This is an automated email from the git hooks/post-receive script. malex-guest pushed a commit to branch master in repository cufflinks.
commit 27b51c38f643c227de12471178f904648dbdda96 Author: Alexandre Mestiashvili <[email protected]> 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 <[email protected]> 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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