[med-svn] [gatb-core] 01/03: Fix hdf5 includes

[Andreas Tille]

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tille pushed a commit to branch master
in repository gatb-core.

commit 3a669c4b39cca7f81f04f920ea39ef3624d3e138
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 28 22:11:29 2017 +0100

    Fix hdf5 includes
---
 debian/patches/fix_hdf5_includes.patch | 126 +++++++++++++++++++++++++++++++++
 debian/patches/series                  |   1 +
 2 files changed, 127 insertions(+)

diff --git a/debian/patches/fix_hdf5_includes.patch b/debian/patches/fix_hdf5_includes.patch
new file mode 100644
index 0000000..56110cd
--- /dev/null
+++ b/debian/patches/fix_hdf5_includes.patch
@@ -0,0 +1,126 @@
+Author: Christian Seiler <christian at iwakd.de>
+Last-Update: Tue, 28 Nov 2017 22:00:48 +0100
+Description: Fix hdf5 includes.
+  --> https://lists.debian.org/debian-mentors/2017/11/msg00227.html
+
+--- a/gatb-core/src/gatb/tools/math/LargeInt.hpp
++++ b/gatb-core/src/gatb/tools/math/LargeInt.hpp
+@@ -35,7 +35,7 @@
+ #include <stdint.h>
+ #include <algorithm>
+ #include <iostream>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ #include <gatb/system/api/Exception.hpp>
+ #include <gatb/system/api/config.hpp>
+--- a/gatb-core/src/gatb/tools/math/NativeInt128.hpp
++++ b/gatb-core/src/gatb/tools/math/NativeInt128.hpp
+@@ -33,7 +33,7 @@
+ /********************************************************************************/
+ 
+ #include <iostream>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+--- a/gatb-core/src/gatb/tools/math/NativeInt16.hpp
++++ b/gatb-core/src/gatb/tools/math/NativeInt16.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+--- a/gatb-core/src/gatb/tools/math/NativeInt32.hpp
++++ b/gatb-core/src/gatb/tools/math/NativeInt32.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+--- a/gatb-core/src/gatb/tools/math/NativeInt64.hpp
++++ b/gatb-core/src/gatb/tools/math/NativeInt64.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ extern const unsigned char revcomp_4NT[];
+ extern const unsigned char comp_NT    [];
+--- a/gatb-core/src/gatb/tools/math/NativeInt8.hpp
++++ b/gatb-core/src/gatb/tools/math/NativeInt8.hpp
+@@ -31,7 +31,7 @@
+ #include <iostream>
+ #include <gatb/system/api/types.hpp>
+ #include <gatb/tools/misc/api/Abundance.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb  {
+--- a/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
++++ b/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
+@@ -31,7 +31,7 @@
+ /********************************************************************************/
+ 
+ #include <sys/types.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+--- a/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
++++ b/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
+@@ -28,7 +28,7 @@
+ 
+ #include <gatb/system/api/ISmartPointer.hpp>
+ #include <gatb/tools/storage/impl/Storage.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+--- a/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
++++ b/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+--- a/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
++++ b/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
+@@ -40,7 +40,7 @@
+ #include <string>
+ #include <vector>
+ #include <stdarg.h>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ 
+ /********************************************************************************/
+ namespace gatb      {
+--- a/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
++++ b/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
+@@ -33,7 +33,7 @@
+ #include <gatb/tools/storage/impl/CollectionHDF5.hpp>
+ #include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp>
+ #include <gatb/system/impl/System.hpp>
+-#include <hdf5/hdf5.h>
++#include <hdf5.h>
+ #include <sstream>
+ 
+ /********************************************************************************/
diff --git a/debian/patches/series b/debian/patches/series
index f8768ac..8f6d780 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 use_debian_packaged_hdf5.patch
+fix_hdf5_includes.patch

-- 
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