioperl-run/tags/1.6.9-1/debian/rules
Removed:
trunk/packages/bioperl-run/tags/1.6.9-1/debian/changelog
trunk/packages/bioperl-run/tags/1.6.9-1/debian/control
trunk/packages/bioperl-run/tags/1.6.9-1/debian/copyright
trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/install-scripts.patch
trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/series
trunk/packages/bioperl-run/tags/1.6.9-1/debian/rules
Log:
[svn-buildpackage] Tagging bioperl-run 1.6.9-1
Deleted: trunk/packages/bioperl-run/tags/1.6.9-1/debian/changelog
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/changelog 2011-06-17 14:19:23 UTC (rev 7078)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/changelog 2011-06-18 05:19:05 UTC (rev 7088)
@@ -1,61 +0,0 @@
-bioperl-run (1.6.9-1) UNRELEASED; urgency=low
-
- TODO: make renamed EMBOSS programs accessible.
-
- * New upstream release.
- * debian/rules:
- - Re-enabled the tests.
- * debian/control:
- - Refreshed the list of packages for which wrappers are provided, in the
- Suggests field as well as in an experimental Build-Recommends field.
- - Incremented Standards-Version to reflect conformance with Policy 3.9.2.
- No other changes needed.
- - Vcs-Browser URL made redirectable to viewvc.
- - Removed useless ‘svn’ in the Vcs-Svn URL.
- * Point debian/watch to CPAN.
- * Tiny style with Debhelper 8 (debian/rules, debian/compat, debian/control).
- * Split scripts in bioperl-run and modules in libbio-perl-run-perl.
- (debian/rules, debian/control, debian/bioperl-run.install,
- debian/libbio-perl-run-perl.install)
- * debian/patches/install-scripts.patch for Build.PL option --install_scripts.
- (debian/rules, debian/patches/series, debian/control)
- * Trigger network tests with DEB_MAINTAINER_MODE (debian/rules,
- debian/README.test).
-
- -- Charles Plessy <plessy at debian.org> Fri, 17 Jun 2011 09:05:14 +0900
-
-bioperl-run (1.6.1-1) unstable; urgency=low
-
- * New upstream release.
- * debian/patches/10-wrong-path-for-interpreter.patch: removed
- (fixed upstream).
- * debian/watch updated (bioperl -> BioPerl).
- * debian/rules refreshed with dh-make-perl 0.53.
- - Disabled installation of examples (removed upstream).
- - Removed the correction of file permission of Pise documentation
- (removed upstream).
- - Removed patching facilities (no patches anymore).
- - Disabled tests as I experience failures with t/Eponine.t despite
- this program is not installed.
- * debian/copyright:
- - Removed vanity lines about debianization and debian copyright.
- - Incremented years to 2009.
- - Updated to latest experimentation of the machine-readable license summary.
- * debian/control:
- - Incremented Standards-Version to reflect conformance on new Policy
- (dropped versionned build-dependancy on Perl).
- - Removed build-dependancy on quilt (no patches anymore).
- - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0.
- - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl,
- libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES.
- - Build-depends on libarray-compare-perl and libtree-dagnode-perl
- (otherwise tests fail).
- - Depend on amap-align instead of amap (Closes: #541274).
-
- -- Charles Plessy <plessy at debian.org> Thu, 03 Sep 2009 11:00:03 +0900
-
-bioperl-run (1.5.2.100-1) unstable; urgency=low
-
- * Initial Release (Closes: #505112).
-
- -- Charles Plessy <plessy at debian.org> Mon, 10 Nov 2008 09:11:17 +0900
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/changelog (from rev 7087, trunk/packages/bioperl-run/trunk/debian/changelog)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/changelog (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/changelog 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,60 @@
+bioperl-run (1.6.9-1) unstable; urgency=low
+
+ * New upstream release.
+ * Converted and validated debian/copyright to latest machine-readable format.
+ * debian/control:
+ - Refreshed the list of packages for which wrappers are provided, in the
+ Suggests field as well as in an experimental Build-Recommends field.
+ - Incremented Standards-Version to reflect conformance with Policy 3.9.2.
+ No other changes needed.
+ - Vcs-Browser URL made redirectable to viewvc.
+ - Removed useless ‘svn’ in the Vcs-Svn URL.
+ * Point debian/watch to CPAN.
+ * Tiny style with Debhelper 8 (debian/rules, debian/compat, debian/control).
+ * Split scripts in bioperl-run and modules in libbio-perl-run-perl.
+ (debian/rules, debian/control, debian/bioperl-run.install,
+ debian/libbio-perl-run-perl.install)
+ * debian/rules, debian/patches/series, debian/control:
+ - debian/patches/install-scripts.patch for non-interactive script install.
+ - debian/patches/Use-system-s-Perl.patch against /usr/local/bin/perl.
+ - debian/patches/Some-spellchecking.patch.
+ * Trigger network tests with DEB_MAINTAINER_MODE (debian/rules,
+ debian/README.test).
