[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-24-gb9a99b5
Andreas Tille
tille at debian.org
Wed May 22 11:33:53 UTC 2013
The following commit has been merged in the master branch:
commit e5beb6e4942c1f12f01d73bcfce64ddf73dea998
Author: Andreas Tille <tille at debian.org>
Date: Wed May 22 13:29:43 2013 +0200
Upstream release 2.1.1 (+ adapted patches)
diff --git a/debian/changelog b/debian/changelog
index 50e8d0f..4c5ea75 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-cufflinks (2.0.2-1) UNRELEASED; urgency=low
+cufflinks (2.1.1-1) UNRELEASED; urgency=low
[Carlos Borroto]
* New upstream release.
@@ -9,7 +9,11 @@ cufflinks (2.0.2-1) UNRELEASED; urgency=low
[ Alexandre Mestiashvili ]
* Imported debian/patches/0004-fix-m64-usage-and-lfs.patch, Closes: #675985
- -- Carlos Borroto <carlos.borroto at gmail.com> Fri, 08 Jun 2012 11:45:00 -0400
+ [ Andreas Tille ]
+ * Upstream release 2.1.1 (+ adapted patches)
+ Closes: #687968
+
+ -- Andreas Tille <tille at debian.org> Wed, 22 May 2013 13:27:40 +0200
cufflinks (1.3.0-2) unstable; urgency=low
diff --git a/debian/patches/0001-fix_spelling.patch b/debian/patches/0001-fix_spelling.patch
index 4308e78..31c6756 100644
--- a/debian/patches/0001-fix_spelling.patch
+++ b/debian/patches/0001-fix_spelling.patch
@@ -7,9 +7,9 @@ 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
-@@ -410,7 +410,7 @@
+--- a/src/locfit/arith.c
++++ b/src/locfit/arith.c
+@@ -410,7 +410,7 @@ double (*f)();
INT i;
if (l==NULL)
{
@@ -18,9 +18,9 @@ Subject: fix_spelling
return NULL;
}
v = createvar("_vvec1",STHIDDEN,l->n,VDOUBLE);
---- cufflinks.orig/src/locfit/lfd.c
-+++ cufflinks/src/locfit/lfd.c
-@@ -78,7 +78,7 @@
+--- a/src/locfit/lfd.c
++++ b/src/locfit/lfd.c
+@@ -78,7 +78,7 @@ INT fp;
}
}
if (access("LFData",W_OK)==-1)
@@ -29,9 +29,9 @@ Subject: fix_spelling
return(0);
}
}
---- cufflinks.orig/src/abundances.cpp
-+++ cufflinks/src/abundances.cpp
-@@ -2019,7 +2019,7 @@
+--- a/src/abundances.cpp
++++ b/src/abundances.cpp
+@@ -2901,7 +2901,7 @@ bool AbundanceGroup::calculate_gammas(co
vector<double> gammas;
diff --git a/debian/patches/0002-bam2samtools.patch b/debian/patches/0002-bam2samtools.patch
index 1270a71..2c45845 100644
--- a/debian/patches/0002-bam2samtools.patch
+++ b/debian/patches/0002-bam2samtools.patch
@@ -6,8 +6,6 @@ Subject: bam2samtools
ax_bam.m4 | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-diff --git a/ax_bam.m4 b/ax_bam.m4
-index 7d463b7..8641172 100644
--- a/ax_bam.m4
+++ b/ax_bam.m4
@@ -102,7 +102,7 @@ if test "x$want_bam" = "xyes"; then
@@ -19,4 +17,3 @@ index 7d463b7..8641172 100644
]], [[
]])],[
AC_MSG_RESULT(yes)
---
diff --git a/debian/patches/0003-fix_includes_path.patch b/debian/patches/0003-fix_includes_path.patch
index 141b5f0..4858a1a 100644
--- a/debian/patches/0003-fix_includes_path.patch
+++ b/debian/patches/0003-fix_includes_path.patch
@@ -6,8 +6,8 @@ Subject: fix_includes_path.patch
src/hits.h | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
---- cufflinks.orig/src/hits.h
-+++ cufflinks/src/hits.h
+--- a/src/hits.h
++++ b/src/hits.h
@@ -16,7 +16,7 @@
#include <boost/shared_ptr.hpp>
@@ -17,9 +17,9 @@ Subject: fix_includes_path.patch
#include "common.h"
#include "multireads.h"
---- cufflinks.orig/ax_check_eigen.m4
-+++ cufflinks/ax_check_eigen.m4
-@@ -66,7 +66,7 @@
+--- a/ax_check_eigen.m4
++++ b/ax_check_eigen.m4
+@@ -66,7 +66,7 @@ export EIGEN_CPPFLAGS
AC_LANG_PUSH(C++)
AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
@@ -28,9 +28,9 @@ Subject: fix_includes_path.patch
]], [[
]])],[
AC_MSG_RESULT(yes)
---- cufflinks.orig/configure
-+++ cufflinks/configure
-@@ -5674,7 +5674,7 @@
+--- a/configure
++++ b/configure
+@@ -6279,7 +6279,7 @@ cat confdefs.h >>conftest.$ac_ext
cat >>conftest.$ac_ext <<_ACEOF
/* end confdefs.h. */
@@ -39,19 +39,19 @@ Subject: fix_includes_path.patch
int
main ()
---- cufflinks.orig/src/abundances.cpp
-+++ cufflinks/src/abundances.cpp
-@@ -41,7 +41,7 @@
- #include <boost/random/negative_binomial_distribution.hpp>
+--- a/src/abundances.cpp
++++ b/src/abundances.cpp
+@@ -49,7 +49,7 @@
+ #include "negative_binomial_distribution.h"
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
//using Eigen::MatrixXd;
-
---- cufflinks.orig/src/abundances.h
-+++ cufflinks/src/abundances.h
+ //#ifdef __USE_ISOC99
+--- a/src/abundances.h
++++ b/src/abundances.h
@@ -18,7 +18,7 @@
#include <boost/numeric/ublas/matrix.hpp>
#include <boost/numeric/ublas/vector.hpp>
@@ -61,8 +61,8 @@ Subject: fix_includes_path.patch
#include "hits.h"
#include "scaffolds.h"
---- cufflinks.orig/src/jensen_shannon.h
-+++ cufflinks/src/jensen_shannon.h
+--- a/src/jensen_shannon.h
++++ b/src/jensen_shannon.h
@@ -14,7 +14,7 @@
#include <boost/numeric/ublas/io.hpp>
@@ -72,8 +72,8 @@ Subject: fix_includes_path.patch
namespace ublas = boost::numeric::ublas;
---- cufflinks.orig/src/sampling.h
-+++ cufflinks/src/sampling.h
+--- a/src/sampling.h
++++ b/src/sampling.h
@@ -35,7 +35,7 @@
#include <boost/random/variate_generator.hpp>
#include <boost/math/constants/constants.hpp>
diff --git a/debian/patches/0004-fix-m64-usage-and-lfs.patch b/debian/patches/0004-fix-m64-usage-and-lfs.patch
index 14609ac..97f33ae 100644
--- a/debian/patches/0004-fix-m64-usage-and-lfs.patch
+++ b/debian/patches/0004-fix-m64-usage-and-lfs.patch
@@ -4,11 +4,9 @@ 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).
-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 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -69,11 +69,6 @@ case "${host_cpu}-${host_os}" in
i*86-darwin*)
CFLAGS="-m64"
AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
diff --git a/debian/patches/gcc-4.7.patch b/debian/patches/gcc-4.7.patch
deleted file mode 100644
index 63bfaed..0000000
--- a/debian/patches/gcc-4.7.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Mon, 14 May 2012 08:38:03 +0200
-Bug-Debian: http://bugs.debian.org/672744
-Description: Fixes FTBFS with gcc-4.7 by simply
- following the advise given by gcc
-
---- cufflinks-1.3.0.orig/src/lemon/bits/base_extender.h
-+++ cufflinks-1.3.0/src/lemon/bits/base_extender.h
-@@ -359,10 +359,10 @@
- }
-
- Node source(const UEdge& edge) const {
-- return aNode(edge);
-+ return this->aNode(edge);
- }
- Node target(const UEdge& edge) const {
-- return bNode(edge);
-+ return this->bNode(edge);
- }
-
- void firstInc(UEdge& edge, bool& dir, const Node& node) const {
diff --git a/debian/patches/series b/debian/patches/series
index 683174c..bc2b9b1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,4 +2,3 @@
0001-fix_spelling.patch
0002-bam2samtools.patch
0003-fix_includes_path.patch
-gcc-4.7.patch
--
Transcript assembly, differential expression, and differential regulation for RNA-Seq.
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