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commit c435e524abee308b93415681c215c74a586af289 Author: Steffen Moeller <moel...@debian.org> Date: Fri Sep 15 14:17:53 2017 +0200 Getting 0.6.2 to build binaries. --- debian/changelog | 14 ++++++++++++++ debian/patches/functional.patch | 12 ++++++++++++ debian/patches/hdf5include.patch | 13 +++++++++++++ debian/patches/rpath.patch | 22 +++++++++++----------- debian/patches/series | 6 ++++-- debian/rules | 2 ++ 6 files changed, 56 insertions(+), 13 deletions(-) diff --git a/debian/changelog b/debian/changelog index b35768f..4a34d20 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,17 @@ +fast5 (0.6.2-1) UNRELEASED; urgency=medium + + * Team upload. + * New upstream version. + * Updated policy to 4.1.0 (no changes reguired) + * Patches + - Uncommented two older patches that do not seem to fit current + build structure + - Added patch for gcc-7 compatibility + - Added patch to adjusted include path for hdf5.h + * ./debian/rules binary works, still trouble with generated files + + -- Steffen Moeller <moel...@debian.org> Fri, 15 Sep 2017 13:46:49 +0200 + fast5 (0.5.9-1) UNRELEASED; urgency=medium * Imported Upstream version 0.5.9 diff --git a/debian/patches/functional.patch b/debian/patches/functional.patch new file mode 100644 index 0000000..bca2b63 --- /dev/null +++ b/debian/patches/functional.patch @@ -0,0 +1,12 @@ +Index: fast5/src/logger.hpp +=================================================================== +--- fast5.orig/src/logger.hpp ++++ fast5/src/logger.hpp +@@ -72,6 +72,7 @@ + #include <iostream> + #include <mutex> + #include <stdexcept> ++#include <functional> + + namespace logger + { diff --git a/debian/patches/hdf5include.patch b/debian/patches/hdf5include.patch new file mode 100644 index 0000000..6dd31ea --- /dev/null +++ b/debian/patches/hdf5include.patch @@ -0,0 +1,13 @@ +Index: fast5/src/hdf5_tools.hpp +=================================================================== +--- fast5.orig/src/hdf5_tools.hpp ++++ fast5/src/hdf5_tools.hpp +@@ -27,7 +27,7 @@ + + namespace hdf5 + { +-#include <hdf5.h> ++#include <hdf5/serial/hdf5.h> + } + + namespace hdf5_tools diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch index 94fe9e7..0bd2438 100644 --- a/debian/patches/rpath.patch +++ b/debian/patches/rpath.patch @@ -2,16 +2,16 @@ Description: Don't set RPATH for compiled Python extensions Author: Afif Elghraoui <a...@debian.org> Forwarded: not-needed Last-Update: 2016-10-20 +Index: fast5/python/setup.py +=================================================================== --- fast5.orig/python/setup.py +++ fast5/python/setup.py -@@ -69,10 +69,6 @@ - hdf5_lib_dir, - boost_lib_dir, - ], -- runtime_library_dirs=[ -- hdf5_lib_dir, -- boost_lib_dir, -- ], - libraries=[ - hdf5_lib, - boost_python_lib, +@@ -53,7 +53,7 @@ extensions = [ + sources=['fast5/fast5.' + ['cpp', 'pyx'][use_cython]], + include_dirs=[fast5_src_dir], + library_dirs=[hdf5_lib_dir], +- runtime_library_dirs=[hdf5_lib_dir], ++ #runtime_library_dirs=[hdf5_lib_dir], + libraries=[hdf5_lib], + extra_compile_args=extra_compile_args, + extra_link_args=extra_link_args, diff --git a/debian/patches/series b/debian/patches/series index 7dc224e..2f38c1c 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,5 @@ -relative-paths.patch -examples.patch +#relative-paths.patch +#examples.patch rpath.patch +functional.patch +hdf5include.patch diff --git a/debian/rules b/debian/rules index f8f630d..e517f10 100755 --- a/debian/rules +++ b/debian/rules @@ -10,6 +10,8 @@ export HDF5_INCLUDE_DIR=/usr/include/hdf5/serial export HDF5_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial export BOOST_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH) +export CXXFLAGS += -std=c++11 + %: dh $@ --with python2,python3 --buildsystem=pybuild \ --sourcedirectory=python -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fast5.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit