Commit 7b9eb571 authored by Andreas Tille's avatar Andreas Tille

New upstream version 2.3.1

parent e1f3f065
This source diff could not be displayed because it is too large. You can view the blob instead.
# CMake script for Bio++ Sequence-Omics library
# Author: Sylvain Gaillard and Julien Dutheil
# Authors:
# Sylvain Gaillard
# Julien Dutheil
# Francois Gindraud (2017)
# Created: 30/07/2012
# Global parameters
CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
PROJECT(bpp-seq-omics CXX)
cmake_minimum_required (VERSION 2.8.11)
project (bpp-seq-omics CXX)
# Compile options
set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
IF(NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
"Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
FORCE)
ENDIF(NOT CMAKE_BUILD_TYPE)
SET(CMAKE_CXX_FLAGS "-Wall -Weffc++ -Wshadow -Wconversion")
IF(NOT NO_VIRTUAL_COV)
SET(NO_VIRTUAL_COV FALSE CACHE BOOL
"Disable covariant return type with virtual inheritance, for compilers that do not support it."
FORCE)
ENDIF(NOT NO_VIRTUAL_COV)
IF(NO_VIRTUAL_COV)
MESSAGE("-- Covariant return with virtual inheritance disabled.")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNO_VIRTUAL_COV=1")
ENDIF(NO_VIRTUAL_COV)
IF(NOT NO_DEP_CHECK)
SET(NO_DEP_CHECK FALSE CACHE BOOL
"Disable dependencies check for building distribution only."
......@@ -41,47 +35,46 @@ ELSE(NO_DEP_CHECK)
# library implements.
# In other words, the library implements all the interface numbers in the
# range from number current - age to current.
SET(BPPSEQOMICS_VERSION_CURRENT "1")
SET(BPPSEQOMICS_VERSION_REVISION "0")
SET(BPPSEQOMICS_VERSION_AGE "0")
SET(${PROJECT_NAME}_VERSION_CURRENT "2")
SET(${PROJECT_NAME}_VERSION_REVISION "0")
SET(${PROJECT_NAME}_VERSION_AGE "0")
# Effective version number computation
math(EXPR BPPSEQOMICS_VERSION_MAJOR "${BPPSEQOMICS_VERSION_CURRENT} - ${BPPSEQOMICS_VERSION_AGE}")
SET(BPPSEQOMICS_VERSION_MINOR ${BPPSEQOMICS_VERSION_AGE})
SET(BPPSEQOMICS_VERSION_PATCH ${BPPSEQOMICS_VERSION_REVISION})
SET(BPPSEQOMICS_VERSION "${BPPSEQOMICS_VERSION_MAJOR}.${BPPSEQOMICS_VERSION_MINOR}.${BPPSEQOMICS_VERSION_PATCH}")
# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
# standard install location
IF(CMAKE_INSTALL_PREFIX)
SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
ENDIF(CMAKE_INSTALL_PREFIX)
MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
#start:
FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find} )
SET(${lib_name}_NAMES ${lib_name} ${lib_name}lib ${lib_name}dll)
FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX})
IF(${lib_name}_LIBRARY)
MESSAGE("-- Library ${lib_name} found here:")
MESSAGE(" includes : ${${lib_name}_INCLUDE_DIR}")
MESSAGE(" libraries: ${${lib_name}_LIBRARY}")
ELSE(${lib_name}_LIBRARY)
MESSAGE(FATAL_ERROR "${lib_name} required but not found.")
