[med-svn] r4309 - trunk/packages/emboss-explorer/trunk/debian/patches
Charles Plessy
plessy at alioth.debian.org
Wed Nov 4 10:22:44 UTC 2009
Author: plessy
Date: 2009-11-04 10:22:43 +0000 (Wed, 04 Nov 2009)
New Revision: 4309
Added:
trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.diff
trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.diff
trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.diff
trunk/packages/emboss-explorer/trunk/debian/patches/series
Removed:
trunk/packages/emboss-explorer/trunk/debian/patches/00list
trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.dpatch
trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch
trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.dpatch
Log:
Converted to quilt.
See ?\226?\128?\152http://blog.orebokech.com/2007/08/converting-debian-packages-from-dpatch.html?\226?\128?\153.
Deleted: trunk/packages/emboss-explorer/trunk/debian/patches/00list
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/00list 2009-11-03 17:21:35 UTC (rev 4308)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/00list 2009-11-04 10:22:43 UTC (rev 4309)
@@ -1,3 +0,0 @@
-01-fix_examples.dpatch
-02-fix_Conf.pm.dpatch
-05-build-manpages.dpatch
Copied: trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.diff (from rev 4308, trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.dpatch)
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.diff (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.diff 2009-11-04 10:22:43 UTC (rev 4309)
@@ -0,0 +1,21 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 02-fix_examples.dpatch by David Paleino <d.paleino at gmail.com>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: The Debian package for EMBOSS installs its files in /usr/share/EMBOSS.
+## DP: This patch is necessary for the test of the ACD module to function.
+## DP: As it is Debian-specific, it has not been forwarded upstream.
+
+ at DPATCH@
+diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
+--- emboss-explorer~/t/ACD.t 2006-11-13 00:38:39.000000000 +0100
++++ emboss-explorer/t/ACD.t 2007-05-20 15:33:09.000000000 +0200
+@@ -15,7 +15,7 @@
+ BEGIN {
+ # locate the EMBOSS ACD files in order to validate against them...
+ #
+- @ACDFILES = glob "/usr/local/share/EMBOSS/acd/*.acd";
++ @ACDFILES = glob "/usr/share/EMBOSS/acd/*.acd";
+
+ $XHTML = EMBOSS::GUI::XHTML->new(
+ script_url => 'dummy'
Deleted: trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.dpatch
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.dpatch 2009-11-03 17:21:35 UTC (rev 4308)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/01-fix_examples.dpatch 2009-11-04 10:22:43 UTC (rev 4309)
@@ -1,21 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 02-fix_examples.dpatch by David Paleino <d.paleino at gmail.com>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: The Debian package for EMBOSS installs its files in /usr/share/EMBOSS.
-## DP: This patch is necessary for the test of the ACD module to function.
-## DP: As it is Debian-specific, it has not been forwarded upstream.
-
- at DPATCH@
-diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
---- emboss-explorer~/t/ACD.t 2006-11-13 00:38:39.000000000 +0100
-+++ emboss-explorer/t/ACD.t 2007-05-20 15:33:09.000000000 +0200
-@@ -15,7 +15,7 @@
- BEGIN {
- # locate the EMBOSS ACD files in order to validate against them...
