From 5e8702bcbbed438e6c6cce023e7ef0cc9baa3e02 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 22 Apr 2018 14:25:03 +0100 Subject: gentoo resync : 22.04.2018 --- sci-chemistry/Manifest.gz | Bin 17232 -> 17233 bytes sci-chemistry/ball/Manifest | 17 +- sci-chemistry/ball/ball-1.4.2-r2.ebuild | 83 ----- sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild | 100 ++++++ .../ball/files/ball-1.4.1-BondOrder.xml.patch | 30 -- .../ball/files/ball-1.4.1-missing-signed.patch | 26 -- sci-chemistry/ball/files/ball-1.4.1-multilib.patch | 39 --- ...1.4.2-Fix-compilation-of-sipModularWidget.patch | 40 --- ....4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch | 28 -- ..._OPTIONS-CMake-macro-changed-in-CMake-2.8.patch | 44 --- .../files/ball-1.4.2-fix-python-bindings.patch | 22 -- .../files/ball-1.4.2-std-namespace-isnan.patch | 16 - .../files/ball-1.4.2-struct-swap-attribute.patch | 80 ----- .../ball/files/ball-1.4.2-underlinking.patch | 16 - .../ball/files/ball-1.5.0-gnuinstalldirs.patch | 355 +++++++++++++++++++++ sci-chemistry/ball/metadata.xml | 25 +- 16 files changed, 474 insertions(+), 447 deletions(-) delete mode 100644 sci-chemistry/ball/ball-1.4.2-r2.ebuild create mode 100644 sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild delete mode 100644 sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.1-multilib.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch delete mode 100644 sci-chemistry/ball/files/ball-1.4.2-underlinking.patch create mode 100644 sci-chemistry/ball/files/ball-1.5.0-gnuinstalldirs.patch (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 6514084e97f4..6d67d7fc607c 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/ball/Manifest b/sci-chemistry/ball/Manifest index c31e5573eae0..1c087ccb3314 100644 --- a/sci-chemistry/ball/Manifest +++ b/sci-chemistry/ball/Manifest @@ -1,13 +1,4 @@ -AUX ball-1.4.1-BondOrder.xml.patch 1675 BLAKE2B e2a36d281239fc5524b106a926060dd5631b5f10505561dad5c3479f75329fa213610119cd3456c06fbc765ecc3ea4b47812a377447e2fef06df56cf64c2a54a SHA512 77e04209bebff5057ad549d1c1d7b638391fb063efb8635a72b46287a4c4975c2d0940267bce9002f3c9dc0f6fab7e21a3099506f57a44e0a325149ee134b2e0 -AUX ball-1.4.1-missing-signed.patch 985 BLAKE2B 230f5a89086431483206253cd6da74e39c62b653b97d505ebbe7a237541bae239d1e8f4056c592d151266845ed9b60dc78845ff7abf02fc1b86e1ac1739be703 SHA512 ea50bbceb38e80416e4f49a247816ccaf1318c45676669388f681eca5be525b5ed6d472c1b20afe37d3d95ae5334d90831269c77bce922207b515e8c5a46f20a -AUX ball-1.4.1-multilib.patch 1585 BLAKE2B 4b61cf04883ef98de4471584376796c5d6534e78ec6da7b181bdc139794e730c8d57dcd04cf9e37e0d57af2734a5bdf6194053b0283160912046a929e82fd41e SHA512 5eebfdce5fba25967c252d0c83f6187079efc55c9481045d6c9e111930e1bb2bed31666b913eb12f46a723aa875559b54f658460efd7be10bbbe4c7cd2982341 -AUX ball-1.4.2-Fix-compilation-of-sipModularWidget.patch 1565 BLAKE2B 853823ab0a5b174bad52290f933257ab9a3e8227855bf6a7769c11d008bcdc56914825ce9addb10b24d0c9c67fbf2be3b7f88997dd96bf2a76e50657f4e873eb SHA512 15cc7b8583b5dfcefa152dac0fcf300ad2369f147dc4bb4061fd06586eea403a67442389b2eecca93144b02f73c0eb252794604b87348e63dddcaa03d2775882 -AUX ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch 1011 BLAKE2B aa08be283cd17947e93c09f5020b08b5fa3f35fe9b94b138fb2df329e5f2bfecd204ffa5dab836a3a201cc415b2e074b29906822a943dcdf4676edc3b48069d4 SHA512 f99d0b42b6798b0f97aeb93f9aedf9dfd68c62f948dabab4cc1e7b6a4251b10ec8b4e109936f86456f77b1faecad5eff05bb40200d55490c7f82787b3f6951a1 -AUX ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch 1470 BLAKE2B db660cfc8414d913dd2473396d20622da9bc9629cd90843dcad4f2f004177f0b2c1d42ecbf95540d677e779f948223e0fbbf20126e34c8b72adfb541a0b1dc41 SHA512 18cd445e4867878f73d74afef1ae74d02bb3a118fdeb379beb2463cef501a79eacfa9c5d487fa2656993f652cc0a7432c7d139a2df101416cc6d7139dc4af034 -AUX ball-1.4.2-fix-python-bindings.patch 643 BLAKE2B 2d5d9a437d90ac52cc865d96419739d1ad5948cd5893fdc988b1530f6ce3bb9ea8cbdf11d1c4b0aa0bfd2352ebbc03b8ce1bffe3e1785f35c142f49f2845cabb SHA512 af1d61a2f4b6b1a0e567e0257e575ffe75f62bb0d0a49379bc08861d0c5bb9dee458a254966a88ecb62eefcd3c6fbb9426b734265627bf7a936111df0f7e61ef -AUX ball-1.4.2-std-namespace-isnan.patch 716 BLAKE2B 86a5edd70115ba20cb34a4665840a7013d25e4b32cba6a31133a1c7429f7c56be7eba44450725c865e5657e66f5243bd9b8f385ab1650f4d7f9b817c863d73d4 SHA512 2fb87783e7d97d12c4841e9e475eb8d99c2a20b0e162f37394182236a6c1ca3c24c0193110671c296dbb2ae244aab720680b17b0862c3da54ab65061f49be9d2 -AUX ball-1.4.2-struct-swap-attribute.patch 1997 BLAKE2B 