[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/, sci-chemistry/openbabel/files/
commit: 4a0dcf6b2ab6b2bc5725cc51b813bfa478bee3cf
Author: Sam James gentoo org>
AuthorDate: Sun Jun 12 10:26:07 2022 +
Commit: Sam James gentoo org>
CommitDate: Sun Jun 12 10:36:25 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4a0dcf6b
sci-chemistry/openbabel: fix build with GCC 12
Closes: https://bugs.gentoo.org/851510
Signed-off-by: Sam James gentoo.org>
.../openbabel-3.1.1-fix-time-check-cmake.patch | 32 ++
.../openbabel/openbabel-3.1.1_p20210225.ebuild | 4 +++
2 files changed, 36 insertions(+)
diff --git
a/sci-chemistry/openbabel/files/openbabel-3.1.1-fix-time-check-cmake.patch
b/sci-chemistry/openbabel/files/openbabel-3.1.1-fix-time-check-cmake.patch
new file mode 100644
index ..69e41211023b
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.1.1-fix-time-check-cmake.patch
@@ -0,0 +1,32 @@
+https://github.com/openbabel/openbabel/pull/2493
+
+From: Sam James
+Date: Sun, 12 Jun 2022 11:23:59 +0100
+Subject: [PATCH] CMake: fix time check typo (fixes build failure w/ GCC 12)
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Without this fixed check, we get a build failure with GCC 12:
+```
+/var/tmp/portage/sci-chemistry/openbabel-3.1.1_p20210225/work/openbabel-08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b/include/openbabel/obutil.h:65:14:
error: ‘clock’ was not declared in this scope; did you mean ‘clock_t’?
+ 65 | start= clock();
+ | ^
+ | clock_t
+```
+
+Bug: https://bugs.gentoo.org/851510
+--- a/src/config.h.cmake
b/src/config.h.cmake
+@@ -182,8 +182,8 @@
+ #define OB_MODULE_PATH "@OB_MODULE_PATH@"
+
+ #ifndef TIME_WITH_SYS_TIME
+- #ifdef HAVE_SYS_TIME
+-#ifdef HAVE_TIME
++ #ifdef HAVE_SYS_TIME_H
++#ifdef HAVE_TIME_H
+ #define TIME_WITH_SYS_TIME 1
+ #else
+ #define TIME_WITH_SYS_TIME 0
+
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
index 61a6ad498b66..0eb8ddaa0cf5 100644
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
+++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20210225.ebuild
@@ -80,6 +80,10 @@ RDEPEND="
)
"
+PATCHES=(
+ "${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
+)
+
pkg_pretend() {
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
}
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/, sci-chemistry/openbabel/files/
commit: e4d21e84be5fb16ae0d7f9bee7f7ab33fcb93eee
Author: Peter Levine gmail com>
AuthorDate: Sun Mar 21 07:54:12 2021 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Wed Dec 15 10:09:01 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4d21e84
sci-chemistry/openbabel: Add openbabel-
Add an up-to-date live ebuild with a templated versioning scheme,
and match the bindings to USE flags.
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Peter Levine gmail.com>
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-chemistry/openbabel/Manifest | 1 +
.../openbabel/files/openbabel-python.cmake | 104
sci-chemistry/openbabel/metadata.xml | 4 +
sci-chemistry/openbabel/openbabel-.ebuild | 272 +
4 files changed, 381 insertions(+)
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index b22751d4a860..ac334bea30ea 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,2 +1,3 @@
DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B
8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125
SHA512
427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
+DIST openbabel.jpg 12159 BLAKE2B
b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7
SHA512
998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0
DIST openbabel.png 29060 BLAKE2B
8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3
SHA512
bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
diff --git a/sci-chemistry/openbabel/files/openbabel-python.cmake
b/sci-chemistry/openbabel/files/openbabel-python.cmake
new file mode 100644
index ..425b4656a9d2
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-python.cmake
@@ -0,0 +1,104 @@
+# The following is a cmake fragment taken from scripts/CMakeLists.txt and
+# edited for Gentoo python multibuild compatibility.
