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authorAvatar Heiko Becker <heirecka@exherbo.org> 2017-05-07 23:02:38 +0200
committerAvatar Heiko Becker <heirecka@exherbo.org> 2017-05-13 11:19:12 +0200
commit41bd471c201dc163c82b53f052a9e839a0bebe91 (patch)
tree1c36ac27c3fc2f5bd63733fa423f9e0429238ab9
parent394727cb27b49599f7e18b9db0d2d0fbd3ce6e40 (diff)
downloadscientific-41bd471c201dc163c82b53f052a9e839a0bebe91.tar.gz
scientific-41bd471c201dc163c82b53f052a9e839a0bebe91.tar.xz
openbabel: Version bump to 2.4.1
This version fixes building against gcc6/7. Change-Id: Ia0fa88b545f8d6d37a57a9f80c463f5f4135c4a4
-rw-r--r--packages/sci-chemistry/openbabel/files/openbabel-2.3.2-CMakeLists.txt-Allow-configuring-BABEL_DATADIR.patch60
-rw-r--r--packages/sci-chemistry/openbabel/files/openbabel-2.3.2-fix-build-with-gcc-5.patch27
-rw-r--r--packages/sci-chemistry/openbabel/files/openbabel-Fix-GCC-version-check-resolves-353.patch27
-rw-r--r--packages/sci-chemistry/openbabel/files/openbabel-cmake.patch23
-rw-r--r--packages/sci-chemistry/openbabel/openbabel-2.4.1.exheres-0 (renamed from packages/sci-chemistry/openbabel/openbabel-2.3.2-r1.exheres-0)12
5 files changed, 36 insertions, 113 deletions
diff --git a/packages/sci-chemistry/openbabel/files/openbabel-2.3.2-CMakeLists.txt-Allow-configuring-BABEL_DATADIR.patch b/packages/sci-chemistry/openbabel/files/openbabel-2.3.2-CMakeLists.txt-Allow-configuring-BABEL_DATADIR.patch
deleted file mode 100644
index 3cb345e..0000000
--- a/packages/sci-chemistry/openbabel/files/openbabel-2.3.2-CMakeLists.txt-Allow-configuring-BABEL_DATADIR.patch
+++ /dev/null
@@ -1,60 +0,0 @@
-Upstream: yes
-
-From 417361bb9f19c78434b067293980085464760c20 Mon Sep 17 00:00:00 2001
-From: Heiko Becker <heirecka@exherbo.org>
-Date: Thu, 2 Apr 2015 15:49:47 +0200
-Subject: [PATCH] CMakeLists.txt: Allow configuring BABEL_DATADIR
-
-This allows installing the architecture independent data outside
-the prefix, for example on a multiarch layout where the prefix
-is /usr/{host-triplet}.
----
- CMakeLists.txt | 4 +++-
- data/CMakeLists.txt | 2 +-
- doc/CMakeLists.txt | 4 ++--
- 3 files changed, 6 insertions(+), 4 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 262cc0b..812f817 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -38,7 +38,9 @@ if(EMBED_OPENBABEL)
- else()
- set(BABEL_VERSION "${BABEL_MAJ_VER}.${BABEL_MIN_VER}.${BABEL_PATCH_VER}")
- endif()
--set(BABEL_DATADIR "${CMAKE_INSTALL_PREFIX}/share/openbabel")
-+set(BABEL_DATAROOTDIR "${CMAKE_INSTALL_PREFIX}/share"
-+ CACHE PATH "Install dir for arch independent data")
-+set(BABEL_DATADIR "${BABEL_DATAROOTDIR}/openbabel")
-
- option(ENABLE_VERSIONED_FORMATS
- "Enable versioning of the format plugin directory" ON)
-diff --git a/data/CMakeLists.txt b/data/CMakeLists.txt
-index 6af378a..1d4450c 100644