+
+ -- Charles Plessy <plessy at debian.org> Sat, 18 Jun 2011 13:21:36 +0900
+
+bioperl-run (1.6.1-1) unstable; urgency=low
+
+ * New upstream release.
+ * debian/patches/10-wrong-path-for-interpreter.patch: removed
+ (fixed upstream).
+ * debian/watch updated (bioperl -> BioPerl).
+ * debian/rules refreshed with dh-make-perl 0.53.
+ - Disabled installation of examples (removed upstream).
+ - Removed the correction of file permission of Pise documentation
+ (removed upstream).
+ - Removed patching facilities (no patches anymore).
+ - Disabled tests as I experience failures with t/Eponine.t despite
+ this program is not installed.
+ * debian/copyright:
+ - Removed vanity lines about debianization and debian copyright.
+ - Incremented years to 2009.
+ - Updated to latest experimentation of the machine-readable license summary.
+ * debian/control:
+ - Incremented Standards-Version to reflect conformance on new Policy
+ (dropped versionned build-dependancy on Perl).
+ - Removed build-dependancy on quilt (no patches anymore).
+ - Depend and Build-Depend on bioperl versions superior or equal to 1.6.0.
+ - Build-depends on, and Recommdnes libalgorithm-diff-perl, libipc-run-perl,
+ libio-string-perl and libxml-twig-perl, that are listed in DEPENDANCIES.
+ - Build-depends on libarray-compare-perl and libtree-dagnode-perl
+ (otherwise tests fail).
+ - Depend on amap-align instead of amap (Closes: #541274).
+
+ -- Charles Plessy <plessy at debian.org> Thu, 03 Sep 2009 11:00:03 +0900
+
+bioperl-run (1.5.2.100-1) unstable; urgency=low
+
+ * Initial Release (Closes: #505112).
+
+ -- Charles Plessy <plessy at debian.org> Mon, 10 Nov 2008 09:11:17 +0900
Deleted: trunk/packages/bioperl-run/tags/1.6.9-1/debian/control
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/control 2011-06-17 14:19:23 UTC (rev 7078)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/control 2011-06-18 05:19:05 UTC (rev 7088)
@@ -1,42 +0,0 @@
-Source: bioperl-run
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 8), quilt, libmodule-build-perl
-Build-Depends-Indep: perl, bioperl (>= 1.6.0), libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl,
- libarray-compare-perl, libtree-dagnode-perl
-# Here is a list of all the packages and prospective packages for which wrappers are provided.
-XS-Build-Recommends: coils, emboss, eponine, footprinter, wise, genscan, hmmer,
- pise, ensembl, fingerprintscan, prscan, repeatmasker, seg, signalp, tmhmm,
- tribe, paml, molphy, phylip, clustalw, sim4, t-coffee, blast2, fasta, lagan,
- vista-align, amap-align, blat,
-# This Perl library is needed for the network tests.
- libwww-perl
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-Standards-Version: 3.9.2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bioperl-run/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bioperl-run/trunk/
-Homepage: http://www.bioperl.org/wiki/Run_package
-
-Package: bioperl-run
-Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends}, bioperl (>= 1.6.0), libbio-perl-run-perl (= ${source:Version})
-Recommends: amap-align, blast2, clustalw, emboss, ensembl, hmmer, sim4, t-coffee, wise
-Suggests: coils, eponine, footprinter, genscan, pise, fingerprintscan, prscan, repeatmasker,
- seg, signalp, tmhmm, tribe, paml, molphy, phylip, fasta, lagan, vista-align, blat
-Description: BioPerl wrappers: scripts
- Contains scripts from the the BioPerl-Run package. This package will also install all
- wrappable applications packaged in Debian. The ones that are not available or not Free are
- "Suggested" by this package.
-
-Package: libbio-perl-run-perl
-Architecture: all
-Breaks: bioperl-run (<< 1.6.9)
-Replaces: bioperl-run (<< 1.6.9)
-Depends: ${misc:Depends}, ${perl:Depends}, libbio-perl-perl (>= 1.6.0)
-Recommends: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libwww-perl
-Description: BioPerl wrappers: modules
- Contains modules that provide a Perl interface to various
- bioinformatics applications to allow them to be
- used with common BioPerl objects.
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/control (from rev 7087, trunk/packages/bioperl-run/trunk/debian/control)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/control (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/control 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,59 @@
+Source: bioperl-run
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 8), quilt, libmodule-build-perl
+Build-Depends-Indep: perl, bioperl (>= 1.6.9),
+# Recommended in Build.PL:
+ libalgorithm-diff-perl,
+ libipc-run-perl,
+ libio-string-perl,
+ libxml-twig-perl,
+# Not yet available: libfile-sort-perl
+# Needed for the tests, but not documented Upstream
+ libarray-compare-perl, libtree-dagnode-perl,
+# Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.
+# amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate,
+# hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons,
+# samtools, sim4, t-coffee, tigr-glimmer, wise,
+# Needed for the network tests:
+ libwww-perl
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+Standards-Version: 3.9.2
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bioperl-run/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bioperl-run/trunk/
+Homepage: http://www.bioperl.org/wiki/Run_package
+
+Package: bioperl-run
+Architecture: all
+Depends: ${misc:Depends}, ${perl:Depends}, bioperl (>= 1.6.0), libbio-perl-run-perl (= ${source:Version})
+Recommends: amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate,
+ hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons,
+ samtools, sim4, t-coffee, tigr-glimmer, wise
+Suggests:
+# Non-Free.
+ gmap, paml, molphy, phylip,
+# Not available.
+# blat, cap3, coils, condense, drawgram, drawtree, eponine, fasta, footprinter, genemark-hmm,
+# genscan, gerp, glimmer2, hyphy, lagan, lvb, match, mcs, mdust, meme, minimo,
+# neighbor, newbler, njtree, pal2nal, phastcons, phrap, primate, prints, probalign, profile,
+# promoterwise, protdist, protpars, pseudowise, quikctree, repeatmasker, sablastplus, seg,
+# semphy, seqboot, signalp, simprot, slr, soapeu, tigr-assembler, tmhmm, tribe, trnascan, vista-align,
+# Available, but needs interactive setup.
+ ensembl
+Description: BioPerl wrappers: scripts
+ Contains scripts from the BioPerl-Run package. This package will also install
+ all wrappable applications packaged in Debian. The ones that are not Free are
+ "Suggested" by this package.
+
+Package: libbio-perl-run-perl
+Section: perl
+Architecture: all
+Breaks: bioperl-run (<< 1.6.9)
+Replaces: bioperl-run (<< 1.6.9)
+Depends: ${misc:Depends}, ${perl:Depends}, libbio-perl-perl (>= 1.6.0)
+Recommends: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libwww-perl
+Description: BioPerl wrappers: modules
+ Contains modules that provide a Perl interface to various bioinformatics
+ applications to allow them to be used with common BioPerl objects.
Deleted: trunk/packages/bioperl-run/tags/1.6.9-1/debian/copyright
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/copyright 2011-06-17 14:19:23 UTC (rev 7078)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/copyright 2011-06-18 05:19:05 UTC (rev 7088)
@@ -1,74 +0,0 @@
-Machine-readable license summary, see ’http://dep.debian.net/deps/dep5/’.
-
-Name : BioPerl-run
-Contact : Bioperl Team <bioperl-l at bioperl.org>
-Source : http://www.bioperl.org/DIST/BioPerl-run-1.6.1.tar.gz
-
-Copyright: 1997-2009 Bioperl Team <bioperl-l at bioperl.org>
- Sendu Bala <bix at sendu.me.uk>
- Jer-Ming Chia <giscjm at nus.edu.sg>
- Rob Edwards <redwards at utmem.edu>
- Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
- Shawn Hoon <shawnh at fugu-sg.org>
- Donald Jackson <donald.jackson at bms.com>
- Keith James <kdj at sanger.ac.uk>
- Ratnapu Kiran Kumar <kiran at fugu-sg.org>
- Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
- Catherine Letondal <letondal at pasteur.fr>
- Heikki Lehvaslaiho <heikki at ebi.ac.uk>
- Stephen Montgomery <smontgom at bcgsc.bc.ca>
- Brian Osborne <bosborne at alum.mit.edu>
- Tania Oh <gisoht at nus.edu.sg>
- Peter Schattner <schattner at alum.mit.edu>
- Martin Senger <senger at ebi.ac.uk>
- Marc Sohrmann <ms2 at sanger.ac.uk>
- Jason Stajich <jason at bioperl.org>
- Elia Stupka <elia at fugu-sg.org>
- David Vilanova <david.vilanova at urbanet.ch>
- Albert Vilella <avilella at gmail.com>
- Tiequan Zhang <tqzhang1973 at yahoo.com>
- Juguang Xiao <juguang at tll.org.sg>
-License: Perl
-
- Everyone can use it! We don't care if you are academic, corporate, or
- government. BioPerl is licensed under the same terms as Perl itself, which
- means it is dually-licensed under either the Artistic or GPL licenses. The Perl
- Artistic License, or the GNU GPL covers all the legalese and what you can and
- can't do with the source code.
-
- We do appreciate:
-
- * You letting us know you sell or use a product that uses BioPerl. This helps
- us show people how useful our toolkit is. It also helps us if we seek funding
- from a government source, to identify the utility of the code to many different
- groups of users. Add your project and institution to our BioPerl Users page.
-
- * If you fix bugs, please let us know about them. Because Bioperl is
- dual-licensed under the GPL or Artistic licenses, you can choose the Artistic
- license, which means that you are not required to submit the code fixes, but in
- the spirit of making a better product we hope you'll contribute back to the
- community any insight or code improvements.
-
- * Please include the AUTHORS file and ascribe credit to the original BioPerl
- toolkit where appropriate.
-
- * If you are an academic and you use the software, please cite the article.
- See the BioPerl publications for a list of papers which describe components in
- the toolkit.
