[med-svn] [tophat] 05/07: d/patches: updated debian/patches/fix_includes_path.patch to exclude SeqAn-1.3 from configure.ac d/control: new Homepage d/copyright: new Source

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository tophat.

commit 9fbdf45147940c4b9862e868a9b014aea3d52313
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Jul 7 13:27:42 2014 +0200

    d/patches: updated debian/patches/fix_includes_path.patch
     to exclude SeqAn-1.3 from configure.ac
    d/control: new Homepage
    d/copyright: new Source
---
 debian/changelog                                              |  9 +++++----
 debian/control                                                |  2 +-
 debian/copyright                                              |  4 ++--
 .../{fix4seqan1.4.patch => fix_build_w_seqan1.4.patch}        |  0
 debian/patches/fix_includes_path.patch                        | 11 +++++++++++
 debian/patches/series                                         |  2 +-
 6 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 84313e3..9bc6bde 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,12 @@
 tophat (2.0.12+dfsg-1) UNRELEASED; urgency=medium
 
-  [ Andreas Tille ]
-  * Commit Diane's patch
-
   [ Alexandre Mestiashvili ]
-  *  d/watch: new url
+  * d/watch: new url
   * Imported Upstream version 2.0.12+dfsg
+  * d/patches/fix_build_w_seqan1.4.patch: patch from Manuel Holtgrewe resolving #733352.
+     removed const_ness_part1.patch as the new patch solves the problem completely
+    Closes: #733352
+  * debian/patches/fix_includes_path.patch: exclude SeqAn-1.3 from configure.ac
 
  -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 03 Jul 2014 21:06:10 +0200
 
diff --git a/debian/control b/debian/control
index 9ad56ab..4372394 100644
--- a/debian/control
+++ b/debian/control
@@ -18,7 +18,7 @@ Build-Depends: debhelper (>= 9),
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/tophat.git
 Vcs-Git: git://anonscm.debian.org/debian-med/tophat.git
-Homepage: http://tophat.cbcb.umd.edu/
+Homepage: http://ccb.jhu.edu/software/tophat
 
 Package: tophat
 Architecture: any
diff --git a/debian/copyright b/debian/copyright
index 33fc0f6..1109e44 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: TopHat
 Upstream-Contact: Daehwan Kim <infphilo at gmail.com>
-Source: http://tophat.cbcb.umd.edu/downloads/tophat-2.0.10.tar.gz
+Source: http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.12.tar.gz
 Comment:
  Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by
  Ben Langmead and Cole Trapnell.  Daehwan Kim and Geo Pertea added support
@@ -90,7 +90,7 @@ License:
 
 Files: debian/*
 Copyright: © 2011 Carlos Borroto <carlos.borroto at gmail.com>
-           © 2013 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+           © 2014 Alex Mestiashvili <alex at biotec.tu-dresden.de>
 License: GPL-2+
 
 License: GAP
diff --git a/debian/patches/fix4seqan1.4.patch b/debian/patches/fix_build_w_seqan1.4.patch
similarity index 100%
rename from debian/patches/fix4seqan1.4.patch
rename to debian/patches/fix_build_w_seqan1.4.patch
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 337b5c2..87c44f8 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -74,3 +74,14 @@ Subject: Corrected location for samtools .h files
  	]], [[
  	]])],[
          AC_MSG_RESULT(yes)
+--- tophat.orig/configure.ac
++++ tophat/configure.ac
+@@ -93,7 +93,7 @@
+ 	  
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
+ CXXFLAGS="$CFLAGS"
+-CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3"
++CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS"
+ LDFLAGS="$user_LDFLAGS"
+ 
+ AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
diff --git a/debian/patches/series b/debian/patches/series
index 2ef3aff..d51df39 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,3 @@
-fix4seqan1.4.patch
+fix_build_w_seqan1.4.patch
 fix_includes_path.patch
 bashism_in_shell_script.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/tophat.git