---- a/data/CMakeLists.txt
-+++ b/data/CMakeLists.txt
-@@ -52,7 +52,7 @@ set(to_install
- )
-
- if(NOT MSVC)
-- install(FILES ${to_install} DESTINATION share/openbabel/${BABEL_VERSION})
-+ install(FILES ${to_install} DESTINATION "${BABEL_DATADIR}/${BABEL_VERSION}")
- else(NOT MSVC)
- install(FILES ${to_install} DESTINATION bin/data)
- endif(NOT MSVC)
-diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
-index 8cd71f1..9d72ead 100644
---- a/doc/CMakeLists.txt
-+++ b/doc/CMakeLists.txt
-@@ -1,6 +1,6 @@
- file(GLOB man_1 *.1)
--install(FILES ${man_1} DESTINATION share/man/man1)
--install(FILES splash.png DESTINATION share/openbabel/${BABEL_VERSION})
-+install(FILES ${man_1} DESTINATION "${BABEL_DATAROOTDIR}/man/man1")
-+install(FILES splash.png DESTINATION "${BABEL_DATADIR}/${BABEL_VERSION}")
-
- OPTION(BUILD_DOCS "Build Open Babel documentation" OFF)
- IF(BUILD_DOCS)
---
-2.3.3
-
diff --git a/packages/sci-chemistry/openbabel/files/openbabel-2.3.2-fix-build-with-gcc-5.patch b/packages/sci-chemistry/openbabel/files/openbabel-2.3.2-fix-build-with-gcc-5.patch
deleted file mode 100644
index 4db968b..0000000
--- a/packages/sci-chemistry/openbabel/files/openbabel-2.3.2-fix-build-with-gcc-5.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-Upstream: yes, cherry-picked from 04d0fe305c28965cafb252945d4afd23c2b98468
-
-From aab34665d0ed00f99175affc5d7f285a61d85609 Mon Sep 17 00:00:00 2001
-From: David Hall <david@acpharis.com>
-Date: Thu, 12 Feb 2015 08:46:21 -0500
-Subject: [PATCH] GCC5 patch from fedora packager
-
----
- include/openbabel/shared_ptr.h | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/include/openbabel/shared_ptr.h b/include/openbabel/shared_ptr.h
-index 169f8a8..7c79991 100644
---- a/include/openbabel/shared_ptr.h
-+++ b/include/openbabel/shared_ptr.h
-@@ -21,7 +21,7 @@ GNU General Public License for more details.
- #define shared_ptr boost::shared_ptr
- #else
- #include <memory>
-- #if __GNUC__ == 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of Konstantin Tokarev
-+ #if __GNUC__ >= 4 //&& __GNUC_MINOR__ < 3 removed at the suggestion of Konstantin Tokarev
- #include <tr1/memory>
- #endif
- using std::tr1::shared_ptr;
---
-2.3.3
-
diff --git a/packages/sci-chemistry/openbabel/files/openbabel-Fix-GCC-version-check-resolves-353.patch b/packages/sci-chemistry/openbabel/files/openbabel-Fix-GCC-version-check-resolves-353.patch
new file mode 100644
index 0000000..beee318
--- /dev/null
+++ b/packages/sci-chemistry/openbabel/files/openbabel-Fix-GCC-version-check-resolves-353.patch
@@ -0,0 +1,27 @@
+Upstream: yes
+
+From 1bde79933149fb02c2e5b50d3a2f80a82f39c508 Mon Sep 17 00:00:00 2001
+From: Geoff Hutchison <geoff.hutchison@gmail.com>
+Date: Sat, 3 Dec 2016 11:10:00 -0500
+Subject: [PATCH] Fix GCC version check, resolves #353.
