[med-svn] [gatb-core] 02/05: Build-Depends: libcppunit-dev, libhdf5-dev; try to use Debian packaged hdf5

[Andreas Tille]

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

commit 70cf3c9305b72d99250ab0fc715583eea83552d1
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 28 10:17:22 2017 +0100

    Build-Depends: libcppunit-dev, libhdf5-dev; try to use Debian packaged hdf5
---
 debian/changelog                              |  2 +-
 debian/control                                |  7 ++--
 debian/patches/series                         |  1 +
 debian/patches/use_debian_packaged_hdf5.patch | 52 +++++++++++++++++++++++++++
 4 files changed, 59 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index c25e28b..40cf6bd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,4 +2,4 @@ gatb-core (1.3.0+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #873044)  
 
- -- Nadiya Sitdykova <rovenskasa at gmail.com>  Wed, 23 Aug 2017 23:59:46 -0400
+ -- Andreas Tille <tille at debian.org>  Tue, 28 Nov 2017 10:37:22 +0100
diff --git a/debian/control b/debian/control
index 7c16b7d..4c00595 100644
--- a/debian/control
+++ b/debian/control
@@ -1,10 +1,13 @@
 Source: gatb-core
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Nadiya Sitdykova <rovenskasa at gmail.com>
+Uploaders: Nadiya Sitdykova <rovenskasa at gmail.com>,
+           Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
-               cmake
+               cmake,
+               libcppunit-dev,
+               libhdf5-dev
 Standards-Version: 4.1.1
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/gatb-core.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/gatb-core.git
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..f8768ac
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_hdf5.patch
diff --git a/debian/patches/use_debian_packaged_hdf5.patch b/debian/patches/use_debian_packaged_hdf5.patch
new file mode 100644
index 0000000..c0cafef
--- /dev/null
+++ b/debian/patches/use_debian_packaged_hdf5.patch
@@ -0,0 +1,52 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 28 Nov 2017 10:37:22 +0100
+Description: Use Debian packaged hdf5
+
+--- a/gatb-core/thirdparty/CMakeLists.txt
++++ b/gatb-core/thirdparty/CMakeLists.txt
+@@ -5,6 +5,8 @@
+ #SET (HDF5_ENABLE_THREADSAFE       ON)
+ #SET (H5_HAVE_THREADSAFE 1)
+ 
++FIND_PACKAGE(HDF5 COMPONENTS C REQUIRED)
++
+ ##########  MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED  ##########
+ SET (HDF5_BUILD_TOOLS             ON CACHE BOOL "Build HDF5 Tools")
+ #SET (CMAKE_EXE_LINKER_FLAGS       "-lpthread -lz")
+@@ -16,9 +18,9 @@ SET (HDF5_EXTERNALLY_CONFIGURED     ON)
+ SET (HDF5_INSTALL_BIN_DIR           bin)
+ SET (HDF5_INSTALL_LIB_DIR           lib)
+ 
+-SET (HDF5_INSTALL_INCLUDE_DIR       ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5)
+-SET (HDF5_INSTALL_DATA_DIR          ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
+-SET (HDF5_INSTALL_CMAKE_DIR         ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE})
++SET (HDF5_INSTALL_INCLUDE_DIR       /usr/include/${CMAKE_BUILD_TYPE}/hdf5)
++SET (HDF5_INSTALL_DATA_DIR          /usr/share/${CMAKE_BUILD_TYPE})
++SET (HDF5_INSTALL_CMAKE_DIR         /usr/share/${CMAKE_BUILD_TYPE})
+ 
+ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE)
+     SET (HDF5_EXPORTED_TARGETS          "gatb-hdf5")
+@@ -32,23 +34,6 @@ ENDIF()
+ set (COMPILE_DEFINITIONS  "${COMPILE_DEFINITIONS}  -w")
+ add_definitions (${COMPILE_DEFINITIONS})
+ 
+-# add HDF5 generation
+-ADD_SUBDIRECTORY (hdf5)
+-
+-# We add a custom target for copying header files.
+-add_custom_target (hdf5_postbuild ALL)
+-
+-# We build the output directory
+-add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR})
+-
+-# We define all the header files to be copied
+-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h)
+-
+-# We copy each header file
+-foreach (header ${headerfiles})
+-  add_custom_command (TARGET hdf5_postbuild POST_BUILD  COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR}  )
+-endforeach()
+-
+ # include other smaller libraries (json, Boophf)
+ 
+ add_custom_target (thirdparty_copy ALL)

-- 
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