[med-svn] [cufflinks] 03/07: d/patches: refreshed d/changelog: imported new upstream version 2.2.0

Fri Apr 11 18:58:13 UTC 2014

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

commit 27b51c38f643c227de12471178f904648dbdda96
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Fri Apr 11 13:15:40 2014 +0200

     d/patches: refreshed
     d/changelog: imported new upstream version 2.2.0
---
 debian/changelog                                | 10 +++++++
 debian/patches/0001-fix_spelling.patch          | 18 ++++++-------
 debian/patches/0002-bam2samtools.patch          |  6 ++---
 debian/patches/0003-fix_includes_path.patch     | 36 ++++++++++++-------------
 debian/patches/0004-fix-m64-usage-and-lfs.patch |  6 ++---
 5 files changed, 43 insertions(+), 33 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index c6a4f9b..67ba4e2 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+cufflinks (2.2.0-1) UNRELEASED; urgency=medium
+
+  [ James McCoy ]
+  * Move debian/upstream to debian/upstream/metadata
+
+  [ Alexandre Mestiashvili ]
+  * Imported Upstream version 2.2.0
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Fri, 11 Apr 2014 13:12:25 +0200
+
 cufflinks (2.1.1-4) unstable; urgency=low
 
   * Force use boost_system, boost_thread when linking. Fixing FTBFS in
diff --git a/debian/patches/0001-fix_spelling.patch b/debian/patches/0001-fix_spelling.patch
index 31c6756..7efa73c 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(-)
 
---- a/src/locfit/arith.c
-+++ b/src/locfit/arith.c
-@@ -410,7 +410,7 @@ double (*f)();
+--- cufflinks.orig/src/locfit/arith.c
++++ cufflinks/src/locfit/arith.c
+@@ -410,7 +410,7 @@
      INT i;
      if (l==NULL) 
      {
@@ -18,9 +18,9 @@ Subject: fix_spelling
          return NULL;
      }
      v = createvar("_vvec1",STHIDDEN,l->n,VDOUBLE);
---- a/src/locfit/lfd.c
-+++ b/src/locfit/lfd.c
-@@ -78,7 +78,7 @@ INT fp;
+--- cufflinks.orig/src/locfit/lfd.c
++++ cufflinks/src/locfit/lfd.c
+@@ -78,7 +78,7 @@
          }
        }
        if (access("LFData",W_OK)==-1)
@@ -29,9 +29,9 @@ Subject: fix_spelling
          return(0);
        }
      }
---- a/src/abundances.cpp
-+++ b/src/abundances.cpp
-@@ -2901,7 +2901,7 @@ bool AbundanceGroup::calculate_gammas(co
+--- cufflinks.orig/src/abundances.cpp
++++ cufflinks/src/abundances.cpp
+@@ -3132,7 +3132,7 @@
  	
  	vector<double> gammas;
  	
diff --git a/debian/patches/0002-bam2samtools.patch b/debian/patches/0002-bam2samtools.patch
index 2c45845..b1d20fb 100644
--- a/debian/patches/0002-bam2samtools.patch
+++ b/debian/patches/0002-bam2samtools.patch
@@ -6,9 +6,9 @@ Subject: bam2samtools
  ax_bam.m4 |    2 +-
  1 files changed, 1 insertions(+), 1 deletions(-)
 
---- a/ax_bam.m4
-+++ b/ax_bam.m4
-@@ -102,7 +102,7 @@ if test "x$want_bam" = "xyes"; then
+--- cufflinks.orig/ax_bam.m4
++++ cufflinks/ax_bam.m4
+@@ -102,7 +102,7 @@
  
  	AC_LANG_PUSH(C++)
       	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
diff --git a/debian/patches/0003-fix_includes_path.patch b/debian/patches/0003-fix_includes_path.patch
index 4858a1a..c6aa5f9 100644
--- a/debian/patches/0003-fix_includes_path.patch
+++ b/debian/patches/0003-fix_includes_path.patch
@@ -6,9 +6,9 @@ Subject: fix_includes_path.patch
  src/hits.h |    2 +-
  1 files changed, 1 insertions(+), 1 deletions(-)
 
---- a/src/hits.h
-+++ b/src/hits.h
-@@ -16,7 +16,7 @@
+--- cufflinks.orig/src/hits.h
++++ cufflinks/src/hits.h
+@@ -18,7 +18,7 @@
  
  #include <boost/shared_ptr.hpp>
  
@@ -17,9 +17,9 @@ Subject: fix_includes_path.patch
  
  #include "common.h"
  #include "multireads.h"
---- a/ax_check_eigen.m4
-+++ b/ax_check_eigen.m4
-@@ -66,7 +66,7 @@ export EIGEN_CPPFLAGS
+--- cufflinks.orig/ax_check_eigen.m4
++++ cufflinks/ax_check_eigen.m4
+@@ -66,7 +66,7 @@
  
  AC_LANG_PUSH(C++)
  AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
@@ -28,9 +28,9 @@ Subject: fix_includes_path.patch
  ]], [[
  ]])],[
  AC_MSG_RESULT(yes)
---- a/configure
-+++ b/configure
-@@ -6279,7 +6279,7 @@ cat confdefs.h >>conftest.$ac_ext
+--- cufflinks.orig/configure
++++ cufflinks/configure
+@@ -6723,7 +6723,7 @@
  cat >>conftest.$ac_ext <<_ACEOF
  /* end confdefs.h.  */
  
@@ -39,9 +39,9 @@ Subject: fix_includes_path.patch
  
  int
  main ()
---- a/src/abundances.cpp
-+++ b/src/abundances.cpp
-@@ -49,7 +49,7 @@
+--- cufflinks.orig/src/abundances.cpp
++++ cufflinks/src/abundances.cpp
+@@ -50,7 +50,7 @@
  #include "negative_binomial_distribution.h"
  
  
@@ -50,8 +50,8 @@ Subject: fix_includes_path.patch
  //using Eigen::MatrixXd;
  
  //#ifdef  __USE_ISOC99
---- a/src/abundances.h
-+++ b/src/abundances.h
+--- cufflinks.orig/src/abundances.h
++++ cufflinks/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"
---- a/src/jensen_shannon.h
-+++ b/src/jensen_shannon.h
+--- cufflinks.orig/src/jensen_shannon.h
++++ cufflinks/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;
  
---- a/src/sampling.h
-+++ b/src/sampling.h
+--- cufflinks.orig/src/sampling.h
++++ cufflinks/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 97f33ae..8f52a33 100644
--- a/debian/patches/0004-fix-m64-usage-and-lfs.patch
+++ b/debian/patches/0004-fix-m64-usage-and-lfs.patch
@@ -4,9 +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).
 
---- a/configure.ac
-+++ b/configure.ac
-@@ -69,11 +69,6 @@ case "${host_cpu}-${host_os}" in
+--- cufflinks.orig/configure.ac
++++ cufflinks/configure.ac
+@@ -71,11 +71,6 @@
    i*86-darwin*)
  	CFLAGS="-m64"
  	AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;

-- 
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