93c59eca3ea8f49d8b7ec225c0ddb68ed476acd3c8ab1fba81dc183fa504489248033c52a027f04060ab2cd7e6a1badff646805c8c9a55a0651b5f567e7abcf0 SHA512 a8b7e2eaf094a97008fb69030549a4c4bb2eabaf3d06ee5191ae5512c3af73198f88c26dca5e0b63cc19d9e3b1e21c323494017f81339b4a30caf1ae8f0f98f0 -AUX ball-1.4.2-underlinking.patch 665 BLAKE2B d34df60aee08bccfe31aa208d912feee7446fd186b7f7b6db09cb213a7e90a8f1159ccabb8cb06457f4cc441c2c36774f12e0a44e08a5378158526af17cbcb24 SHA512 b122e4f6e87be39642355869a42730263ec9d5e66d9887af5e2c4040eef4fce1306a57b106731bba8136197eecc3f72ca99b863aead70f89825ae6724268c688 -DIST BALL-1.4.2.tar.xz 16080664 BLAKE2B 15faa5f1aed0701ab318ac965ece216be0ff653ab1e57b0a1f2c253cf97b1ac89800ab528c9d044da903b154e16d1dfde936bd1475d6b1903acfa867904a55a7 SHA512 c719af4ef2dc1076818d59b72350b704fbffea06bd44737519fb50d88da113ea509333d407f2330aa59bf1c4e6b81adfd3d28e05459f66d7c9707f8d85db7a87 -EBUILD ball-1.4.2-r2.ebuild 2037 BLAKE2B 55f985f97248c5581f802e370afb586f82b18efd312618aa425ce831b9f5b37f7f112722735535b1a8deb04e1eca4700cb32f630ec4aad5d5f4dc387236352ac SHA512 81f51cdb2e6d7d988aa7f180bf506804d8eb76e2e8a5a297ed50068afc536ece9b42b381123b1bfddc2f69c315aa3cbdba4fe7b60912d82907c0f5ed6ae02479 -MISC metadata.xml 1431 BLAKE2B 74b306217177742cba96db2095cdb43d118a1e76fb41ee847c147dbe73800535c563a9131c62bcc8bda91a5a6dd2bf83cd07a7449af07b97481c0ff6c22fe080 SHA512 c12eaa309bc4e2f6fb51415b943144974a23a92e0705dd7368e402c1be7244485b66bf2d1f0dc11a6b2b673be7189b2543b999924e5ecb94ca00ec9bd1ba32b2 +AUX ball-1.5.0-gnuinstalldirs.patch 14265 BLAKE2B abb1795e7e322e532d041d16e919b59bfa0430df2e06c3b179ae94e8462ed98369e32056c4cc63d181c2d5af59109a4a0b602cf1af47384350c6ef29871d4b0d SHA512 cdf71a863347c3b8716f7e54ded4df15e2615e3375adeaf4c3de1659d52ffde0e3bcd82f7eb26f6f27d03517d279fb4b19fd1c06f12e2191bf81d19d54161906 +DIST ball-1.5.0_pre20180419.tar.gz 37577697 BLAKE2B 44db256dad4703115ca381c4bc7f8393657d9d205b78c9ed55328769129dc38a2898d838bea2beb2e1e5e25184944a5724dd808917928f79c41b8216d98a6677 SHA512 a5cf9680468636c6b3de950f058d1bedb9c2d9ef7b5ba1af60e4b79fab3e6bae9cd814ec3238703075ae66c5a637d1ba8281ce7f11ac842133af91c000c983c3 +EBUILD ball-1.5.0_pre20180419.ebuild 2389 BLAKE2B 45982157a733cbcd4cf785a33071dffcf3f37211bf697876cc64e6e2d9602c44b6dbb0e58c752085c60a23b84cd971f2693ec4da6089e4300f4741aa37af4593 SHA512 5cd1d8d7c87af7720c5ccfbad4ca824fabadd9fbecf129d30ae179379d34c3b5218298c745fe36c77b0bfc0a8080eb330ac72df81bb936f2bd0b8d10ad29b55f +MISC metadata.xml 1920 BLAKE2B 5c44bceae9d74d6e720184b0e2c1eb2fef57c96c05ae7224065e83b088dcf159cf51875390e651d906daa5cb08f714d3808783cccba0935c73dd6ae5b14bf8bc SHA512 8a4ab19d094b8d538cd2494e43572420fb3dd9fdc474056f18c10c6baa4bbb6fad8c89095df3914c9639d4396a7cddbab16ed9b0cd050521e92f1bf3ef162288 diff --git a/sci-chemistry/ball/ball-1.4.2-r2.ebuild b/sci-chemistry/ball/ball-1.4.2-r2.ebuild deleted file mode 100644 index 89c96a194b67..000000000000 --- a/sci-chemistry/ball/ball-1.4.2-r2.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-single-r1 - -DESCRIPTION="Biochemical Algorithms Library" -HOMEPAGE="http://www.ball-project.org/" -SRC_URI="http://www.ball-project.org/Downloads/v${PV}/BALL-${PV}.tar.xz" - -SLOT="0" -LICENSE="LGPL-2 GPL-3" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="cuda mpi +python sql test +threads" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -RDEPEND=" - dev-cpp/eigen:3 - dev-libs/boost:= - dev-qt/qtcore:4 - dev-qt/qtgui:4 - dev-qt/qtopengl:4 - dev-qt/qttest:4 - media-libs/glew:0 - sci-libs/fftw:3.0[threads?] - sci-libs/gsl - sci-libs/libsvm - sci-mathematics/lpsolve - virtual/opengl - x11-libs/libX11 - cuda? ( dev-util/nvidia-cuda-toolkit ) - mpi? ( virtual/mpi ) - python? ( ${PYTHON_DEPS} ) - sql? ( dev-qt/qtsql:4 )" -DEPEND="${RDEPEND} - dev-python/sip - sys-devel/bison - virtual/yacc" - -S="${WORKDIR}"/BALL-${PV} - -PATCHES=( - "${FILESDIR}"/${PN}-1.4.1-multilib.patch - "${FILESDIR}"/${PN}-1.4.1-missing-signed.patch - "${FILESDIR}"/${P}-PDBFile-Fix-compilation-with-gcc-4.8.patch - "${FILESDIR}"/${P}-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch - "${FILESDIR}"/${PN}-1.4.1-BondOrder.xml.patch - "${FILESDIR}"/${P}-Fix-compilation-of-sipModularWidget.patch - "${FILESDIR}"/${P}-underlinking.patch - "${FILESDIR}"/${P}-fix-python-bindings.patch - "${FILESDIR}"/${P}-std-namespace-isnan.patch - "${FILESDIR}"/${P}-struct-swap-attribute.patch -) - -pkg_setup() { - use python && python-single-r1_pkg_setup -} - -src_configure() { - local mycmakeargs=( - -DUSE_FFTW_THREADS=$(usex threads) - -DMT_ENABLE_CUDA=$(usex cuda) - -DMT_ENABLE_MPI=$(usex mpi) - -DBALL_HAS_QTSQL=$(usex sql) - -DBALL_PYTHON_SUPPORT=$(usex python) - ) - cmake-utils_src_configure - - local i - for i in "${S}"/data/*; do - ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die - ln -sf "${i}" "${S}"/source/TEST/ || die - done -} - -src_compile() { - cmake-utils_src_compile - use test && cmake-utils_src_make build_tests -} diff --git a/sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild b/sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild new file mode 100644 index 000000000000..b4d49d1fb14b --- /dev/null +++ b/sci-chemistry/ball/ball-1.5.0_pre20180419.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 ) +COMMIT=e80b5e2021a72faa36bf9e35207998d4590f2cf4 +inherit cmake-utils python-single-r1 + +DESCRIPTION="Biochemical Algorithms Library" +HOMEPAGE="https://github.com/BALL-Project/ball" +SRC_URI="https://github.com/BALL-Project/${PN}/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="LGPL-2 fftw? ( GPL-3 ) openbabel? ( GPL-3 )" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="cuda doc +fftw +gui lpsolve mpi openbabel +python svm test threads webengine" + +REQUIRED_USE=" + python? ( ${PYTHON_REQUIRED_USE} ) + threads? ( fftw ) + webengine? ( gui ) +" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/boost:= + dev-qt/qtcore:5 + dev-qt/qtnetwork:5 + dev-qt/qtxml:5 + media-libs/glew:0= + virtual/opengl + x11-libs/libX11 + cuda? ( dev-util/nvidia-cuda-toolkit ) + fftw? ( sci-libs/fftw:3.0=[threads?] ) + gui? ( + dev-qt/qtgui:5 + dev-qt/qtopengl:5 + dev-qt/qtprintsupport:5 + dev-qt/qttest:5 + dev-qt/qtwidgets:5 + ) + lpsolve? ( sci-mathematics/lpsolve ) + mpi? ( virtual/mpi ) + openbabel? ( sci-chemistry/openbabel:= ) + python? ( ${PYTHON_DEPS} ) + svm? ( sci-libs/libsvm:= ) + webengine? ( + dev-qt/qtwebchannel:5 + dev-qt/qtwebengine:5[widgets] + ) +" +DEPEND="${RDEPEND} + sys-devel/bison + virtual/yacc + doc? ( app-doc/doxygen[dot] ) + gui? ( dev-qt/linguist-tools:5 ) + python? ( dev-python/sip ) +" + +S="${WORKDIR}"/${PN}-${COMMIT} + +PATCHES=( "${FILESDIR}"/${PN}-1.5.0-gnuinstalldirs.patch ) + +RESTRICT="test" + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_configure() { + local mycmakeargs=( + -DUPDATE_TRANSLATIONS=ON + -DCMAKE_DISABLE_FIND_PACKAGE_LATEX=ON + -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF} + -DUSE_CUDA=$(usex cuda) + -DCMAKE_DISABLE_FIND_PACKAGE_Doxygen=$(usex !doc) + -DCMAKE_DISABLE_FIND_PACKAGE_FFTW=$(usex !fftw) + -DUSE_LPSOLVE=$(usex lpsolve) + -DUSE_MPI=$(usex mpi) + -DREQUIRE_MPI=$(usex mpi) + -DCMAKE_DISABLE_FIND_PACKAGE_OpenBabel2=$(usex !openbabel) + -DBALL_PYTHON_SUPPORT=$(usex python) + -DBALL_HAS_VIEW=$(usex gui) + -DUSE_LIBSVM=$(usex svm) + -DUSE_FFTW_THREADS=$(usex threads) + -DUSE_QTWEBENGINE=$(usex webengine) + ) + + if use fftw || use openbabel; then + mycmakeargs+=( -DBALL_LICENSE=GPL ) + fi + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile + use test && cmake-utils_src_make build_tests +} diff --git a/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch b/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch deleted file mode 100644 index 51e592806999..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.1-BondOrder.xml.patch +++ /dev/null @@ -1,30 +0,0 @@ - source/STRUCTURE/assignBondOrderProcessor.C | 2 +- - source/TEST/AssignBondOrderProcessor_test.C | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/source/STRUCTURE/assignBondOrderProcessor.C b/source/STRUCTURE/assignBondOrderProcessor.C -index f8acc4f..035fffc 100644 ---- a/source/STRUCTURE/assignBondOrderProcessor.C -+++ b/source/STRUCTURE/assignBondOrderProcessor.C -@@ -100,7 +100,7 @@ namespace BALL - const bool AssignBondOrderProcessor::Default::KEKULIZE_RINGS = true; - - const char* AssignBondOrderProcessor::Option::INIFile = "iniFile"; -- const String AssignBondOrderProcessor::Default::INIFile = "/bond_lengths/BondOrder.xml"; -+ const String AssignBondOrderProcessor::Default::INIFile = "bond_lengths/BondOrder.xml"; - - const char* AssignBondOrderProcessor::Option::MAX_BOND_ORDER = "max_bond_order"; - const int AssignBondOrderProcessor::Default::MAX_BOND_ORDER = 3; -diff --git a/source/TEST/AssignBondOrderProcessor_test.C b/source/TEST/AssignBondOrderProcessor_test.C -index 6dfafcc..3405ef5 100644 ---- a/source/TEST/AssignBondOrderProcessor_test.C -+++ b/source/TEST/AssignBondOrderProcessor_test.C -@@ -1834,7 +1834,7 @@ CHECK(Option::INIFile) - // There is really not much we can test here, so we just execute the processor - // to have a chance of catching bugs with valgrind if they sneak in - AssignBondOrderProcessor abop; -- abop.options.set(AssignBondOrderProcessor::Option::INIFile, "/bond_lengths/BondOrderGAFF.xml"); -+ abop.options.set(AssignBondOrderProcessor::Option::INIFile, "bond_lengths/BondOrderGAFF.xml"); - - System sys40; - MOL2File mol40(BALL_TEST_DATA_PATH(AssignBondOrderProcessor_test_C4_input.mol2), std::ios::in); diff --git a/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch b/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch deleted file mode 100644 index 6868871b3dc4..