[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-7-g2fb02e8

[Carlos Borroto]

The following commit has been merged in the master branch:
commit 2673e1e1f0637727441baf9f437351e1458c80f6
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Fri Jun 8 11:47:34 2012 -0400

    patches refreshed

diff --git a/debian/patches/0001-fix_spelling.patch b/debian/patches/0001-fix_spelling.patch
index d3cca57..fe708dc 100644
--- a/debian/patches/0001-fix_spelling.patch
+++ b/debian/patches/0001-fix_spelling.patch
@@ -7,8 +7,10 @@ Subject: fix_spelling
  src/locfit/lfd.c   |    2 +-
  2 files changed, 2 insertions(+), 2 deletions(-)
 
---- cufflinks.orig/src/locfit/arith.c
-+++ cufflinks/src/locfit/arith.c
+Index: cufflinks/src/locfit/arith.c
+===================================================================
+--- cufflinks.orig/src/locfit/arith.c	2012-06-08 11:44:22.468790509 -0400
++++ cufflinks/src/locfit/arith.c	2012-06-08 11:46:41.156792714 -0400
 @@ -410,7 +410,7 @@
      INT i;
      if (l==NULL) 
@@ -18,8 +20,10 @@ Subject: fix_spelling
          return NULL;
      }
      v = createvar("_vvec1",STHIDDEN,l->n,VDOUBLE);
---- cufflinks.orig/src/locfit/lfd.c
-+++ cufflinks/src/locfit/lfd.c
+Index: cufflinks/src/locfit/lfd.c
+===================================================================
+--- cufflinks.orig/src/locfit/lfd.c	2012-06-08 11:44:22.468790509 -0400
++++ cufflinks/src/locfit/lfd.c	2012-06-08 11:46:41.156792714 -0400
 @@ -78,7 +78,7 @@
          }
        }
@@ -29,9 +33,11 @@ Subject: fix_spelling
          return(0);
        }
      }
---- cufflinks.orig/src/abundances.cpp
-+++ cufflinks/src/abundances.cpp
-@@ -1751,7 +1751,7 @@
+Index: cufflinks/src/abundances.cpp
+===================================================================
+--- cufflinks.orig/src/abundances.cpp	2012-06-08 11:44:33.688790686 -0400
++++ cufflinks/src/abundances.cpp	2012-06-08 11:46:41.156792714 -0400
+@@ -1995,7 +1995,7 @@
  	
  	vector<double> gammas;
  	
diff --git a/debian/patches/0004-fix-m64-usage-and-lfs.patch b/debian/patches/0004-fix-m64-usage-and-lfs.patch
index ab78e2d..14609ac 100644
--- a/debian/patches/0004-fix-m64-usage-and-lfs.patch
+++ b/debian/patches/0004-fix-m64-usage-and-lfs.patch
@@ -4,9 +4,11 @@ Just because the compiler supports it, doesn't mean it can compile
 natively to it (e.g. on powerpc, you can compile -m64, but there are
 no headers for it plus it cannot run on 32-bit systems).
 
---- cufflinks/configure.ac~	2012-01-02 13:34:14.000000000 +0000
-+++ cufflinks/configure.ac	2012-01-18 22:13:30.000000000 +0000
-@@ -64,12 +64,7 @@
+Index: cufflinks/configure.ac
+===================================================================
+--- cufflinks.orig/configure.ac	2012-06-08 11:44:33.688790686 -0400
++++ cufflinks/configure.ac	2012-06-08 11:46:28.724792515 -0400
+@@ -66,11 +66,6 @@
    i*86-darwin*)
  	CFLAGS="-m64"
  	AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
@@ -18,4 +20,3 @@ no headers for it plus it cannot run on 32-bit systems).
  esac
  
  AC_ARG_ENABLE(vectorize,    [  --enable-vectorize        Enable GCC auto-vectorization],
- 			  [ext_CFLAGS="${ext_CFLAGS} -ftree-vectorize -msse3 -ffast-math -ftree-vectorizer-verbose=99"], [])

-- 
Transcript assembly, differential expression, and differential regulation for RNA-Seq.