ENDIF(${lib_name}_LIBRARY)
#add the dependency:
INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR})
SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY})
ENDMACRO(IMPROVED_FIND_LIBRARY)
#Find the Bio++ libraries:
IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h)
IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h)
# Subdirectories
ADD_SUBDIRECTORY(src)
MATH(EXPR ${PROJECT_NAME}_VERSION_MAJOR "${${PROJECT_NAME}_VERSION_CURRENT} - ${${PROJECT_NAME}_VERSION_AGE}")
SET(${PROJECT_NAME}_VERSION_MINOR ${${PROJECT_NAME}_VERSION_AGE})
SET(${PROJECT_NAME}_VERSION_PATCH ${${PROJECT_NAME}_VERSION_REVISION})
SET(${PROJECT_NAME}_VERSION "${${PROJECT_NAME}_VERSION_MAJOR}.${${PROJECT_NAME}_VERSION_MINOR}.${${PROJECT_NAME}_VERSION_PATCH}")
set (PROJECT_VERSION ${${PROJECT_NAME}_VERSION})
# Find dependencies (add install directory to search)
if (CMAKE_INSTALL_PREFIX)
set (CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
endif (CMAKE_INSTALL_PREFIX)
include (GNUInstallDirs)
find_package (bpp-seq 11.0.0 REQUIRED)
# CMake package
set (cmake-package-location ${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME})
include (CMakePackageConfigHelpers)
configure_package_config_file (
package.cmake.in
${CMAKE_CURRENT_BINARY_DIR}/package.cmake
INSTALL_DESTINATION ${cmake-package-location}
)
write_basic_package_version_file (
${CMAKE_CURRENT_BINARY_DIR}/package-version.cmake
VERSION ${PROJECT_VERSION}
COMPATIBILITY SameMajorVersion
)
install (FILES ${CMAKE_CURRENT_BINARY_DIR}/package.cmake DESTINATION ${cmake-package-location}
RENAME ${PROJECT_NAME}-config.cmake)
install (FILES ${CMAKE_CURRENT_BINARY_DIR}/package-version.cmake DESTINATION ${cmake-package-location}
RENAME ${PROJECT_NAME}-config-version.cmake)
# Define the libraries
add_subdirectory (src)
# Doxygen
FIND_PACKAGE(Doxygen)
......@@ -102,47 +95,22 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
SET(CPACK_PACKAGE_VERSION "2.2.0")
SET(CPACK_PACKAGE_VERSION "2.3.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "2")
SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_VERSION_MINOR "3")
SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence-Omics library")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt")
SET(CPACK_SOURCE_GENERATOR "TGZ")
SET(CPACK_SOURCE_IGNORE_FILES
"CMakeFiles"
"Makefile"
"_CPack_Packages"
"CMakeCache.txt"
".*\\\\.cmake"
".*\\\\.git"
".*\\\\.gz"
".*\\\\.deb"
".*\\\\.rpm"
".*\\\\.dmg"
".*\\\\..*\\\\.swp"
"src/\\\\..*"
"src/libbpp*"
"debian/tmp"
"debian/libbpp.*/"
"debian/libbpp.*\\\\.so.*"
"debian/libbpp.*\\\\.a"
"debian/libbpp.*\\\\.substvars"
"debian/libbpp.*\\\\.debhelper"
"debian/debhelper\\\\.log"
"html"
"Seq.tag"
"Testing"
"build-stamp"
"install_manifest.txt"
"DartConfiguration.tcl"
${CPACK_SOURCE_IGNORE_FILES}
)
IF (MACOS)
SET(CPACK_GENERATOR "Bundle")
ENDIF()
# /!\ This assumes that an external build is used
SET(CPACK_SOURCE_IGNORE_FILES
"/build/"
"/\\\\.git/"
"/\\\\.gitignore"
${CPACK_SOURCE_IGNORE_FILES}
)
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "lib${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig")
......@@ -150,22 +118,9 @@ INCLUDE(CPack)
#This adds the 'dist' target
ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
# 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources:
IF("${CMAKE_GENERATOR}" MATCHES "Make")
ADD_CUSTOM_TARGET(make_clean
COMMAND ${CMAKE_MAKE_PROGRAM} clean
WORKING_DIRECTORY ${CMAKE_CURRENT_DIR}
)
ADD_DEPENDENCIES(dist make_clean)
ENDIF()
IF(NOT NO_DEP_CHECK)
IF (UNIX)
#This creates deb packages:
ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz)
ADD_DEPENDENCIES(origdist dist)
ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
ADD_DEPENDENCIES(deb origdist)
#This creates rpm packages:
ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
......@@ -177,10 +132,11 @@ SET(CTEST_UPDATE_TYPE git)
SET(UPDATE_COMMAND "git")
SET(UPDATE_OPTIONS "")
ENABLE_TESTING()
INCLUDE(CTest)
IF (BUILD_TESTING)
ADD_SUBDIRECTORY(test)
ENDIF(BUILD_TESTING)
# Tests
enable_testing ()
include (CTest)
if (BUILD_TESTING)
add_subdirectory (test)
endif (BUILD_TESTING)
ENDIF(NOT NO_DEP_CHECK)
## This file should be placed in the root directory of your project.
## Then modify the CMakeLists.txt file in the root directory of your
## project to incorporate the testing dashboard.
## # The following are required to uses Dart and the Cdash dashboard
## ENABLE_TESTING()
## INCLUDE(CTest)
set(CTEST_PROJECT_NAME "bpp-seq-omics")
set(CTEST_NIGHTLY_START_TIME "00:00:00 CEST")
set(CTEST_DROP_METHOD "http")
set(CTEST_DROP_SITE "biopp.univ-montp2.fr")
set(CTEST_DROP_LOCATION "/dashboard/submit.php?project=bpp-seq-omics")
set(CTEST_DROP_SITE_CDASH TRUE)
10/05/17 -*- Version 2.3.0 -*-
03/04/17 Julien Dutheil
* VCF export now can export all position, including non-variable ones.
