[med-svn] r10032 - in trunk/packages/qiime/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2012-03-20 13:46:03 +0000 (Tue, 20 Mar 2012)
New Revision: 10032

Removed:
   trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch
Modified:
   trunk/packages/qiime/trunk/debian/changelog
   trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
   trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch
   trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch
   trunk/packages/qiime/trunk/debian/patches/series
Log:
New upstream version


Modified: trunk/packages/qiime/trunk/debian/changelog
===================================================================
--- trunk/packages/qiime/trunk/debian/changelog	2012-03-20 13:39:51 UTC (rev 10031)
+++ trunk/packages/qiime/trunk/debian/changelog	2012-03-20 13:46:03 UTC (rev 10032)
@@ -1,9 +1,12 @@
-qiime (1.3.0-4) UNRELEASED; urgency=low
+qiime (1.4.0-1) UNRELEASED; urgency=low
 
+  * New upstream version (updated patches)
+  * debian/patches/fix_shebang_lines.patch: Removed because file
+    to patch was removed upstream
   * debian/copyright: rewritten to confirm DEP5 and verified using
       cme fix dpkg-copyright
 
- -- Andreas Tille <tille at debian.org>  Tue, 20 Mar 2012 14:23:22 +0100
+ -- Andreas Tille <tille at debian.org>  Tue, 20 Mar 2012 14:41:20 +0100
 
 qiime (1.3.0-3) unstable; urgency=low
 

Modified: trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	2012-03-20 13:39:51 UTC (rev 10031)
+++ trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch	2012-03-20 13:46:03 UTC (rev 10032)
@@ -1,5 +1,5 @@
---- a/qiime/denoiser/utils.py
-+++ b/qiime/denoiser/utils.py
+--- Qiime-1.4.0.orig/qiime/denoiser/utils.py
++++ Qiime-1.4.0/qiime/denoiser/utils.py
 @@ -41,9 +41,12 @@
  def get_flowgram_ali_exe():
      """Return the path to the flowgram alignment prog

Deleted: trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch	2012-03-20 13:39:51 UTC (rev 10031)
+++ trunk/packages/qiime/trunk/debian/patches/fix_shebang_lines.patch	2012-03-20 13:46:03 UTC (rev 10032)
@@ -1,8 +0,0 @@
---- a/scripts/denoiser_postprocess.py
-+++ b/scripts/denoiser_postprocess.py
-@@ -1,4 +1,4 @@
-- #!/usr/bin/env python 
-+#!/usr/bin/python
- 
- __author__ = "Jens Reeder"
- __copyright__ = "Copyright 2011, The QIIME Project" 

Modified: trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch	2012-03-20 13:39:51 UTC (rev 10031)
+++ trunk/packages/qiime/trunk/debian/patches/ghc_7.4.2_compatibility.patch	2012-03-20 13:46:03 UTC (rev 10032)
@@ -5,8 +5,8 @@
 Date: Mon, 19 Mar 2012 15:26:02 +0100
 Bug-Debian: http://bugs.debian.org/663889
 
---- qiime-1.3.0.orig/qiime/support_files/denoiser/FlowgramAlignment/FlowgramUtils.lhs
-+++ qiime-1.3.0/qiime/support_files/denoiser/FlowgramAlignment/FlowgramUtils.lhs
+--- Qiime-1.4.0.orig/qiime/support_files/denoiser/FlowgramAlignment/FlowgramUtils.lhs
++++ Qiime-1.4.0/qiime/support_files/denoiser/FlowgramAlignment/FlowgramUtils.lhs
 @@ -1,6 +1,6 @@
  > module FlowgramUtils where
  
@@ -15,8 +15,8 @@
  > import System.IO.Unsafe (unsafePerformIO)
  
  > type FlowSignalDistrib = Array (Int,Int) Float
---- qiime-1.3.0.orig/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
-+++ qiime-1.3.0/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
+--- Qiime-1.4.0.orig/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
++++ Qiime-1.4.0/qiime/support_files/denoiser/FlowgramAlignment/FlowgramAli_4frame.lhs
 @@ -1,13 +1,12 @@
  > module Main where
  
@@ -35,9 +35,9 @@
  > import Text.Printf(printf)
  
  The signature:
---- qiime-1.3.0.orig/qiime/support_files/denoiser/FlowgramAlignment/ADPCombinators.lhs
-+++ qiime-1.3.0/qiime/support_files/denoiser/FlowgramAlignment/ADPCombinators.lhs
-@@ -7,7 +7,7 @@ programming.
+--- Qiime-1.4.0.orig/qiime/support_files/denoiser/FlowgramAlignment/ADPCombinators.lhs
++++ Qiime-1.4.0/qiime/support_files/denoiser/FlowgramAlignment/ADPCombinators.lhs
+@@ -7,7 +7,7 @@
  ----------------------------------------------------------------------
  
  > module ADPCombinators where

Modified: trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch	2012-03-20 13:39:51 UTC (rev 10031)
+++ trunk/packages/qiime/trunk/debian/patches/python26_trim_sff_primers.patch	2012-03-20 13:46:03 UTC (rev 10032)
@@ -1,7 +1,5 @@
-Index: Qiime-1.2.1/qiime/trim_sff_primers.py
-===================================================================
---- Qiime-1.2.1.orig/qiime/trim_sff_primers.py	2011-03-02 22:27:48.000000000 +0100
-+++ Qiime-1.2.1/qiime/trim_sff_primers.py	2011-03-02 22:29:00.000000000 +0100
+--- Qiime-1.4.0.orig/qiime/trim_sff_primers.py
++++ Qiime-1.4.0/qiime/trim_sff_primers.py
 @@ -101,8 +101,8 @@
          clipped_header, clipped_reads = set_clip_qual_left(sff_data, readlength)
          

Modified: trunk/packages/qiime/trunk/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series	2012-03-20 13:39:51 UTC (rev 10031)
+++ trunk/packages/qiime/trunk/debian/patches/series	2012-03-20 13:46:03 UTC (rev 10032)
@@ -1,4 +1,3 @@
 python26_trim_sff_primers.patch
-fix_shebang_lines.patch
 fix_binary_helper_location.patch
 ghc_7.4.2_compatibility.patch