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.1-missing-signed.patch +++ /dev/null @@ -1,26 +0,0 @@ -Index: ball/include/BALL/DATATYPE/hashGrid.h -=================================================================== ---- ball.orig/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:49:26.000000000 +0100 -+++ ball/include/BALL/DATATYPE/hashGrid.h 2011-12-09 13:51:09.000000000 +0100 -@@ -37,7 +37,7 @@ - { - namespace __private - { -- extern const char BALL_EXPORT neighbour_table_[27][3]; -+ extern const signed char BALL_EXPORT neighbour_table_[27][3]; - } - - template class HashGrid3; -Index: ball/source/DATATYPE/hashGrid.C -=================================================================== ---- ball.orig/source/DATATYPE/hashGrid.C 2011-12-09 13:49:26.000000000 +0100 -+++ ball/source/DATATYPE/hashGrid.C 2011-12-09 13:50:49.000000000 +0100 -@@ -9,7 +9,7 @@ - { - namespace __private - { -- const char neighbour_table_[27][3] = -+ const signed char neighbour_table_[27][3] = - { - { 0, 0, 0 }, { 0, 0, -1 }, { 0, 0, 1 }, - { 0, -1, -1 }, { 0, -1, 0 }, { 0, -1, 1 }, diff --git a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch deleted file mode 100644 index 317c4029c678..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch +++ /dev/null @@ -1,39 +0,0 @@ -From 5b8f4e58b4e54bcdfa6f287e01f91d9dfd4e5a14 Mon Sep 17 00:00:00 2001 -From: Justin Lecher -Date: Sun, 25 Mar 2012 14:12:21 +0200 -Subject: [PATCH] Correct path for multilib installation. - -Libraries should go into lib64 not lib on native 64bit. Therefore we can use the LIBDIR detected by cmake. ---- - CMakeLists.txt | 8 ++++---- - 1 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 940ebf4..7eb3db4 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -426,8 +426,8 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") - ## These variables are used in all install-targets - IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin") -- SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib") -- SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib") -+ SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) -+ SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) - SET(BALL_HEADER_INSTALL_DIRECTORY ".") - SET(BALL_DATA_INSTALL_DIRECTORY "share/BALL") - SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY "share/BALL/doc") -@@ -435,8 +435,8 @@ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin") - SET(BALL_PYTHON_INSTALL_DIRECTORY "bin") - SET(BALL_PLUGIN_INSTALL_DIRECTORY "bin") - ELSE() -- SET(BALL_PYTHON_INSTALL_DIRECTORY "lib") -- SET(BALL_PLUGIN_INSTALL_DIRECTORY "lib") -+ SET(BALL_PYTHON_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) -+ SET(BALL_PLUGIN_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) - ENDIF() - ELSE() - SET(BALL_BUNDLE_INSTALL_DIRECTORY "Applications") --- -1.7.8.5 - diff --git a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch deleted file mode 100644 index 3ec2f6e983a8..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch +++ /dev/null @@ -1,40 +0,0 @@ -From da49802f8620562f91ac2c947520dccd223ee26b Mon Sep 17 00:00:00 2001 -From: Andreas Hildebrandt -Date: Wed, 15 Jan 2014 17:42:01 +0100 -Subject: [PATCH] Fix compilation of sipModularWidget - ---- - source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip | 10 +++++----- - 1 file changed, 5 insertions(+), 5 deletions(-) - -diff --git a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip -index 522b0ed..7b8ba3e 100644 ---- a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip -+++ b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip -@@ -22,18 +22,18 @@ class ModularWidget - static Size countInstances(); - static ModularWidget* getInstance(Position); - -- ModularWidget(const char* = "") throw(); -- ModularWidget(const ModularWidget&) throw(); -+ ModularWidget(const char* = ""); -+ ModularWidget(const ModularWidget&); - ~ModularWidget() throw(); - -- virtual void destroy() throw(); -- virtual void clear() throw(); -+// virtual void destroy(); -+ virtual void clear(); - - static void registerWidget(ModularWidget*) throw(NullPointer); - // virtual void initializeWidget(MainControl&); - // virtual void finalizeWidget(MainControl&); - virtual void checkMenu(MainControl&) throw(); --// virtual void initializePreferencesTab(Preferences&) throw(); -+// virtual void initializePreferencesTab(Preferences&); - // virtual void finalizePreferencesTab(Preferences&) throw(); - virtual void applyPreferences() throw(); - virtual void fetchPreferences(INIFile&) throw(); --- -1.9.1 - diff --git a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch deleted file mode 100644 index f6b8ff45fa7f..