debian/changelog

@@ -12,6 +12,7 @@ minia (3.2.0-1) UNRELEASED; urgency=medium
   * Remove trailing whitespace in debian/copyright
   * Build-Depends: libboost-dev, libhdf5-dev
   * Versioned Build-Depends: libgatbcore-dev (>= 1.4.1+git20181225.44d5a44~)
+  * Do not set rpath
 
  -- Andreas Tille <tille@debian.org>  Mon, 21 Jan 2019 09:01:19 +0100
 

debian/copyright

@@ -2,35 +2,6 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: minia
 Source: http://minia.genouest.org
 
-Files: ttmath/*
-Copyright: Tomasz Sowa <t.sowa@ttmath.org>
-License: BSD-3-clause
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
-  * Redistributions of source code must retain the above copyright notice,
-    this list of conditions and the following disclaimer.
- .
-  * Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
- .
-  * Neither the name Tomasz Sowa nor the names of contributors to this
-    project may be used to endorse or promote products derived
-    from this software without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
- LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
- THE POSSIBILITY OF SUCH DAMAGE.
-
 Files: *
 Copyright: 2012 Rayan Chiki <rayan.chikhi@ens-cachan.org>
            2012 Guillaume Rizk
@@ -354,7 +325,7 @@ License: CeCILL
  terms  and  conditions  of  such  technical  assistance,  and/or   such
  maintenance, shall then be set forth in  a  separate  instrument.  Only  the
  Licensor offering said  maintenance  and/or  technical  assistance  services
- shall incur liability therefor.
+ shall incur liability therefore.
  .
  7.2. Similarly, any or all Licensor  shall  be  entitled  to  offer  to  its
  Licensees, under its own responsibility, a  warranty,  that  shall  only  be
@@ -532,6 +503,7 @@ License: CeCILL
 
 Files: debian/*
 Copyright: 2013 Olivier Sallou <osallou@debian.org>
+           2016-2019 Andreas Tille <tille@debian.org>
 License: GPL-2+
  The Debian packaging is licensed under the GPL which is available at
  `/usr/share/common-licenses/GPL-2'.

debian/docs

 debian/README.test
 debian/tests/run-unit-test
-test/read50x_ref10K_e001.fa*
-
+test
+README*

debian/install

+obj-*/bin	usr

debian/patches/no_install_to_wrong_dir.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Failed to fix these install dirs, deactivate completely and use dh_install
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -121,9 +121,9 @@ SET (CPACK_SOURCE_IGNORE_FILES
+ )
+ 
+ # We copy the project binary to the 'bin' directory
+-INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
+-INSTALL (DIRECTORY "${PROJECT_SOURCE_DIR}/test/" DESTINATION test)
+-INSTALL (FILES LICENSE README.md DESTINATION bin/..)
++#INSTALL (TARGETS ${PROJECT_NAME} DESTINATION bin)
++#INSTALL (DIRECTORY "${PROJECT_SOURCE_DIR}/test/" DESTINATION test)
++#INSTALL (FILES LICENSE README.md DESTINATION bin/..)
+ 
+ # We include the "bin" tag into binary archive file name
+ set (CPACK_PACKAGE_FILE_NAME  ${PROJECT_NAME}-${CPACK_PACKAGE_VERSION}-bin-${CMAKE_SYSTEM_NAME})

debian/patches/series

 use_debian_packaged_gatb-core.patch
 link_libraries.patch
+no_install_to_wrong_dir.patch
+skip-rpath.patch

debian/patches/skip-rpath.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Jan 2019 09:01:19 +0100
+Description: Do not set rpath
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -75,6 +75,7 @@ file (GLOB_RECURSE  ProjectFiles  ${PROG
+ include(GNUInstallDirs)
+ LINK_DIRECTORIES( /usr/${CMAKE_INSTALL_LIBDIR}/hdf5/serial )
+ add_executable(${PROJECT_NAME} ${ProjectFiles})
++set_target_properties(${PROJECT_NAME} PROPERTIES SKIP_BUILD_RPATH TRUE)
+ target_link_libraries(${PROJECT_NAME} gatbcore hdf5 )
+ 
+ # merci
+@@ -82,6 +83,7 @@ set (MERCI_SOURCE_DIR ${PROJECT_SOURCE_D
+ include_directories (${MERCI_SOURCE_DIR})
+ file (GLOB_RECURSE  MerciFiles  ${MERCI_SOURCE_DIR}/*.cpp)
+ add_executable("merci"  ${MerciFiles})
++set_target_properties("merci" PROPERTIES SKIP_BUILD_RPATH TRUE)
+ target_link_libraries("merci" gatbcore hdf5 )
+ 
+