+
+if (PYTHON_BINDINGS)
+ # Tags should be edited to reflect the active python implementation
+ set(EPYTHON @@EPYTHON@@)
+ set(PYTHON_INCUDE_DIR @@PYTHON_INCUDE_DIR@@)
+ set(PYTHON_LIBS @@PYTHON_LIBS@@)
+ set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@)
+
+ include_directories(${PYTHON_INCUDE_DIR})
+
+ add_custom_command(
+ OUTPUT
${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp
${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
+ COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O
-templatereduce -naturalvar -I${CMAKE_SOURCE_DIR}/include
-I${CMAKE_BINARY_DIR}/include -o
${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define}
-outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}
${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i
+ MAIN_DEPENDENCY openbabel-python.i
+ VERBATIM
+ )
+
+
configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
+ ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py)
+
+ add_library(bindings_python_${EPYTHON} MODULE
${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp)
+ target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS}
${BABEL_LIBRARY})
+
+ set_target_properties(bindings_python_${EPYTHON}
+ PROPERTIES
+ OUTPUT_NAME _openbabel
+ LIBRARY_OUTPUT_DIRECTORY
${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel
+ PREFIX ""
+ SUFFIX .so )
+
+ add_dependencies(bindings_python_${EPYTHON} openbabel)
+
+ install(TARGETS bindings_python_${EPYTHON}
+ LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+ install(FILES
${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py
+ DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+ install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
+ DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+ install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py
+ DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+
+ if (ENABLE_TESTS)
+ # Make sure all module files are together in the same directory
for testing
+ add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD
+ COMMAND ${CMAKE_COMMAND} -E copy
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/, sci-chemistry/openbabel/files/
commit: 81ccd60f63092c825376eb6dd8897edc9eb86820
Author: Pacho Ramos gentoo org>
AuthorDate: Sun Mar 28 00:17:34 2021 +
Commit: Pacho Ramos gentoo org>
CommitDate: Sun Mar 28 00:17:34 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=81ccd60f
sci-chemistry/openbabel: Fix gcc10 build and use wxGTK:gtk3.0
Thanks-to: Michelangelo Scopelliti
Bug: https://bugs.gentoo.org/722860
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Pacho Ramos gentoo.org>
.../openbabel/files/openbabel-2.4.1-gcc10.patch| 62 +
sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild | 101 +
2 files changed, 163 insertions(+)
diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch
b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch
new file mode 100644
index 000..88d8c2add64
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch
@@ -0,0 +1,62 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 2e66dd1..ef4f16b 100644
+--- a/CMakeLists.txt
b/CMakeLists.txt
+@@ -1,16 +1,11 @@
+ # Please ensure that any changes remain compliant with 2.4.8.
+ if(NOT EMBED_OPENBABEL)
+- cmake_minimum_required(VERSION 2.4.8)
++ cmake_minimum_required(VERSION 2.4.10)
+ endif()
+
+ project(openbabel)
+ set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules)
+
+-# Allow loose loop constructs, i.e. no matching in if/else/endif or loops.
+-# Note that this is true by default in CMake 2.6.0, but we currently only
+-# require CMake 2.4.8 - remove this when the CMake requirement is bumped.
+-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS 1)
+-
+ if(COMMAND cmake_policy)
+ cmake_policy(SET CMP0003 NEW)
+ cmake_policy(SET CMP0005 OLD) # add_definitions need updating to set to NEW
+@@ -20,7 +15,6 @@ if(COMMAND cmake_policy)
+ endif()
+
+ include (CheckCXXCompilerFlag)
+-include (MacroEnsureVersion)
+
+ # Version numbering - should be bumped for each release
+ # Note that for "beta" releases, we should start at x.90.0 -- we've
+@@ -238,16 +232,21 @@ check_type_size(clock_t CLOCK_T)
+
+ # Get the GCC version - from KDE4 cmake files
+ if(CMAKE_COMPILER_IS_GNUCXX)
+- exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE
_gcc_version_info)
+- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version
"${_gcc_version_info}")
+- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+- # patch level, handle this here:
+- if (NOT _gcc_version)
+-string (REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0"
_gcc_version "${_gcc_version_info}")
+- endif ()
+- macro_ensure_version("4.0.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_0)
+- macro_ensure_version("4.1.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_1)
+- macro_ensure_version("4.2.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_2)
++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.0.0))
++set(GCC_IS_NEWER_THAN_4_0 TRUE)
++ else()
++set(GCC_IS_NEWER_THAN_4_0 FALSE)
++ endif()
++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.1.0))
++set(GCC_IS_NEWER_THAN_4_1 TRUE)
++ else()
++set(GCC_IS_NEWER_THAN_4_1 FALSE)
++ endif()
++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.2.0))
++set(GCC_IS_NEWER_THAN_4_2 TRUE)