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch +++ /dev/null @@ -1,28 +0,0 @@ -From e7cc50705bed20e160bd4b637b23f57270f580a8 Mon Sep 17 00:00:00 2001 -From: Daniel Stoeckel -Date: Sat, 6 Apr 2013 01:06:55 +0200 -Subject: [PATCH] PDBFile:Fix compilation with gcc 4.8 - -Apparently the automatic conversion from boost::shared_ptr -to boost::shared_ptr is no longer supported. -Just change the type of the pointer and work around this issue. ---- - source/FORMAT/PDBFileDetails.C | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/source/FORMAT/PDBFileDetails.C b/source/FORMAT/PDBFileDetails.C -index 97c2572..aedc5db 100644 ---- a/source/FORMAT/PDBFileDetails.C -+++ b/source/FORMAT/PDBFileDetails.C -@@ -901,7 +901,7 @@ namespace BALL - { - if (!(current_protein_->hasProperty("CRYSTALINFO"))) - { -- boost::shared_ptr temp_ptr(new CrystalInfo()); -+ boost::shared_ptr temp_ptr(new CrystalInfo()); - current_protein_->setProperty(NamedProperty("CRYSTALINFO", temp_ptr)); - } - --- -1.9.1 - diff --git a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch deleted file mode 100644 index 615a92290805..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch +++ /dev/null @@ -1,44 +0,0 @@ -From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001 -From: Luis de la Garza -Date: Fri, 22 Nov 2013 15:18:55 +0100 -Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12; - fixed BALLMacros.cmake - ---- - cmake/BALLMacros.cmake | 14 ++++++++++---- - 1 file changed, 10 insertions(+), 4 deletions(-) - -diff --git a/cmake/BALLMacros.cmake b/cmake/BALLMacros.cmake -index f81ab89..0ac1b87 100644 ---- a/cmake/BALLMacros.cmake -+++ b/cmake/BALLMacros.cmake -@@ -6,16 +6,22 @@ - ### minor modifications (marked with ## BALL ###) - ### - MACRO(QT4_WRAP_UI_BALL outfiles ) -- QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) -- -- ### BALL ### -+ # since 2.8.12 qt4_extract_options has an additional argument -+ # copied fix from OpenMS -+ IF(${CMAKE_VERSION} VERSION_LESS "2.8.12") -+ QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN}) -+ ELSE() -+ QT4_EXTRACT_OPTIONS(ui_files ui_options ui_target ${ARGN}) -+ ENDIF() -+ -+ ### BALL ### - # create output directory (will not exist for out-of-source builds) - FILE(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/) - - FOREACH (it ${ui_files}) - GET_FILENAME_COMPONENT(outfile ${it} NAME_WE) - GET_FILENAME_COMPONENT(infile ${it} ABSOLUTE) -- ### BALL ### -+ ### BALL ### - SET(outfile ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/ui_${outfile}.h) - ADD_CUSTOM_COMMAND(OUTPUT ${outfile} - COMMAND ${QT_UIC_EXECUTABLE} --- -1.9.1 - diff --git a/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch deleted file mode 100644 index a13ea2f36ec0..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 38a955ad9588817073a330c79d4b4476afcf69d5 Mon Sep 17 00:00:00 2001 -From: Daniel Stoeckel -Date: Thu, 14 Apr 2016 19:30:04 +0200 -Subject: [PATCH] Fix Python bindings for Box - ---- - source/PYTHON/EXTENSIONS/VIEW/box.sip | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/source/PYTHON/EXTENSIONS/VIEW/box.sip b/source/PYTHON/EXTENSIONS/VIEW/box.sip -index 341b1a4..592765e 100644 ---- a/source/PYTHON/EXTENSIONS/VIEW/box.sip -+++ b/source/PYTHON/EXTENSIONS/VIEW/box.sip -@@ -6,7 +6,7 @@ - - class Box - : GeometricObject, -- Vertex2 -+ Box3 - { - %TypeHeaderCode - #include diff --git a/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch deleted file mode 100644 index cea6377b6a20..