+
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 0ee545cf..7f4b944e 100755
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T)
+ # Get the GCC version - from KDE4 cmake files
+ if(CMAKE_COMPILER_IS_GNUCXX)
+ exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
+- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
++ string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
+ # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+ # patch level, handle this here:
+ if (NOT _gcc_version)
+--
+2.12.2
+
diff --git a/packages/sci-chemistry/openbabel/files/openbabel-cmake.patch b/packages/sci-chemistry/openbabel/files/openbabel-cmake.patch
deleted file mode 100644
index aa711e7..0000000
--- a/packages/sci-chemistry/openbabel/files/openbabel-cmake.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Upstream: reported
-Reason: newer cmake versions complain about a duplicated target
-Source: http://sourceforge.net/p/openbabel/bugs/839/
-
-diff -up openbabel-2.3.2/scripts/CMakeLists.txt.cmakepol openbabel-2.3.2/scripts/CMakeLists.txt
---- openbabel-2.3.2/scripts/CMakeLists.txt.cmakepol 2012-10-03 22:08:52.000000000 +0300
-+++ openbabel-2.3.2/scripts/CMakeLists.txt 2013-07-18 10:31:52.295263987 +0300
-@@ -222,15 +222,6 @@ if (DO_PERL_BINDINGS)
- endif (NOT WIN32)
- endif (RUN_SWIG)
-
-- add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp)
-- target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS})
-- set_target_properties(bindings_perl PROPERTIES
-- PREFIX ""
-- OUTPUT_NAME OpenBabel)
-- add_dependencies(bindings_perl openbabel)
-- install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-- install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR})
--
- set(PERL_INSTALLDIRS_TEXT "")
- if (OBPERL_INSTALLDIRS)
- set(PERL_INSTALLDIRS_TEXT "INSTALLDIRS=${OBPERL_INSTALLDIRS}")
diff --git a/packages/sci-chemistry/openbabel/openbabel-2.3.2-r1.exheres-0 b/packages/sci-chemistry/openbabel/openbabel-2.4.1.exheres-0
index 07807b7..04de924 100644
--- a/packages/sci-chemistry/openbabel/openbabel-2.3.2-r1.exheres-0
+++ b/packages/sci-chemistry/openbabel/openbabel-2.4.1.exheres-0
@@ -21,6 +21,7 @@ MYOPTIONS="doc
gui [[ description = [ Build a GUI using wxWidgets ] ]]
java [[ description = [ Adds bindings for Java ] ]]
openmp [[ description = [ Enable parallel processing using OpenMP ] ]]
+ R [[ description = [ Adds bindings for R ] ]]
perl python"
RESTRICT="test" # Tests are still utterly broken (2.3.2)
@@ -49,19 +50,22 @@ DEPENDENCIES="
dev-lang/python:=
dev-lang/swig[>=2.0]
)
+ R? (
+ dev-lang/swig[>=2.0]
+ sci-lang/R
+ )
"
UPSTREAM_RELEASE_NOTES="http://openbabel.org/wiki/Open_Babel_${PV}"
DEFAULT_SRC_PREPARE_PATCHES=(
- "${FILES}"/${PN}-cmake.patch
- "${FILES}"/${PNV}-CMakeLists.txt-Allow-configuring-BABEL_DATADIR.patch
- "${FILES}"/${PNV}-fix-build-with-gcc-5.patch
+ "${FILES}"/${PN}-Fix-GCC-version-check-resolves-353.patch
)
src_configure() {
local cmakeparams=(
-DBABEL_DATAROOTDIR:PATH=/usr/share
+ -DBINDINGS_ONLY:BOOL=FALSE
-DBUILD_EXAMPLES:BOOL=FALSE
-DBUILD_SHARED:BOOL=TRUE
-DCSHARP_BINDINGS:BOOL=FALSE
@@ -71,6 +75,7 @@ src_configure() {
-DINCHI_INCLUDE_DIR=/usr/$(exhost --target)/inchi
-DINCHI_LIBRARY=/usr/$(exhost --target)/lib/libinchi.so.1
-DOPENBABEL_USE_SYSTEM_INCHI:BOOL=TRUE
+ -DPHP_BINDINGS:BOOL=FALSE
# Ruby bindings currently fail to build with ruby:2.2
-DRUBY_BINDINGS:BOOL=FALSE
-DWITH_INCHI:BOOL=TRUE
@@ -81,6 +86,7 @@ src_configure() {
$(cmake_option java JAVA_BINDINGS)
$(cmake_option perl PERL_BINDINGS)
$(cmake_option python PYTHON_BINDINGS)
+ $(cmake_option R R_BINDINGS)
$(expecting_tests -DENABLE_TESTS:BOOL=TRUE -DENABLE_TESTS:BOOL=FALSE)
)