[med-svn] r12783 - trunk/packages/meme/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2013-01-14 09:14:46 +0000 (Mon, 14 Jan 2013)
New Revision: 12783

Modified:
   trunk/packages/meme/trunk/debian/patches/fix_doc_location
   trunk/packages/meme/trunk/debian/patches/fix_installer_paths
   trunk/packages/meme/trunk/debian/patches/fix_plib_path
   trunk/packages/meme/trunk/debian/patches/no_libxml_configure
   trunk/packages/meme/trunk/debian/patches/perl-include.patch
Log:
Refreshed patches


Modified: trunk/packages/meme/trunk/debian/patches/fix_doc_location
===================================================================
--- trunk/packages/meme/trunk/debian/patches/fix_doc_location	2013-01-14 09:07:42 UTC (rev 12782)
+++ trunk/packages/meme/trunk/debian/patches/fix_doc_location	2013-01-14 09:14:46 UTC (rev 12783)
@@ -2,7 +2,7 @@
 
 --- a/scripts/meme.csh.in
 +++ b/scripts/meme.csh.in
-@@ -59,7 +59,7 @@
+@@ -59,7 +59,7 @@ exit $exe_status
  
  # Describe MEME and its output format:
  usage:

Modified: trunk/packages/meme/trunk/debian/patches/fix_installer_paths
===================================================================
--- trunk/packages/meme/trunk/debian/patches/fix_installer_paths	2013-01-14 09:07:42 UTC (rev 12782)
+++ trunk/packages/meme/trunk/debian/patches/fix_installer_paths	2013-01-14 09:14:46 UTC (rev 12783)
@@ -2,7 +2,7 @@
 
 --- a/Makefile.am
 +++ b/Makefile.am
-@@ -18,11 +18,11 @@
+@@ -18,11 +18,11 @@ ARCHIVE_REVISION:
  install-data-hook: dbdir
  
  dbdir:
@@ -19,7 +19,7 @@
  
 --- a/doc/examples/Makefile.am
 +++ b/doc/examples/Makefile.am
-@@ -52,7 +52,7 @@
+@@ -52,7 +52,7 @@ exdir = $(WEBDIR)/examples
  other_exdir = $(WEBDIR)/doc/examples
  else
  exdir = $(prefix)/doc/examples

Modified: trunk/packages/meme/trunk/debian/patches/fix_plib_path
===================================================================
--- trunk/packages/meme/trunk/debian/patches/fix_plib_path	2013-01-14 09:07:42 UTC (rev 12782)
+++ trunk/packages/meme/trunk/debian/patches/fix_plib_path	2013-01-14 09:14:46 UTC (rev 12783)
@@ -14,7 +14,7 @@
  
  #define ROUNDERROR (1E-12)
  
-@@ -496,9 +497,11 @@
+@@ -495,9 +496,11 @@ void init_meme(
          plib_name = DNA_PLIB;   /* default mixture prior for DNA */
        }
        /* prepend meme_directory to file name */

Modified: trunk/packages/meme/trunk/debian/patches/no_libxml_configure
===================================================================
--- trunk/packages/meme/trunk/debian/patches/no_libxml_configure	2013-01-14 09:07:42 UTC (rev 12782)
+++ trunk/packages/meme/trunk/debian/patches/no_libxml_configure	2013-01-14 09:14:46 UTC (rev 12783)
@@ -2,12 +2,12 @@
 
 --- a/src/Makefile.am
 +++ b/src/Makefile.am
-@@ -21,7 +21,7 @@
+@@ -21,7 +21,7 @@ else
  PARALLEL_DIR =
  endif
  
--SUBDIRS = filters libxml2 libxslt libexslt . $(PARALLEL_DIR)
-+SUBDIRS = filters libexslt . $(PARALLEL_DIR)
+-SUBDIRS = filters libxml2 libxslt libexslt wiggle . $(PARALLEL_DIR)
++SUBDIRS = filters libexslt wiggle . $(PARALLEL_DIR)
  