- #
-- @ACDFILES = glob "/usr/local/share/EMBOSS/acd/*.acd";
-+ @ACDFILES = glob "/usr/share/EMBOSS/acd/*.acd";
-
- $XHTML = EMBOSS::GUI::XHTML->new(
- script_url => 'dummy'
Copied: trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.diff (from rev 4308, trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch)
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.diff (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.diff 2009-11-04 10:22:43 UTC (rev 4309)
@@ -0,0 +1,95 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 01-fix_Conf.pm.dpatch by David Paleino <d.paleino at gmail.com>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Moving configuration to /etc/emboss-explorer.conf
+## DP: Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1992075&group_id=124389&atid=699414
+
+ at DPATCH@
+diff -urNad emboss-explorer~/lib/EMBOSS/GUI/Conf.pm emboss-explorer/lib/EMBOSS/GUI/Conf.pm
+--- emboss-explorer~/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:23.000000000 +0200
++++ emboss-explorer/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:57.000000000 +0200
+@@ -43,79 +43,16 @@
+
+ package EMBOSS::GUI::Conf;
+
+-use strict;
+ use warnings;
+
+ use Carp;
+
+ our $VERSION = 1.10;
+
+-# path to the EMBOSS::GUI HTML files
+-our $HTML_PATH = "/var/www/emboss/html";
+-
+-# URL corresponding to $HTML_PATH above
+-our $HTML_URL = "/emboss";
+-
+-# URL specifying the style sheet to use
+-our $STYLE_URL = "$HTML_URL/style/emboss.css";
+-
+-# URL prefix to place before image links
+-our $IMAGE_URL = "$HTML_URL/images";
+-
+-# URL prefix to place before manual links (only used in static pages)
+-our $MANUAL_URL = "$HTML_URL/manual";
+-
+-# path to the EMBOSS::GUI temporary output directory
+-our $OUTPUT_PATH = "$HTML_PATH/output";
+-
+-# URL corresponding to $OUTPUT_PATH above
+-our $OUTPUT_URL = "$HTML_URL/output";
+-
+-# prefix under which EMBOSS was installed
+-our $EMBOSS_PREFIX = "/usr/local";
+-
+-# path to EMBOSS binaries
+-our $EMBOSS_BIN = "$EMBOSS_PREFIX/bin";
+-
+-# path to EMBOSS installation
+-our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS";
+-
+-# path to EMBOSS ACD files
+-our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd";
+-
+-# path to EMBOSS data
+-our $EMBOSS_DATA = "$EMBOSS_HOME/data";
+-
+-# path to EMBOSS application manuals
+-our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html";
+-
+-# list of groups and applications to exclude from the main menu
+-our @EXCLUDED = (
+- "ACD",
+- "acdc",
+- "acdpretty",
+- "acdtable",
+- "acdtrace",
+- "acdvalid",
+- "UTILS DATABASE CREATION",
+- "aaindexextract",
+- "cutgextract",
+- "printsextract",
+- "prosextract",
+- "rebaseextract",
+- "tfextract",
+- "UTILS DATABASE INDEXING",
+- "dbiblast",
+- "dbifasta",
+- "dbiflat",
+- "dbigcg",
+-);
+-
+-# number of seconds to delay between placeholder page refreshes
+-our $REFRESH_DELAY = 1;
+-
+-# whether or not to display using frames
+-our $FRAMES = 1;
++open (config_file, "</etc/emboss-explorer/emboss-explorer.conf") or die "Cannot load /etc/emboss-explorer.conf!";
++my @conf = <config_file>;
++eval join("\n", @conf);
++die $@ if $@;
+
+ =item new()
+
Deleted: trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch 2009-11-03 17:21:35 UTC (rev 4308)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/02-fix_Conf.pm.dpatch 2009-11-04 10:22:43 UTC (rev 4309)
@@ -1,95 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 01-fix_Conf.pm.dpatch by David Paleino <d.paleino at gmail.com>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: Moving configuration to /etc/emboss-explorer.conf
-## DP: Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1992075&group_id=124389&atid=699414
-
- at DPATCH@
-diff -urNad emboss-explorer~/lib/EMBOSS/GUI/Conf.pm emboss-explorer/lib/EMBOSS/GUI/Conf.pm
---- emboss-explorer~/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:23.000000000 +0200
-+++ emboss-explorer/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:57.000000000 +0200
-@@ -43,79 +43,16 @@
-
- package EMBOSS::GUI::Conf;
-
--use strict;
- use warnings;
-
- use Carp;
-
- our $VERSION = 1.10;
-
--# path to the EMBOSS::GUI HTML files
--our $HTML_PATH = "/var/www/emboss/html";
--
--# URL corresponding to $HTML_PATH above
--our $HTML_URL = "/emboss";
--
--# URL specifying the style sheet to use
--our $STYLE_URL = "$HTML_URL/style/emboss.css";
--
--# URL prefix to place before image links
--our $IMAGE_URL = "$HTML_URL/images";
--