-
-See http://www.bioperl.org/wiki/Licensing_BioPerl
-
-License: Perl
- This program is free software; you can redistribute it and/or modify
- it under the terms of either:
-
- a) the GNU General Public License as published by the Free Software
- Foundation; either version 1, or (at your option) any later
- version, or
-
- b) the "Artistic License" which comes with Perl.
-
-On Debian systems, the complete text of the Artistic License can be found in
-‘/usr/share/common-licenses/Artistic’, and the complete text of the latest
-version of the GNU General Public License can be found in
-‘/usr/share/common-licenses/GPL’.
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/copyright (from rev 7079, trunk/packages/bioperl-run/trunk/debian/copyright)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/copyright (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/copyright 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,70 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
+
+Files: *
+Copyright: © 1997–2011 Bioperl Team <bioperl-l at bioperl.org>
+ Sendu Bala <bix at sendu.me.uk>
+ Jer-Ming Chia <giscjm at nus.edu.sg>
+ Rob Edwards <redwards at utmem.edu>
+ Mauricio Herrera Cuadra <mauricio at open-bio.org>
+ Shawn Hoon <shawnh at fugu-sg.org>
+ Donald Jackson <donald.jackson at bms.com>
+ Keith James <kdj at sanger.ac.uk>
+ Ratnapu Kiran Kumar <kiran at fugu-sg.org>
+ Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
+ Catherine Letondal <letondal at pasteur.fr>
+ Heikki Lehvaslaiho <heikki at ebi.ac.uk>
+ Stephen Montgomery <smontgom at bcgsc.bc.ca>
+ Brian Osborne <bosborne at alum.mit.edu>
+ Tania Oh <gisoht at nus.edu.sg>
+ Peter Schattner <schattner at alum.mit.edu>
+ Martin Senger <senger at ebi.ac.uk>
+ Marc Sohrmann <ms2 at sanger.ac.uk>
+ Jason Stajich <jason at bioperl.org>
+ Elia Stupka <elia at fugu-sg.org>
+ David Vilanova <david.vilanova at urbanet.ch>
+ Albert Vilella <avilella at gmail.com>
+ Tiequan Zhang <tqzhang1973 at yahoo.com>
+ Juguang Xiao <juguang at tll.org.sg>
+Comment:
+ Everyone can use it! We don't care if you are academic, corporate, or
+ government. BioPerl is licensed under the same terms as Perl itself, which
+ means it is dually-licensed under either the Artistic or GPL licenses. The Perl
+ Artistic License, or the GNU GPL covers all the legalese and what you can and
+ can't do with the source code.
+ .
+ We do appreciate:
+ .
+ * You letting us know you sell or use a product that uses BioPerl. This helps
+ us show people how useful our toolkit is. It also helps us if we seek funding
+ from a government source, to identify the utility of the code to many different
+ groups of users. Add your project and institution to our BioPerl Users page.
+ .
+ * If you fix bugs, please let us know about them. Because Bioperl is
+ dual-licensed under the GPL or Artistic licenses, you can choose the Artistic
+ license, which means that you are not required to submit the code fixes, but in
+ the spirit of making a better product we hope you'll contribute back to the
+ community any insight or code improvements.
+ .
+ * Please include the AUTHORS file and ascribe credit to the original BioPerl
+ toolkit where appropriate.
+ .
+ * If you are an academic and you use the software, please cite the article.
+ See the BioPerl publications for a list of papers which describe components in
+ the toolkit.
+ .
+ See http://www.bioperl.org/wiki/Licensing_BioPerl
+License: Perl
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of either:
+ .
+ a) the GNU General Public License as published by the Free Software
+ Foundation; either version 1, or (at your option) any later
+ version, or
+ .
+ b) the "Artistic License" which comes with Perl.
+ .
+ On Debian systems, the complete text of the Artistic License can be found in
+ ‘/usr/share/common-licenses/Artistic’, and the complete text of the latest
+ version of the GNU General Public License version 1 can be found in
+ ‘/usr/share/common-licenses/GPL-1’.
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Some-spellchecking.patch (from rev 7086, trunk/packages/bioperl-run/trunk/debian/patches/Some-spellchecking.patch)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Some-spellchecking.patch (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Some-spellchecking.patch 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,311 @@
+Forwarded: https://redmine.open-bio.org/issues/3256
+From b6c1d10797c2fbb6c5fe3c0fe2e5f74d252889cb Mon Sep 17 00:00:00 2001
+From: Charles Plessy <plessy at debian.org>
+Date: Sat, 18 Jun 2011 13:13:43 +0900
+Subject: [PATCH] Some spellchecking.
