[med-svn] [sra-sdk] 01/01: Adapt to hdf5_serial

[Andreas Tille]

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tille pushed a commit to branch master
in repository sra-sdk.

commit 7c0f4b5542d5e4664d1c70b46f0b84912e73b7c1
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 21 23:39:09 2016 +0200

    Adapt to hdf5_serial
---
 debian/patches/find_ncbi-vdb.patch |  4 ++++
 debian/patches/find_ngs-sdk.patch  |  4 ++++
 debian/patches/lib_hdf5.patch      | 44 ++++++++++++++++++++++++++++++++++++++
 debian/patches/series              |  1 +
 4 files changed, 53 insertions(+)

diff --git a/debian/patches/find_ncbi-vdb.patch b/debian/patches/find_ncbi-vdb.patch
index ab27d40..e3bf52b 100644
--- a/debian/patches/find_ncbi-vdb.patch
+++ b/debian/patches/find_ncbi-vdb.patch
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
+Description: Make sure ncbi-vdb will be found
+
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
 @@ -1301,6 +1301,9 @@ sub find_in_dir {
diff --git a/debian/patches/find_ngs-sdk.patch b/debian/patches/find_ngs-sdk.patch
index 5d770c8..da5b0c5 100644
--- a/debian/patches/find_ngs-sdk.patch
+++ b/debian/patches/find_ngs-sdk.patch
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
+Description: Make sure ngs-sdk will be found
+
 --- a/setup/konfigure.perl
 +++ b/setup/konfigure.perl
 @@ -435,6 +435,7 @@ if ($TOOLS =~ /gcc$/) {
diff --git a/debian/patches/lib_hdf5.patch b/debian/patches/lib_hdf5.patch
new file mode 100644
index 0000000..9d84e52
--- /dev/null
+++ b/debian/patches/lib_hdf5.patch
@@ -0,0 +1,44 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 12 Jul 2016 16:15:32 +0200
+Description: Use hdf5_serial
+
+--- a/libs/hdf5/hdf5arrayfile-priv.h
++++ b/libs/hdf5/hdf5arrayfile-priv.h
+@@ -40,7 +40,7 @@ extern "C" {
+ #endif
+ 
+ #ifndef _HDF5_H
+-#include <hdf5.h>
++#include <hdf5/serial/hdf5.h>
+ #endif
+ 
+ /* object structure */
+@@ -76,4 +76,4 @@ struct HDF5ArrayFile
+ }
+ #endif
+ 
+-#endif /* _h_hdf5arrayfile_priv_ */
+\ No newline at end of file
++#endif /* _h_hdf5arrayfile_priv_ */
+--- a/libs/hdf5/hdf5dir.c
++++ b/libs/hdf5/hdf5dir.c
+@@ -32,7 +32,7 @@ typedef struct HDF5Dir HDF5Dir;
+ 
+ #include <kfs/extern.h> /* may need to be changed */
+ #include <kfs/impl.h>
+-#include <hdf5.h>
++#include <hdf5/serial/hdf5.h>
+ #include <klib/rc.h>
+ #include <klib/namelist.h>
+ #include <klib/text.h>
+--- a/libs/hdf5/Makefile
++++ b/libs/hdf5/Makefile
+@@ -104,7 +104,7 @@ KDF5_OBJ = \
+ 	$(addsuffix .$(LOBX),$(KDF5_SRC))
+ 
+ KDF5_LIB = \
+-	-lhdf5 \
++	-lhdf5_serial \
+ 	-lz \
+ 
+ ifdef HDF5_LIBDIR
diff --git a/debian/patches/series b/debian/patches/series
index 1da8794..67022ca 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ find_hdf5_serial.patch
 find_ngs-sdk.patch
 find_ncbi-vdb.patch
 link_debian_packaged_libz.patch
+lib_hdf5.patch

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