++ else()
++set(GCC_IS_NEWER_THAN_4_2 FALSE)
++ endif()
+ endif()
+
+ if(UNIX)
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild
b/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild
new file mode 100644
index 000..8830108275b
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild
@@ -0,0 +1,101 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+WX_GTK_VER="3.0-gtk3"
+
+inherit cmake-utils desktop optfeature toolchain-funcs wxwidgets
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="http://openbabel.org/wiki/Main_Page;
+SRC_URI="
+ mirror://sourceforge/openbabel/${P}.tar.gz
+ https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
+"
+
+# See src/CMakeLists.txt for LIBRARY_VERSION
+SLOT="0/5.0.0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc openmp test wxwidgets"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-cpp/eigen:3
+ dev-libs/libxml2:2
+ sci-libs/inchi
+ sys-libs/zlib
+ wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ >=dev-util/cmake-2.4.10
+ doc? ( app-doc/doxygen )
+"
+
+DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2}
doc/README.{dioxin.pov,povray} )
+
+PATCHES=(
+ "${FILESDIR}"/${P}-gcc10.patch
+)
+
+pkg_setup() {
+ if use openmp; then
+ if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
+ ewarn "OpenMP is not available in your current selected
gcc"
+ die "need openmp capable gcc"
+ fi
+
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/, sci-chemistry/openbabel/files/
commit: 4ec881ef10b4bcbffd3b56bc78a680b29cd59853
Author: Sergei Trofimovich gentoo org>
AuthorDate: Sun May 6 22:13:04 2018 +
Commit: Sergei Trofimovich gentoo org>
CommitDate: Sun May 6 22:13:32 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4ec881ef
sci-chemistry/openbabel: allow gcc-8, bug #654800
openbabel explicitly whitelists list of major GCC versions.
The change by Milan allow gcc-8. Newer upstream versions
fixed the code to handle in in a more generic way:
https://github.com/openbabel/openbabel/commit/00120f89cf62b121c30d0b2a891b159e19b53624
Fixed-by: milan hodoscek
Closes: https://bugs.gentoo.org/654800
Package-Manager: Portage-2.3.36, Repoman-2.3.9
sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch | 15 +++
sci-chemistry/openbabel/openbabel-2.4.1.ebuild| 3 ++-
2 files changed, 17 insertions(+), 1 deletion(-)
diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
new file mode 100644
index 000..632ffa86761
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
@@ -0,0 +1,15 @@
+https://bugs.gentoo.org/654800
+Fixed-by: milan hodoscek
+diff --git a/../old/CMakeLists.txt b/CMakeLists.txt
+index dc38d1b..801207e 100644
+--- a/../old/CMakeLists.txt
b/CMakeLists.txt
+@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T)
+ # Get the GCC version - from KDE4 cmake files
+ if(CMAKE_COMPILER_IS_GNUCXX)
+ exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE
_gcc_version_info)
+- string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version
"${_gcc_version_info}")
++ string(REGEX MATCH "[345678]\\.[0-9]\\.[0-9]" _gcc_version
"${_gcc_version_info}")
+ # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+ # patch level, handle this here:
+ if (NOT _gcc_version)
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
index 3719af8c81d..4606746af57 100644
--- a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
+++ b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -31,6 +31,7 @@ DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2}
doc/README.{dioxin
PATCHES=(
"${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch
+ "${FILESDIR}"/${P}-gcc-8.patch
)
pkg_setup() {
[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/, sci-chemistry/openbabel/files/
commit: 69b01273253531de9d83902132d9e745a88e94e2
Author: Justin Lecher gentoo org>
AuthorDate: Sat May 13 16:14:26 2017 +
Commit: Justin Lecher gentoo org>
CommitDate: Sat May 13 16:14:26 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=69b01273
sci-chemistry/openbabel: Backport Fix for gcc 6/7
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=594154
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher gentoo.org>
.../files/openbabel-2.3.2-gcc-6_and_7-backport.patch| 13 +
sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild | 7 +--
2 files changed, 18 insertions(+), 2 deletions(-)
diff --git
a/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch
b/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch
new file mode 100644
index 000..e23dc6020ee
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch
@@ -0,0 +1,13 @@
+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
"${_gcc_version_info}")
+ # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+ # patch level, handle this here:
+ if (NOT _gcc_version)
diff --git a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
index ab9bb577790..f84e2a1f51b 100644
--- a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
+++ b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -28,7 +28,10 @@ DEPEND="${RDEPEND}
DOCS="AUTHORS ChangeLog NEWS README THANKS doc/*.inc doc/README* doc/*.mol2"
-PATCHES=( "${FILESDIR}"/${P}-test_lib_path.patch )
+PATCHES=(
+ "${FILESDIR}"/${P}-test_lib_path.patch
+ "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch
+ )
pkg_setup() {
if use openmp; then