04/07/16 Julien Dutheil
* Alignment filters now allow for relative proportions of gaps.
24/05/16 Julien Dutheil
* Added output for SequenceLDhot.
* Added more statistics in SiteMafStatistics: constant, bi-, tri- and quadriallelic site counts.
26/04/16 Julien Dutheil
* Portage to c++11
* Added RemoveEmptySequencesMafFilter class.
10/02/16 Julien Dutheil
* Fixed bug in AlignmentFilter2: also counts gaps at begining of window!
04/02/16 Julien Dutheil
* Added support for features in BedGraph format.
* Added lift over filter as MafIterator.
08/12/15 Julien Dutheil
* Added Tajima's D computation.
22/11/15 Julien Dutheil
* Fix bug in FeatureFilter when two features are exactly following each other.
23/04/15 Julien Dutheil
* Fix another bug in feature extraction on negative strands.
31/03/15 Julien Dutheil
* OutputAlignments now allows to discard coordinates in output.
13/01/15 Julien Dutheil
* OutputAlignments can now use coordinates of ref species infile names.
07/01/15 Julien Dutheil
* Added export filter for MSMC.
22/09/14 -*- Version 2.2.0 -*-
22/08/13 Julien Dutheil
......
This source diff could not be displayed because it is too large. You can view the blob instead.
This software needs cmake >= 2.6 to build.
This software needs cmake >= 2.8.11 and a C++11 capable compiler to build
After installing cmake, run it with the following command:
cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
$ cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
If available, you can also use ccmake instead of cmake for a more user-friendly interface.
Then compile and install the software with
make install
Then compile and install the software with:
$ make install
You may also consider installing and using the software checkinstall for easier system administration.
If you install Bio++ in a non standard path (not /usr/), remember that:
-> if you compile your project with CMake, give it the path with -DCMAKE_PREFIX_PATH=<path>
-> if you compile with something else, give the path to the compiler (-I / -L options)
-> if you use shared libraries, you must also tell programs where to find them at startup:
-> either by adding the path to LD_LIBRARY_PATH environment variable.
-> or by using RPATHs to hard code the path in the executable (generates NON PORTABLE executables !)
-> with CMake, see documentation in bpp-core/cmake/project-template
-> or see your compiler documentation ("-Wl,-rpath,<path>" for clang/gcc)
-> consider installing Bio++ with the "-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE" option
Detailed documentation for using Bio++ with CMake are available in bpp-core/cmake/
%define _basename bpp-seq-omics
%define _version 2.2.0
%define _version 2.3.1
%define _release 1
%define _prefix /usr
......@@ -17,11 +17,11 @@ Requires: bpp-core = %{_version}
Requires: bpp-seq = %{_version}
BuildRoot: %{_builddir}/%{_basename}-root
BuildRequires: cmake >= 2.6.0
BuildRequires: gcc-c++ >= 4.0.0
BuildRequires: libbpp-core2 = %{_version}
BuildRequires: cmake >= 2.8.11
BuildRequires: gcc-c++ >= 4.7.0
BuildRequires: libbpp-core3 = %{_version}
BuildRequires: libbpp-core-devel = %{_version}
BuildRequires: libbpp-seq9 = %{_version}
BuildRequires: libbpp-seq11 = %{_version}
BuildRequires: libbpp-seq-devel = %{_version}
AutoReq: yes
......@@ -31,21 +31,21 @@ AutoProv: yes
This library contains the genomics components of the Bio++ sequence library.
It is part of the Bio++ project.
%package -n libbpp-seq-omics1
%package -n libbpp-seq-omics2
Summary: Bio++ Sequence library: genomics components
Group: Development/Libraries/C and C++
%description -n libbpp-seq-omics1
%description -n libbpp-seq-omics2
This library contains the genomics components of the Bio++ sequence library.
It is part of the Bio++ project.