+
+---
+ lib/Bio/Tools/Run/Alignment/Clustalw.pm | 2 +-
+ lib/Bio/Tools/Run/Alignment/Pal2Nal.pm | 2 +-
+ lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm | 2 +-
+ lib/Bio/Tools/Run/AssemblerBase.pm | 2 +-
+ lib/Bio/Tools/Run/FootPrinter.pm | 2 +-
+ lib/Bio/Tools/Run/Hmmer.pm | 2 +-
+ lib/Bio/Tools/Run/MCS.pm | 2 +-
+ lib/Bio/Tools/Run/Phylo/Gerp.pm | 4 ++--
+ lib/Bio/Tools/Run/Phylo/Gumby.pm | 4 ++--
+ lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm | 2 +-
+ lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm | 6 +++---
+ lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm | 4 ++--
+ lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm | 2 +-
+ lib/Bio/Tools/Run/Phylo/Phyml.pm | 4 ++--
+ lib/Bio/Tools/Run/Phylo/QuickTree.pm | 2 +-
+ lib/Bio/Tools/Run/Phylo/Semphy.pm | 4 ++--
+ lib/Bio/Tools/Run/StandAloneBlastPlus.pm | 2 +-
+ lib/Bio/Tools/Run/TigrAssembler.pm | 2 +-
+ t/lib/Test/Builder/Tester.pm | 2 +-
+ 19 files changed, 26 insertions(+), 26 deletions(-)
+
+diff --git a/lib/Bio/Tools/Run/Alignment/Clustalw.pm b/lib/Bio/Tools/Run/Alignment/Clustalw.pm
+index 2295987..e9afe69 100644
+--- a/lib/Bio/Tools/Run/Alignment/Clustalw.pm
++++ b/lib/Bio/Tools/Run/Alignment/Clustalw.pm
+@@ -205,7 +205,7 @@ clustalw program have not yet been implemented. If you would like
+ that a specific clustalw feature be added to this perl contact
+ bioperl-l at bioperl.org.
+
+-These can be specified as paramters when instantiating a new Clustalw
++These can be specified as parameters when instantiating a new Clustalw
+ object, or through get/set methods of the same name (lowercase).
+
+ =head1 PARAMETER FOR ALIGNMENT COMPUTATION
+diff --git a/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm b/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
+index 072bb7c..ebdc70d 100755
+--- a/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
++++ b/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
+@@ -192,7 +192,7 @@ sub new {
+ Args : The first argument represents a protein alignment, the second
+ argument a set of nucleotide sequences.
+ The alignment can be provided as an alignment file readable by
+- Bio::AlignIO, or a Bio::Align::AlignI complient object (eg. a
++ Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a
+ Bio::SimpleAlign).
+ The nucleotide sequences can be provided as a single filename of a
+ fasta file containing multiple nucleotide sequences, or an array ref
+diff --git a/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm b/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+index d874b81..aee27eb 100644
+--- a/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
++++ b/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+@@ -117,7 +117,7 @@ Email tqzhang1973 at yahoo.com
+ =head1 Appendix
+
+ The rest of the documendation details each of the object
+-methods. Internal methods are preceeded with a underscore
++methods. Internal methods are preceded with a underscore
+
+ =cut
+
+diff --git a/lib/Bio/Tools/Run/AssemblerBase.pm b/lib/Bio/Tools/Run/AssemblerBase.pm
+index bd00780..2941470 100644
+--- a/lib/Bio/Tools/Run/AssemblerBase.pm
++++ b/lib/Bio/Tools/Run/AssemblerBase.pm
+@@ -865,7 +865,7 @@ sub parameters_changed {
+ Usage : @params = $pobj->available_parameters()
+ Function: Returns a list of the available parameters
+ Returns : Array of parameters
+- Args : 'params' for settable program paramters
++ Args : 'params' for settable program parameters
+ 'switches' for boolean program switches
+ default: all
+
+diff --git a/lib/Bio/Tools/Run/FootPrinter.pm b/lib/Bio/Tools/Run/FootPrinter.pm
+index 60294f3..dfaa70f 100644
+--- a/lib/Bio/Tools/Run/FootPrinter.pm
++++ b/lib/Bio/Tools/Run/FootPrinter.pm
+@@ -67,7 +67,7 @@ Written by Mathieu Blanchette and Martin Tompa. Available here:
+
+ =head2 Running Footprinter
+
+-To run FootPrinter, you will need to set the enviroment variable
++To run FootPrinter, you will need to set the environment variable
+ FOOTPRINTER_DIR to where the binary is located (even if the executable
+ is in your path). For example:
+
+diff --git a/lib/Bio/Tools/Run/Hmmer.pm b/lib/Bio/Tools/Run/Hmmer.pm
+index 9ce3f6e..5abebcc 100755
+--- a/lib/Bio/Tools/Run/Hmmer.pm
++++ b/lib/Bio/Tools/Run/Hmmer.pm
+@@ -172,7 +172,7 @@ our @UNSUPPORTED = qw(h verbose a compat pvm);
+ -o is synonymous with -outfile
+
+ # may be specified here, allowing run() to be used, or
+- # it can be ommitted and the corresponding method (eg.
++ # it can be omitted and the corresponding method (eg.
+ # hmmalign()) used later.
+ -program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch
+
+diff --git a/lib/Bio/Tools/Run/MCS.pm b/lib/Bio/Tools/Run/MCS.pm
+index af3570b..5924c49 100755
+--- a/lib/Bio/Tools/Run/MCS.pm
++++ b/lib/Bio/Tools/Run/MCS.pm
+@@ -216,7 +216,7 @@ sub new {
+ third argument represents annotation of the exons in the alignment.
