[med-svn] r14427 - in trunk/packages/cd-hit/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-08-11 09:07:08 +0000 (Sun, 11 Aug 2013)
New Revision: 14427

Removed:
   trunk/packages/cd-hit/trunk/debian/patches/use-dpkg-buildflags.patch
Modified:
   trunk/packages/cd-hit/trunk/debian/changelog
   trunk/packages/cd-hit/trunk/debian/control
   trunk/packages/cd-hit/trunk/debian/patches/enable_help2man.patch
   trunk/packages/cd-hit/trunk/debian/patches/series
Log:
New upstream version with adapted patches; cme fix dpkg-control


Modified: trunk/packages/cd-hit/trunk/debian/changelog
===================================================================
--- trunk/packages/cd-hit/trunk/debian/changelog	2013-08-10 10:26:40 UTC (rev 14426)
+++ trunk/packages/cd-hit/trunk/debian/changelog	2013-08-11 09:07:08 UTC (rev 14427)
@@ -1,3 +1,10 @@
+cd-hit (4.6.1-2012-08-27-1) UNRELEASED; urgency=low
+
+  * New upstream version (adapted patches)
+  * debian/control: cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org>  Sun, 11 Aug 2013 10:51:30 +0200
+
 cd-hit (4.6-2012-04-25-1) unstable; urgency=low
 
   * New upstream version incorporating the previous patches as

Modified: trunk/packages/cd-hit/trunk/debian/control
===================================================================
--- trunk/packages/cd-hit/trunk/debian/control	2013-08-10 10:26:40 UTC (rev 14426)
+++ trunk/packages/cd-hit/trunk/debian/control	2013-08-11 09:07:08 UTC (rev 14427)
@@ -1,19 +1,23 @@
 Source: cd-hit
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
+           Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
- Andreas Tille <tille at debian.org>
-DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 9), mpi-default-dev, help2man
-Standards-Version: 3.9.3
-Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
+Build-Depends: debhelper (>= 9),
+               mpi-default-dev,
+               help2man
+Standards-Version: 3.9.4
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/cd-hit/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cd-hit/trunk/
+Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
 
 Package: cd-hit
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, mpi-default-bin
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${perl:Depends},
+         mpi-default-bin
 Description: suite of programs designed to quickly group sequences
  cd-hit contains a number of programs designed to quickly group
  sequences. cd-hit groups proteins into clusters that meet a user-defined
@@ -22,3 +26,4 @@
  to cd-hit-2d but designed to compare two nucleotide datasets. A number
  of other related programs are also in this package. Please see the
  cd-hit user manual, also part of this package, for further information. 
+

Modified: trunk/packages/cd-hit/trunk/debian/patches/enable_help2man.patch
===================================================================
--- trunk/packages/cd-hit/trunk/debian/patches/enable_help2man.patch	2013-08-10 10:26:40 UTC (rev 14426)
+++ trunk/packages/cd-hit/trunk/debian/patches/enable_help2man.patch	2013-08-11 09:07:08 UTC (rev 14427)
@@ -1,24 +1,25 @@
 Author: Andreas Tille <tille at debian.org>
+LastChanged: Sun, 11 Aug 2013 10:51:30 +0200
 Description: Help help2man to run without producing errors
 
---- cd-hit-v4.6-2012-04-25.orig/cd-hit-2d-para.pl
-+++ cd-hit-v4.6-2012-04-25/cd-hit-2d-para.pl
-@@ -55,7 +55,7 @@
+--- a/cd-hit-2d-para.pl
++++ b/cd-hit-2d-para.pl
+@@ -55,7 +55,7 @@ while ($arg=shift) {
    elsif ($arg eq "--Q" ) { $queue      = shift; }
    elsif ($arg eq "--T" ) { $queue_type = shift; }
    elsif ($arg eq "--R" ) { $restart_in = shift; }
--  else  {$arg_pass         .= " $arg " . shift; }
+-  else  {$arg_pass         .= " $arg "; }
 +  else  {$arg_pass         .= " $arg " ; $arg_pass .= shift if (shift) }
  }
  ($in and $out) || print_usage();
  if (not ($seg_no2 >1)) {
---- cd-hit-v4.6-2012-04-25.orig/cd-hit-para.pl
-+++ cd-hit-v4.6-2012-04-25/cd-hit-para.pl
-@@ -52,7 +52,7 @@
+--- a/cd-hit-para.pl
++++ b/cd-hit-para.pl
+@@ -52,7 +52,7 @@ while ($arg=shift) {
    elsif ($arg eq "--Q") { $queue      = shift; }
    elsif ($arg eq "--T") { $queue_type = shift; }
    elsif ($arg eq "--R") { $restart_in = shift; }
--  else  {$arg_pass       .= " $arg " . shift; }
+-  else  {$arg_pass       .= " $arg "; }
 +  else  {$arg_pass         .= " $arg " ; $arg_pass .= shift if (shift) }
  }
  ($in and $out) || print_usage();

Modified: trunk/packages/cd-hit/trunk/debian/patches/series
===================================================================
--- trunk/packages/cd-hit/trunk/debian/patches/series	2013-08-10 10:26:40 UTC (rev 14426)
+++ trunk/packages/cd-hit/trunk/debian/patches/series	2013-08-11 09:07:08 UTC (rev 14427)
@@ -1,2 +1 @@
-use-dpkg-buildflags.patch
 enable_help2man.patch

Deleted: trunk/packages/cd-hit/trunk/debian/patches/use-dpkg-buildflags.patch
===================================================================
--- trunk/packages/cd-hit/trunk/debian/patches/use-dpkg-buildflags.patch	2013-08-10 10:26:40 UTC (rev 14426)
+++ trunk/packages/cd-hit/trunk/debian/patches/use-dpkg-buildflags.patch	2013-08-11 09:07:08 UTC (rev 14427)
@@ -1,17 +0,0 @@
---- cd-hit-v4.6-2012-04-25.orig/Makefile
-+++ cd-hit-v4.6-2012-04-25/Makefile
-@@ -28,10 +28,13 @@
- endif
- 
- #LDFLAGS = -static -o
--LDFLAGS = -o
-+LDFLAGS += -o
- 
- PROGS = cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div cd-hit-454
- 
-+# Propagate hardening flags
-+CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS)
-+
- .c++.o:
- 	$(CC) $(CCFLAGS) -c $<
-