  BUILT_SOURCES = dir.h projrel.h
  

Modified: trunk/packages/meme/trunk/debian/patches/perl-include.patch
===================================================================
--- trunk/packages/meme/trunk/debian/patches/perl-include.patch	2013-01-14 09:07:42 UTC (rev 12782)
+++ trunk/packages/meme/trunk/debian/patches/perl-include.patch	2013-01-14 09:14:46 UTC (rev 12783)
@@ -1,33 +1,17 @@
 Description: add meme directory to search path
-Index: meme_4.8.1.patch/scripts/meme-chip.pl.in
-===================================================================
---- meme_4.8.1.patch.orig/scripts/meme-chip.pl.in	2012-02-07 04:26:29.000000000 +0100
-+++ meme_4.8.1.patch/scripts/meme-chip.pl.in	2012-06-22 12:40:26.000000000 +0200
-@@ -4,6 +4,7 @@
- use warnings;
+--- a/scripts/meme-chip_webservice.pl.in
++++ b/scripts/meme-chip_webservice.pl.in
+@@ -49,6 +49,7 @@ use Pod::Usage;
  
- use lib qw(@PERLLIBDIR@);
-+use lib qw(/usr/share/perl5/Meme);
  
- use Cwd qw(abs_path);
- use Fcntl qw(O_CREAT O_RDONLY O_WRONLY O_TRUNC SEEK_SET);
-Index: meme_4.8.1.patch/scripts/meme-chip_webservice.pl.in
-===================================================================
---- meme_4.8.1.patch.orig/scripts/meme-chip_webservice.pl.in	2012-01-27 07:05:09.000000000 +0100
-+++ meme_4.8.1.patch/scripts/meme-chip_webservice.pl.in	2012-06-22 12:40:46.000000000 +0200
-@@ -4,6 +4,7 @@
- use warnings;
- 
  use lib qw(@PERLLIBDIR@);
 +use lib qw(/usr/share/perl5/Meme);
  
- use Cwd;
- use File::Basename qw(fileparse);
-Index: meme_4.8.1.patch/scripts/meme2meme.pl.in
-===================================================================
---- meme_4.8.1.patch.orig/scripts/meme2meme.pl.in	2012-01-27 07:05:09.000000000 +0100
-+++ meme_4.8.1.patch/scripts/meme2meme.pl.in	2012-06-22 13:12:53.000000000 +0200
-@@ -10,6 +10,7 @@
+ use ExecUtils qw(stringify_args invoke);
+ use MemeWebUtils qw(is_safe_name add_status_msg update_status loggable_date write_invocation_log);
+--- a/scripts/meme2meme.pl.in
++++ b/scripts/meme2meme.pl.in
+@@ -10,6 +10,7 @@ use warnings;
  use strict;
  
  use lib qw(@PERLLIBDIR@);
@@ -35,10 +19,8 @@
  
  use MotifUtils qw(intern_to_iupac intern_to_meme read_background_file parse_double round);
  
-Index: meme_4.8.1.patch/website/scripts/metameme.txt
-===================================================================
---- meme_4.8.1.patch.orig/website/scripts/metameme.txt	2012-01-27 07:05:12.000000000 +0100
-+++ meme_4.8.1.patch/website/scripts/metameme.txt	2012-06-22 13:13:53.000000000 +0200
+--- a/website/scripts/metameme.txt
++++ b/website/scripts/metameme.txt
 @@ -16,6 +16,7 @@
  #         sorted scores for training set
  #         sorted scores for test set
@@ -47,3 +29,13 @@
  use mhmm_globals;
  
  #########################################################################
+--- a/scripts/meme-chip.pl.in
++++ b/scripts/meme-chip.pl.in
+@@ -69,6 +69,7 @@ use Time::HiRes qw(gettimeofday tv_inter
+ use XML::Simple;
+ 
+ use lib qw(@PERLLIBDIR@);
++use lib qw(/usr/share/perl5/Meme);
+ use Globals;
+ use ExecUtils qw(invoke stringify_args2);
+ use MotifUtils qw(intern_to_meme read_background_file);