+
+ The alignment can be provided as a multi-fasta format alignment
+- filename, or a Bio::Align::AlignI complient object (eg. a
++ filename, or a Bio::Align::AlignI compliant object (eg. a
+ Bio::SimpleAlign).
+
+ The position in the genome can be provided as a Bio::Location::Atomic
+diff --git a/lib/Bio/Tools/Run/Phylo/Gerp.pm b/lib/Bio/Tools/Run/Phylo/Gerp.pm
+index e731b44..9d7c7b5 100755
+--- a/lib/Bio/Tools/Run/Phylo/Gerp.pm
++++ b/lib/Bio/Tools/Run/Phylo/Gerp.pm
+@@ -211,10 +211,10 @@ sub new {
+ Args : The first argument represents an alignment, the second argument
+ a phylogenetic tree with branch lengths.
+ The alignment can be provided as a MAF format alignment
+- filename, or a Bio::Align::AlignI complient object (eg. a
++ filename, or a Bio::Align::AlignI compliant object (eg. a
+ Bio::SimpleAlign).
+ The species tree can be provided as a newick format tree filename
+- or a Bio::Tree::TreeI complient object.
++ or a Bio::Tree::TreeI compliant object.
+
+ In all cases, the alignment sequence names must correspond to node
+ ids in the tree. Multi-word species names should have the
+diff --git a/lib/Bio/Tools/Run/Phylo/Gumby.pm b/lib/Bio/Tools/Run/Phylo/Gumby.pm
+index 6bfd5ee..bf57965 100644
+--- a/lib/Bio/Tools/Run/Phylo/Gumby.pm
++++ b/lib/Bio/Tools/Run/Phylo/Gumby.pm
+@@ -284,10 +284,10 @@ sub annots {
+ Args : The first argument represents an alignment, the second argument
+ a species tree.
+ The alignment can be provided as a multi-fasta format alignment
+- filename, or a Bio::Align::AlignI complient object (eg. a
++ filename, or a Bio::Align::AlignI compliant object (eg. a
+ Bio::SimpleAlign).
+ The species tree can be provided as a newick format tree filename
+- or a Bio::Tree::TreeI complient object. Alternatively a
++ or a Bio::Tree::TreeI compliant object. Alternatively a
+ Bio::DB::Taxonomy object can be supplied, in which case the species
+ tree will be generated by using the alignment sequence names as
+ species names and looking for those in the supplied database.
+diff --git a/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm b/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
+index bf7f66c..3d59846 100644
+--- a/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
++++ b/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
+@@ -554,7 +554,7 @@ sub set_parameter{
+ Returns : none
+ Args : boolean: keep existing parameter values
+ NB : using this isn't an especially good idea! You don't need to do
+- anything to end up using default paramters: hence 'default'!
++ anything to end up using default parameters: hence 'default'!
+
+ =cut
+
+diff --git a/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm b/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
+index 51458f9..0c8ce6b 100644
+--- a/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
++++ b/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
+@@ -331,13 +331,13 @@ sub rho {
+ ('footprinting').
+ Returns : array of Bio::SeqFeature::Annotated (one feature per alignment
+ sequence and prediction)
+- Args : The first arguement represents an alignment, the second arguement
++ Args : The first argument represents an alignment, the second argument
+ a species tree.
+ The alignment can be provided as a multi-fasta format alignment
+- filename, or a Bio::Align::AlignI complient object (eg. a
++ filename, or a Bio::Align::AlignI compliant object (eg. a
+ Bio::SimpleAlign).
+ The species tree can be provided as a newick format tree filename
+- or a Bio::Tree::TreeI complient object. Alternatively a
++ or a Bio::Tree::TreeI compliant object. Alternatively a
+ Bio::DB::Taxonomy object can be supplied, in which case the species
+ tree will be generated by using the alignment sequence names as
+ species names and looking for those in the supplied database.
+diff --git a/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm b/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
+index dfd7e4a..940851d 100644
+--- a/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
++++ b/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
+@@ -241,10 +241,10 @@ sub new {
+ Args : The first argument represents an alignment, the second argument
+ a species tree.
+ The alignment can be provided as a multi-fasta format alignment
+- filename, or a Bio::Align::AlignI complient object (eg. a
++ filename, or a Bio::Align::AlignI compliant object (eg. a
+ Bio::SimpleAlign).
+ The species tree can be provided as a newick format tree filename
+- or a Bio::Tree::TreeI complient object. Alternatively a
++ or a Bio::Tree::TreeI compliant object. Alternatively a
+ Bio::DB::Taxonomy object can be supplied, in which case the species
+ tree will be generated by using the alignment sequence names as
+ species names and looking for those in the supplied database.