%package -n libbpp-seq-omics-devel
Summary: Bio++ Sequence library: genomics components
Group: Development/Libraries/C and C++
Requires: libbpp-seq-omics1 = %{_version}
Requires: libbpp-seq9 = %{_version}
Requires: libbpp-seq-omics2 = %{_version}
Requires: libbpp-seq11 = %{_version}
Requires: libbpp-seq-devel = %{_version}
Requires: libbpp-core2 = %{_version}
Requires: libbpp-core3 = %{_version}
Requires: libbpp-core-devel = %{_version}
%description -n libbpp-seq-omics-devel
......@@ -58,9 +58,6 @@ building applications which use %{_basename}.
%build
CFLAGS="$RPM_OPT_FLAGS"
CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DBUILD_TESTING=OFF"
if [ %{_lib} == 'lib64' ] ; then
CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64"
fi
cmake $CMAKE_FLAGS .
make
......@@ -70,103 +67,11 @@ make DESTDIR=$RPM_BUILD_ROOT install
%clean
rm -rf $RPM_BUILD_ROOT
%post -n libbpp-seq-omics1 -p /sbin/ldconfig
%post -n libbpp-seq-omics-devel
createGeneric() {
echo "-- Creating generic include file: $1.all"
#Make sure we run into subdirectories first:
dirs=()
for file in "$1"/*
do
if [ -d "$file" ]
then
# Recursion:
dirs+=( "$file" )
fi
done
for dir in ${dirs[@]}
do
createGeneric $dir
done
#Now list all files, including newly created .all files:
if [ -f $1.all ]
then
rm $1.all
fi
dir=`basename $1`
for file in "$1"/*
do
if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
then
file=`basename $file`
echo "#include \"$dir/$file\"" >> $1.all
fi
done;
}
# Actualize .all files
createGeneric %{_prefix}/include/Bpp
exit 0
%preun -n libbpp-seq-omics-devel
removeGeneric() {
if [ -f $1.all ]
then
echo "-- Remove generic include file: $1.all"
rm $1.all
fi
for file in "$1"/*
do
if [ -d "$file" ]
then
# Recursion:
removeGeneric $file
fi
done
}
# Actualize .all files
removeGeneric %{_prefix}/include/Bpp
exit 0
%postun -n libbpp-seq-omics1 -p /sbin/ldconfig
%postun -n libbpp-seq-omics-devel
createGeneric() {
echo "-- Creating generic include file: $1.all"
#Make sure we run into subdirectories first:
dirs=()
for file in "$1"/*
do
if [ -d "$file" ]
then
# Recursion:
dirs+=( "$file" )
fi
done
for dir in ${dirs[@]}
do
createGeneric $dir
done
#Now list all files, including newly created .all files:
if [ -f $1.all ]
then
rm $1.all
fi
dir=`basename $1`
for file in "$1"/*
do
if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
then
file=`basename $file`
echo "#include \"$dir/$file\"" >> $1.all
fi
done;
}
# Actualize .all files
createGeneric %{_prefix}/include/Bpp
exit 0
%files -n libbpp-seq-omics1
%post -n libbpp-seq-omics2 -p /sbin/ldconfig
%postun -n libbpp-seq-omics2 -p /sbin/ldconfig
%files -n libbpp-seq-omics2
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
%{_prefix}/%{_lib}/lib*.so.*
......@@ -174,11 +79,23 @@ exit 0
%files -n libbpp-seq-omics-devel
%defattr(-,root,root)
%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
%dir %{_prefix}/%{_lib}/cmake/
%dir %{_prefix}/%{_lib}/cmake/bpp-seq-omics
%{_prefix}/%{_lib}/lib*.so
%{_prefix}/%{_lib}/lib*.a
%{_prefix}/%{_lib}/cmake/bpp-seq-omics/bpp-seq-omics*.cmake
%{_prefix}/include/*
%changelog
* Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
- Increased interface number
* Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1
- Several bugs fixed and performance improvements
- New Maf filters: LiftOver, RemoveEmptySequence
- Support for BED features input
- New output options: MSMC, PLINK
- More options for Vcf and Alignment output
- Upgrade to C++11
* Mon Sep 22 2014 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.2.0-1
- New statistics, including sequence diversity estimators
- Several bugs and memory leaks fixed.
......
libbpp-seq-omics (2.2.0-1) unstable; urgency=low
* New statistics, including sequence diversity estimators
* Several bugs and memory leaks fixed.
-- Julien Dutheil <julien.dutheil@univ-montp2.fr> Mon, 22 Sep 2014 14:00:00 +0100
libbpp-seq-omics (2.1.0-1) unstable; urgency=low
* Maf to VCF tool added as a MafIterator.
