[med-svn] [fast5] 03/03: Getting 0.6.2 to build binaries.

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a commit to branch master
in repository fast5.

commit c435e524abee308b93415681c215c74a586af289
Author: Steffen Moeller <moeller at 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 <moeller at 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 <afif at 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

-- 
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