+diff --git a/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm b/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
+index f68c15b..5aaa208 100644
+--- a/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
++++ b/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
+@@ -97,7 +97,7 @@ this is still experimental as v3.6 is still under alpha release and not all func
+
+ Title : TYPE
+ Description : (optional)
+- Only avaliable in phylip v3.6
++ Only available in phylip v3.6
+
+ This program supports 3 types of consensus generation
+
+diff --git a/lib/Bio/Tools/Run/Phylo/Phyml.pm b/lib/Bio/Tools/Run/Phylo/Phyml.pm
+index 5719281..2004e22 100644
+--- a/lib/Bio/Tools/Run/Phylo/Phyml.pm
++++ b/lib/Bio/Tools/Run/Phylo/Phyml.pm
+@@ -315,7 +315,7 @@ sub version {
+ Returns : Bio::Tree::Tree object
+ Args : file name for your input alignment in a format
+ recognised by AlignIO, OR Bio::Align::AlignI
+- complient object (eg. Bio::SimpleAlign).
++ compliant object (eg. Bio::SimpleAlign).
+
+ =cut
+
+@@ -358,7 +358,7 @@ sub stats {
+ Title : tree_string
+ Usage : $factory->tree_string;
+ $factory->run($align_object);
+- Function: Returns the contents of the phyml '_phyml_tree.txt' ouput file
++ Function: Returns the contents of the phyml '_phyml_tree.txt' output file
+ Returns : string with tree in Newick format, undef before run()
+ Args : none
+
+diff --git a/lib/Bio/Tools/Run/Phylo/QuickTree.pm b/lib/Bio/Tools/Run/Phylo/QuickTree.pm
+index 6c61643..909bf1a 100644
+--- a/lib/Bio/Tools/Run/Phylo/QuickTree.pm
++++ b/lib/Bio/Tools/Run/Phylo/QuickTree.pm
+@@ -240,7 +240,7 @@ sub boot {
+ Function: Runs QuickTree to generate a tree
+ Returns : Bio::Tree::Tree object
+ Args : file name for your input alignment in stockholm format, OR
+- Bio::Align::AlignI complient object (eg. Bio::SimpleAlign).
++ Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).
+
+ =cut
+
+diff --git a/lib/Bio/Tools/Run/Phylo/Semphy.pm b/lib/Bio/Tools/Run/Phylo/Semphy.pm
+index 5d155d4..d4faebf 100755
+--- a/lib/Bio/Tools/Run/Phylo/Semphy.pm
++++ b/lib/Bio/Tools/Run/Phylo/Semphy.pm
+@@ -252,10 +252,10 @@ sub new {
+ argument a species tree (to set an initial tree: normally the -t
+ option to Semphy).
+ The alignment can be provided as a multi-fasta format alignment
+- filename, or a Bio::Align::AlignI complient object (eg. a
++ filename, or a Bio::Align::AlignI compliant object (eg. a
+ Bio::SimpleAlign).
+ The species tree can be provided as a newick format tree filename
+- or a Bio::Tree::TreeI complient object. Alternatively a
++ or a Bio::Tree::TreeI compliant object. Alternatively a
+ Bio::DB::Taxonomy object can be supplied, in which case the species
+ tree will be generated by using the alignment sequence names as
+ species names and looking for those in the supplied database.
+diff --git a/lib/Bio/Tools/Run/StandAloneBlastPlus.pm b/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
+index 82a2aba..089e7cc 100755
+--- a/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
++++ b/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
+@@ -210,7 +210,7 @@ To get the tempfile basename, do:
+
+ =item * Specify data post-construction
+
+-Use the explict attribute setters:
++Use the explicit attribute setters:
+
+ $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
+ -create => 1
+diff --git a/lib/Bio/Tools/Run/TigrAssembler.pm b/lib/Bio/Tools/Run/TigrAssembler.pm
+index 9d76326..757d130 100644
+--- a/lib/Bio/Tools/Run/TigrAssembler.pm
++++ b/lib/Bio/Tools/Run/TigrAssembler.pm
+@@ -179,7 +179,7 @@ TIGR Assembler options available in this module:
+ ignore_tandem_32mers: a flag which causes tandem 32mers (a tandem 32mer is a
+ 32mer which occurs more than once in at least one sequence read) to be
+ ignored (this is now the default behavior and this flag is for backward
+- compatability)
++ compatibility)
+ use_tandem_32mers: a flag which causes tandem 32mers to be used for pairwise
+ comparison opposite of the -t flag which is now the default).
+ safe_merging_stop: a flag which causes merging to stop when only sequences
+diff --git a/t/lib/Test/Builder/Tester.pm b/t/lib/Test/Builder/Tester.pm
+index 289bd60..a6380e1 100644
+--- a/t/lib/Test/Builder/Tester.pm
++++ b/t/lib/Test/Builder/Tester.pm
+@@ -323,7 +323,7 @@ will function normally and cause success/errors for B<Test::Harness>.
+
+ sub test_test
+ {
+- # decode the arguements as described in the pod
++ # decode the arguments as described in the pod
+ my $mess;
+ my %args;
+ if (@_ == 1)
+--
+1.7.2.5
+
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Use-system-s-Perl.patch (from rev 7085, trunk/packages/bioperl-run/trunk/debian/patches/Use-system-s-Perl.patch)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Use-system-s-Perl.patch (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/Use-system-s-Perl.patch 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,23 @@
+Forwarded: https://redmine.open-bio.org/issues/3255
+From 8d4322bea521c457029a00155fe292ef7ef177d4 Mon Sep 17 00:00:00 2001
+From: Charles Plessy <plessy at debian.org>
+Date: Sat, 18 Jun 2011 12:58:08 +0900
+Subject: [PATCH] Use system's Perl.