--# URL prefix to place before manual links (only used in static pages)
--our $MANUAL_URL = "$HTML_URL/manual";
--
--# path to the EMBOSS::GUI temporary output directory
--our $OUTPUT_PATH = "$HTML_PATH/output";
--
--# URL corresponding to $OUTPUT_PATH above
--our $OUTPUT_URL = "$HTML_URL/output";
--
--# prefix under which EMBOSS was installed
--our $EMBOSS_PREFIX = "/usr/local";
--
--# path to EMBOSS binaries
--our $EMBOSS_BIN = "$EMBOSS_PREFIX/bin";
--
--# path to EMBOSS installation
--our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS";
--
--# path to EMBOSS ACD files
--our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd";
--
--# path to EMBOSS data
--our $EMBOSS_DATA = "$EMBOSS_HOME/data";
--
--# path to EMBOSS application manuals
--our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html";
--
--# list of groups and applications to exclude from the main menu
--our @EXCLUDED = (
-- "ACD",
-- "acdc",
-- "acdpretty",
-- "acdtable",
-- "acdtrace",
-- "acdvalid",
-- "UTILS DATABASE CREATION",
-- "aaindexextract",
-- "cutgextract",
-- "printsextract",
-- "prosextract",
-- "rebaseextract",
-- "tfextract",
-- "UTILS DATABASE INDEXING",
-- "dbiblast",
-- "dbifasta",
-- "dbiflat",
-- "dbigcg",
--);
--
--# number of seconds to delay between placeholder page refreshes
--our $REFRESH_DELAY = 1;
--
--# whether or not to display using frames
--our $FRAMES = 1;
-+open (config_file, "</etc/emboss-explorer/emboss-explorer.conf") or die "Cannot load /etc/emboss-explorer.conf!";
-+my @conf = <config_file>;
-+eval join("\n", @conf);
-+die $@ if $@;
-
- =item new()
-
Copied: trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.diff (from rev 4308, trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.dpatch)
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.diff (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.diff 2009-11-04 10:22:43 UTC (rev 4309)
@@ -0,0 +1,20 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 05-build-manpages.dpatch by Charles Plessy <plessy at debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: With this patch, the perl build system will automatically build
+## DP: and install the POD manpages of acdcheckd and mkstatic.
+## DP: Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1994395&group_id=124389&atid=699414
+
+ at DPATCH@
+diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
+--- emboss-explorer-2.2.0/Makefile.PL.old 2008-06-16 07:53:53.000000000 +0900
++++ emboss-explorer-2.2.0/Makefile.PL 2008-06-16 07:55:33.000000000 +0900
+@@ -10,5 +10,6 @@
+ },
+ PREREQ_FATAL => 1,
+ ABSTRACT_FROM => 'lib/EMBOSS/GUI.pm',
+- AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>'
++ AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>',
++ EXE_FILES => => [ qw( bin/acdcheck bin/mkstatic ) ]
+ );
Deleted: trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.dpatch
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.dpatch 2009-11-03 17:21:35 UTC (rev 4308)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/05-build-manpages.dpatch 2009-11-04 10:22:43 UTC (rev 4309)
@@ -1,20 +0,0 @@
-#! /bin/sh /usr/share/dpatch/dpatch-run
-## 05-build-manpages.dpatch by Charles Plessy <plessy at debian.org>
-##
-## All lines beginning with `## DP:' are a description of the patch.
-## DP: With this patch, the perl build system will automatically build
-## DP: and install the POD manpages of acdcheckd and mkstatic.
-## DP: Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1994395&group_id=124389&atid=699414
-
- at DPATCH@
-diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t
---- emboss-explorer-2.2.0/Makefile.PL.old 2008-06-16 07:53:53.000000000 +0900
-+++ emboss-explorer-2.2.0/Makefile.PL 2008-06-16 07:55:33.000000000 +0900
-@@ -10,5 +10,6 @@
- },
- PREREQ_FATAL => 1,
- ABSTRACT_FROM => 'lib/EMBOSS/GUI.pm',
-- AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>'
-+ AUTHOR => 'Luke McCarthy <lukem at gene.pbi.nrc.ca>',
-+ EXE_FILES => => [ qw( bin/acdcheck bin/mkstatic ) ]
- );
Copied: trunk/packages/emboss-explorer/trunk/debian/patches/series (from rev 4308, trunk/packages/emboss-explorer/trunk/debian/patches/00list)
===================================================================
--- trunk/packages/emboss-explorer/trunk/debian/patches/series (rev 0)
+++ trunk/packages/emboss-explorer/trunk/debian/patches/series 2009-11-04 10:22:43 UTC (rev 4309)
@@ -0,0 +1,3 @@
+01-fix_examples.diff
+02-fix_Conf.pm.diff
+05-build-manpages.diff
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