[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-7-g2fb02e8
Carlos Borroto
carlos.borroto at gmail.com
Fri Jun 8 16:47:48 UTC 2012
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.
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