+
+---
+ scripts/bioperl_application_installer.PLS | 2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/scripts/bioperl_application_installer.PLS b/scripts/bioperl_application_installer.PLS
+index 6ab5b5e..f4a05c1 100644
+--- a/scripts/bioperl_application_installer.PLS
++++ b/scripts/bioperl_application_installer.PLS
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl
++#!/usr/bin/perl
+ # BioPerl script for Bio::Installer
+ #
+ # Cared for by Albert Vilella
+--
+1.7.2.5
+
Deleted: trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/install-scripts.patch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch 2011-06-17 14:19:23 UTC (rev 7078)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/install-scripts.patch 2011-06-18 05:19:05 UTC (rev 7088)
@@ -1,21 +0,0 @@
---- a/Build.PL 2011-06-17 18:19:24.491792863 +0900
-+++ b/Build.PL.install-scripts 2011-06-17 18:18:46.371792871 +0900
-@@ -27,7 +27,8 @@
- },
- get_options => {
- accept => { },
-- network => { }
-+ network => { },
-+ install_scripts => { }
- },
- auto_features => {
- Network => {
-@@ -42,7 +43,7 @@
- my $accept = $build->args->{accept};
-
- # Optionally have script files installed.
--if ($accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
-+if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
- my $files = $build->_find_file_by_type('PLS', 'scripts');
-
- my $script_build = File::Spec->catdir($build->blib, 'script');
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/install-scripts.patch (from rev 7084, trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/install-scripts.patch (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/install-scripts.patch 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,36 @@
+Forwarded: https://redmine.open-bio.org/issues/3254
+From 4d1fe98b390c67170d0d23325de5ccd8fdc6ea1a Mon Sep 17 00:00:00 2001
+From: Charles Plessy <plessy at debian.org>
+Date: Sat, 18 Jun 2011 12:43:21 +0900
+Subject: [PATCH] New --install_scripts option to request script installation non-interactively.
+
+---
+ Build.PL | 5 +++--
+ 1 files changed, 3 insertions(+), 2 deletions(-)
+
+diff --git a/Build.PL b/Build.PL
+index a577ecf..531f524 100755
+--- a/Build.PL
++++ b/Build.PL
+@@ -28,7 +28,8 @@ my $build = Module::Build->new(
+ },
+ get_options => {
+ accept => { },
+- network => { }
++ network => { },
++ install_scripts => { }
+ },
+ auto_features => {
+ Network => {
+@@ -43,7 +44,7 @@ my $build = Module::Build->new(
+ my $accept = $build->args->{accept};
+
+ # Optionally have script files installed.
+-if ($accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
++if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
+ my $files = $build->_find_file_by_type('PLS', 'scripts');
+
+ my $script_build = File::Spec->catdir($build->blib, 'script');
+--
+1.7.2.5
+
Deleted: trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/series
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/series 2011-06-17 14:19:23 UTC (rev 7078)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/series 2011-06-18 05:19:05 UTC (rev 7088)
@@ -1 +0,0 @@
-install-scripts.patch
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/series (from rev 7086, trunk/packages/bioperl-run/trunk/debian/patches/series)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/series (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/patches/series 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,3 @@
+install-scripts.patch
+Use-system-s-Perl.patch
+Some-spellchecking.patch
Deleted: trunk/packages/bioperl-run/tags/1.6.9-1/debian/rules
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/rules 2011-06-17 14:19:23 UTC (rev 7078)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/rules 2011-06-18 05:19:05 UTC (rev 7088)
@@ -1,14 +0,0 @@
-#!/usr/bin/make -f
-
-ifneq (,$(DEB_MAINTAINER_MODE))
-NETWORK = --network
-endif
-
-%:
- dh $@ --with quilt
-
-override_dh_auto_configure:
- dh_auto_configure -- --install_scripts $(NETWORK)
-
-override_dh_auto_test:
- PATH=$$PATH:/usr/lib/emboss dh_auto_test
Copied: trunk/packages/bioperl-run/tags/1.6.9-1/debian/rules (from rev 7087, trunk/packages/bioperl-run/trunk/debian/rules)
===================================================================
--- trunk/packages/bioperl-run/tags/1.6.9-1/debian/rules (rev 0)
+++ trunk/packages/bioperl-run/tags/1.6.9-1/debian/rules 2011-06-18 05:19:05 UTC (rev 7088)
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+
+ifneq (,$(DEB_MAINTAINER_MODE))
+NETWORK = --network
+endif
+
+%:
+ dh $@ --with quilt
+
+override_dh_auto_configure:
+ dh_auto_configure -- --install_scripts $(NETWORK)
+
+override_dh_auto_test:
+# PATH=$$PATH:/usr/lib/emboss dh_auto_test
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