-- Julien Dutheil <julien.dutheil@univ-montp2.fr> Wed, 06 Mar 2013 14:34:00 +0100
libbpp-seq-omics (2.0.3-1) unstable; urgency=low
* Initial release, forking from bpp-seq.
-- Julien Dutheil <julien.dutheil@univ-montp2.fr> Tue, 06 Nov 2012 14:05:00 +0100
Source: libbpp-seq-omics
Section: libs
Priority: optional
Maintainer: Loic Dachary <loic@dachary.org>
Uploaders: Julien Dutheil <julien.dutheil@univ-montp2.fr>
Build-Depends: debhelper (>= 5), cmake (>= 2.6),
libbpp-seq-dev (>= 2.2.0)
Standards-Version: 3.9.4
Package: libbpp-seq-omics-dev
Section: libdevel
Architecture: any
Depends: libbpp-seq-omics1 (= ${binary:Version}), ${misc:Depends},
libbpp-seq-dev (>= 2.2.0)
Description: Bio++ Sequence library: genomics components.
Contains the Bio++ sequence classes dedicated to genomics.
Package: libbpp-seq-omics1
Section: libs
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends},
libbpp-seq9 (>= 2.2.0)
Description: Bio++ Sequence library: genomics components.
Contains the Bio++ sequence classes dedicated to genomics.
This package was debianized by Julien Dutheil <julien.dutheil@univ-montp2.fr> on
Wed, 22 Sep 2014 14:00:00 +0100.
It was downloaded from <http://biopp.univ-montp2.fr/Repositories/sources>
Upstream Author:
Julien Dutheil <julien.dutheil@univ-montp2.fr>
Copyright:
Copyright (C) 2014 Bio++ Development Team
License:
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL'.
The Debian packaging is (C) 2014, Julien Dutheil <julien.dutheil@univ-montp2.fr> and
is licensed under the GPL, see above.
The provided software is distributed under the CeCILL license:
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
The complete text of the license may be found here:
http://www.cecill.info/licences/Licence_CeCILL_V2-en.html
debian/tmp/usr/include/*
debian/tmp/usr/lib/lib*.a
debian/tmp/usr/lib/lib*.so
debian/tmp/usr/lib/lib*.so.*
#! /bin/bash
# Abort if any command returns an error value
set -e
createGeneric() {
echo "-- Creating generic include file: $1.all"
#Make sure we run into subdirectories first:
dirs=()
for file in "$1"/*
do
if [ -d "$file" ]
then
# Recursion:
dirs+=( "$file" )
fi
done
for dir in ${dirs[@]}
do
createGeneric $dir
done
#Now list all files, including newly created .all files:
if [ -f $1.all ]
then
rm $1.all
fi
dir=`basename $1`
for file in "$1"/*
do
if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
then
file=`basename $file`
echo "#include \"$dir/$file\"" >> $1.all
fi
done;
}
case "$1" in
configure)
# Actualize .all files
createGeneric /usr/include/Bpp
;;
abort-upgrade|abort-remove|abort-deconfigure)
echo "$1"
;;
*)
echo "postinst called with unknown argument \`\$1'" >&2
exit 0
;;
esac
# dh_installdeb will replace this with shell code automatically
# generated by other debhelper scripts.
#DEBHELPER#
exit 0
#! /bin/bash
# Abort if any command returns an error value
set -e
createGeneric() {
echo "-- Creating generic include file: $1.all"
#Make sure we run into subdirectories first:
dirs=()
for file in "$1"/*
do
if [ -d "$file" ]
then
# Recursion:
dirs+=( "$file" )
fi
done
for dir in ${dirs[@]}
do
createGeneric $dir
done
#Now list all files, including newly created .all files:
if [ -f $1.all ]
then
rm $1.all
fi
dir=`basename $1`
for file in "$1"/*
do
if [ -f "$file" ] && ( [ "${file##*.}" == "h" ] || [ "${file##*.}" == "all" ] )
then
file=`basename $file`
echo "#include \"$dir/$file\"" >> $1.all
fi
done;
}
case "$1" in
remove)
# Automatically added by dh_makeshlibs
ldconfig
# Actualize .all files
createGeneric /usr/include/Bpp
;;
purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
echo $1
;;
*)
echo "postrm called with unknown argument \`\$1'" >&2
exit 0
;;
esac
# dh_installdeb will replace this with shell code automatically
# generated by other debhelper scripts.
#DEBHELPER#
exit 0
#! /bin/bash
# Abort if any command returns an error value
set -e