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch +++ /dev/null @@ -1,16 +0,0 @@ -Fix C++11 changes to isnan(): -* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/source/MOLMEC/MINIMIZATION/shiftedLVMM.C:769:46: required from here -* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/MATHS/common.h:175:18: error: ‘isnan’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive] -* return (isnan(t) != 0); - ---- BALL-1.4.2/include/BALL/MATHS/common.h -+++ BALL-1.4.2/include/BALL/MATHS/common.h -@@ -172,7 +172,7 @@ - #elif defined(BALL_OS_DARWIN) - return ( __inline_isnand(t) != 0); - #else -- return (isnan(t) != 0); -+ return (std::isnan(t) != 0); - #endif - } - diff --git a/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch deleted file mode 100644 index da334915f410..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch +++ /dev/null @@ -1,80 +0,0 @@ -Silence warning pollution due to misplaced attributes: -* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/COMMON/logStream.h:165:22: note: attribute for ‘struct BALL::LogStreamBuf::StreamStruct’ must follow the ‘struct’ keyword - ---- BALL-1.4.2/include/BALL/COMMON/logStream.h -+++ BALL-1.4.2/include/BALL/COMMON/logStream.h -@@ -162,7 +162,7 @@ - virtual int overflow(int c = -1); - //@} - -- BALL_EXPORT struct StreamStruct -+ struct BALL_EXPORT StreamStruct - { - std::ostream* stream; - string prefix; ---- BALL-1.4.2/include/BALL/FORMAT/MOL2File.h -+++ BALL-1.4.2/include/BALL/FORMAT/MOL2File.h -@@ -33,7 +33,7 @@ - public: - - /// A class used for storing TRIPOS sets -- BALL_EXPORT struct SetStruct -+ struct BALL_EXPORT SetStruct - { - String name; - bool is_static; -@@ -136,7 +136,7 @@ - - bool containsAtomChilds_(AtomContainerConstIterator& frag_it); - -- BALL_EXPORT struct AtomStruct -+ struct BALL_EXPORT AtomStruct - { - String name; - Vector3 position; -@@ -146,14 +146,14 @@ - float charge; - }; - -- BALL_EXPORT struct BondStruct -+ struct BALL_EXPORT BondStruct - { - Position atom1; - Position atom2; - String type; - }; - -- BALL_EXPORT struct MoleculeStruct -+ struct BALL_EXPORT MoleculeStruct - { - String name; - Size number_of_atoms; -@@ -166,7 +166,7 @@ - String comment; - }; - -- BALL_EXPORT struct SubstructureStruct -+ struct BALL_EXPORT SubstructureStruct - { - String name; - Size root_atom; -@@ -178,7 +178,7 @@ - String comment; - }; - -- BALL_EXPORT struct CommentStruct -+ struct BALL_EXPORT CommentStruct - { - String name; - String value; ---- BALL-1.4.2/include/BALL/FORMAT/MOLFile.h -+++ BALL-1.4.2/include/BALL/FORMAT/MOLFile.h -@@ -41,7 +41,7 @@ - @see PropertyManager::setProperty - @see PropertyManager::getProperty - */ -- BALL_EXPORT struct Property -+ struct BALL_EXPORT Property - { - /// - static const String ATOM_MASS_DIFFERENCE; diff --git a/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch b/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch deleted file mode 100644 index 825f41978c13..000000000000 --- a/sci-chemistry/ball/files/ball-1.4.2-underlinking.patch +++ /dev/null @@ -1,16 +0,0 @@ - source/APPLICATIONS/BALLVIEW/CMakeLists.txt | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt -index 6d16212..f94ce76 100644 ---- a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt -+++ b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt -@@ -85,7 +85,7 @@ IF (UNIX) - LIST(APPEND BALLVIEW_SUPPORT_LIBRARIES "pthread") - ENDIF () - --TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES}) -+TARGET_LINK_LIBRARIES(BALLView BALL VIEW ${BALLVIEW_SUPPORT_LIBRARIES} X11) - - #Setup the translations - INCLUDE(${CMAKE_SOURCE_DIR}/cmake/BALLViewTranslations.cmake) diff --git a/sci-chemistry/ball/files/ball-1.5.0-gnuinstalldirs.patch b/sci-chemistry/ball/files/ball-1.5.0-gnuinstalldirs.patch new file mode 100644 index 000000000000..f9fedc58bb6f --- /dev/null +++ b/sci-chemistry/ball/files/ball-1.5.0-gnuinstalldirs.patch @@ -0,0 +1,355 @@ +From a8cade5ed7090c704aed53871fb664a0fe07af54 Mon Sep 17 00:00:00 2001 +From: Andreas Sturmlechner +Date: Sat, 21 Apr 2018 20:07:09 +0200 +Subject: [PATCH 1/3] Use GNUInstallDirs + +--- + CMakeLists.txt | 30 ++++++++++++++++-------------- + 1 file changed, 16 insertions(+), 14 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index be57fe90c..1a54446fb 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -65,6 +65,8 @@ INCLUDE(BALLCompilerSpecific) + # Determine BALL configuration + INCLUDE(BALLConfiguration) + ++INCLUDE(GNUInstallDirs) ++ + # We do not have a Component-based installer in MacOS + IF(NOT APPLE) + INCLUDE(BALLComponents) +@@ -473,20 +475,20 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") + + ## These variables are used in all install-targets + IF (NOT APPLE) +- SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin") +- SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib") +- SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib") +- SET(BALL_HEADER_INSTALL_DIRECTORY ".") +- SET(BALL_DATA_INSTALL_DIRECTORY "share/BALL") +- SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY "share/BALL/doc") +- SET(BALL_TOOLS_INSTALL_DIRECTORY "bin/BALLTools") ++ SET(BALL_RUNTIME_INSTALL_DIRECTORY ${CMAKE_INSTALL_BINDIR}) ++ SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_HEADER_INSTALL_DIRECTORY ${CMAKE_INSTALL_INCLUDEDIR}) ++ SET(BALL_DATA_INSTALL_DIRECTORY ${CMAKE_INSTALL_DATAROOTDIR}/BALL) ++ SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY ${CMAKE_INSTALL_DOCDIR}) ++ SET(BALL_TOOLS_INSTALL_DIRECTORY ${CMAKE_INSTALL_BINDIR}/BALLTools) + + IF(WIN32) + SET(BALL_PYTHON_INSTALL_DIRECTORY "bin") + SET(BALL_PLUGIN_INSTALL_DIRECTORY "bin") + ELSE() +- SET(BALL_PYTHON_INSTALL_DIRECTORY "lib") +- SET(BALL_PLUGIN_INSTALL_DIRECTORY "lib") ++ SET(BALL_PYTHON_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) ++ SET(BALL_PLUGIN_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) + ENDIF() + ENDIF() + +@@ -710,21 +712,21 @@ IF(NOT APPLE) + ## care of data files and headers + IF (NOT "${CMAKE_INSTALL_PREFIX}" STREQUAL ".") + ### Install the data directories +- INSTALL(DIRECTORY data DESTINATION "${BALL_DATA_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL}) ++ INSTALL(DIRECTORY data/ DESTINATION "${BALL_DATA_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL}) + + ### Install the includes +- INSTALL(DIRECTORY include DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL_DEV}) ++ INSTALL(DIRECTORY include/ DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL_DEV}) + ENDIF() + + ## The configured files have to be copied in any case + INSTALL(FILES ${PROJECT_BINARY_DIR}/include/BALL/CONFIG/config.h +- DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/include/BALL/CONFIG" ++ DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/CONFIG" + COMPONENT ${COMPONENT_LIBBALL_DEV} + ) + + INSTALL(FILES + ${PROJECT_BINARY_DIR}/include/BALL/PYTHON/BALLPythonConfig.h +- DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/include/BALL/PYTHON" ++ DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/PYTHON" + COMPONENT ${COMPONENT_LIBBALL_DEV} + ) + +@@ -866,7 +868,7 @@ EXPORT(PACKAGE BALL) + # Generate CMake package configuration for BALL installation + IF(NOT APPLE) + # Installation path for BALL CMake package configuration files +- SET(BALL_CMAKE_EXPORT_PATH "lib/cmake/BALL" CACHE PATH "Path to the cmake package configuration files") ++ SET(BALL_CMAKE_EXPORT_PATH ${CMAKE_INSTALL_LIBDIR}/cmake/BALL CACHE PATH "Path to the cmake package configuration files") + + LIST(REMOVE_ITEM BALL_INCLUDE_DIRS "${PROJECT_BINARY_DIR}/include") + LIST(REMOVE_ITEM BALL_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/include") +-- +2.17.0 + + +From 17cbef40ad91cf051ca83b1ccf53dd2ccb22fc8d Mon Sep 17 00:00:00 2001 +From: Andreas Sturmlechner +Date: Sat, 21 Apr 2018 21:20:01 +0200 +Subject: [PATCH 2/3] Drop superfluous cmake variables + +--- + CMakeLists.txt | 34 +++++++------------ + cmake/BALLDoc.cmake | 6 ++-- + source/APPLICATIONS/BALLVIEW/CMakeLists.txt | 4 +-- + source/EXTENSIONS/BALLAXY/CMakeLists.txt | 2 +- + source/EXTENSIONS/JUPYTER/CMakeLists.txt | 2 +- + source/EXTENSIONS/PRESENTABALL/CMakeLists.txt | 2 +- + source/PYTHON/EXTENSIONS/CMakeLists.txt | 12 +++---- + 7 files changed, 27 insertions(+), 35 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1a54446fb..9b9f3513b 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -475,14 +475,6 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") + + ## These variables are used in all install-targets + IF (NOT APPLE) +- SET(BALL_RUNTIME_INSTALL_DIRECTORY ${CMAKE_INSTALL_BINDIR}) +- SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) +- SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR}) +- SET(BALL_HEADER_INSTALL_DIRECTORY ${CMAKE_INSTALL_INCLUDEDIR}) +- SET(BALL_DATA_INSTALL_DIRECTORY ${CMAKE_INSTALL_DATAROOTDIR}/BALL) +- SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY ${CMAKE_INSTALL_DOCDIR}) +- SET(BALL_TOOLS_INSTALL_DIRECTORY ${CMAKE_INSTALL_BINDIR}/BALLTools) +- + IF(WIN32) + SET(BALL_PYTHON_INSTALL_DIRECTORY "bin") + SET(BALL_PLUGIN_INSTALL_DIRECTORY "bin") +@@ -693,18 +685,18 @@ IF(NOT APPLE) + INSTALL(TARGETS BALL + EXPORT BALLExportGroup + COMPONENT "${COMPONENT_LIBBALL}" +- RUNTIME DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}" +- LIBRARY DESTINATION "${BALL_LIBRARY_INSTALL_DIRECTORY}" +- ARCHIVE DESTINATION "${BALL_ARCHIVE_INSTALL_DIRECTORY}" ++ RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" ++ LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" ++ ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" + ) + + IF(BALL_HAS_VIEW) + INSTALL(TARGETS VIEW + EXPORT BALLExportGroup + COMPONENT "${COMPONENT_LIBVIEW}" +- RUNTIME DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}" +- LIBRARY DESTINATION "${BALL_LIBRARY_INSTALL_DIRECTORY}" +- ARCHIVE DESTINATION "${BALL_ARCHIVE_INSTALL_DIRECTORY}" ++ RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" ++ LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}" ++ ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}" + ) + ENDIF() + +@@ -712,21 +704,21 @@ IF(NOT APPLE) + ## care of data files and headers + IF (NOT "${CMAKE_INSTALL_PREFIX}" STREQUAL ".") + ### Install the data directories +- INSTALL(DIRECTORY data/ DESTINATION "${BALL_DATA_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL}) ++ INSTALL(DIRECTORY data/ DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/BALL COMPONENT ${COMPONENT_LIBBALL}) + + ### Install the includes +- INSTALL(DIRECTORY include/ DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}" COMPONENT ${COMPONENT_LIBBALL_DEV}) ++ INSTALL(DIRECTORY include/ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}" COMPONENT ${COMPONENT_LIBBALL_DEV}) + ENDIF() + + ## The configured files have to be copied in any case + INSTALL(FILES ${PROJECT_BINARY_DIR}/include/BALL/CONFIG/config.h +- DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/CONFIG" ++ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/BALL/CONFIG" + COMPONENT ${COMPONENT_LIBBALL_DEV} + ) + + INSTALL(FILES + ${PROJECT_BINARY_DIR}/include/BALL/PYTHON/BALLPythonConfig.h +- DESTINATION "${BALL_HEADER_INSTALL_DIRECTORY}/BALL/PYTHON" ++ DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/BALL/PYTHON" + COMPONENT ${COMPONENT_LIBBALL_DEV} + ) + +@@ -744,14 +736,14 @@ IF(NOT APPLE) + FOREACH(LIB ${BALL_DEP_OPT_DLLS}) + STRING(TOLOWER "${LIB}" LOWER_LIB) + INSTALL(FILES "${LIB}" +- DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}" ++ DESTINATION "${CMAKE_INSTALL_BINDIR}" + COMPONENT ${COMPONENT_LIBBALL}) + ENDFOREACH() + + IF(QT_DEPLOY_EXECUTABLE) + INSTALL(CODE +- "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/BALL.dll) +- EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/VIEW.dll)" ++ "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/BALL.dll) ++ EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/VIEW.dll)" + COMPONENT "${COMPONENT_LIBBALL}") + ENDIF() + ENDIF() +diff --git a/cmake/BALLDoc.cmake b/cmake/BALLDoc.cmake +index 061b9c95f..2d7c17466 100644 +--- a/cmake/BALLDoc.cmake ++++ b/cmake/BALLDoc.cmake +@@ -20,7 +20,7 @@ ENDIF() + + IF(NOT APPLE) + INSTALL(DIRECTORY "${PROJECT_SOURCE_DIR}/doc/examples/" +- DESTINATION "${BALL_DOCUMENTATION_INSTALL_DIRECTORY}/EXAMPLES" ++ DESTINATION "${CMAKE_INSTALL_DOCDIR}/EXAMPLES" + COMPONENT "${COMPONENT_DOCUMENTATION_EXAMPLES}") + ENDIF() + +@@ -53,7 +53,7 @@ IF (DOXYGEN_FOUND) + + IF(NOT APPLE) + INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/doc/html/" +- DESTINATION "${BALL_DOCUMENTATION_INSTALL_DIRECTORY}/BALL" ++ DESTINATION "${CMAKE_INSTALL_DOCDIR}/BALL" + COMPONENT "${COMPONENT_DOCUMENTATION_HTML}" + ) + ENDIF() +@@ -107,7 +107,7 @@ IF (LATEX_COMPILER AND DVIPS_CONVERTER) + + IF(NOT APPLE) + INSTALL(FILES ${PROJECT_BINARY_DIR}/doc/tutorial.pdf +- DESTINATION "${BALL_DOCUMENTATION_INSTALL_DIRECTORY}/TUTORIAL" ++ DESTINATION "${CMAKE_INSTALL_DOCDIR}/TUTORIAL" + COMPONENT "${COMPONENT_DOCUMENTATION_PDF}" + OPTIONAL + ) +diff --git a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +index b4b96c31c..5fd21ee68 100644 +--- a/source/APPLICATIONS/BALLVIEW/CMakeLists.txt ++++ b/source/APPLICATIONS/BALLVIEW/CMakeLists.txt +@@ -59,13 +59,13 @@ IF(APPLE) + ELSE() + INSTALL(TARGETS BALLView + COMPONENT "${COMPONENT_BALLVIEW}" +- RUNTIME DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}" ++ RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}" + BUNDLE DESTINATION "${BALL_BUNDLE_INSTALL_DIRECTORY}" + ) + + IF(WIN32) + IF(QT_DEPLOY_EXECUTABLE) +- INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/BALLView.exe)" ++ INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/BALLView.exe)" + COMPONENT "${COMPONENT_BALLVIEW}") + ENDIF() + ENDIF() +diff --git a/source/EXTENSIONS/BALLAXY/CMakeLists.txt b/source/EXTENSIONS/BALLAXY/CMakeLists.txt +index 2fdfcbeed..1eed12c37 100644 +--- a/source/EXTENSIONS/BALLAXY/CMakeLists.txt ++++ b/source/EXTENSIONS/BALLAXY/CMakeLists.txt +@@ -66,7 +66,7 @@ IF(NOT APPLE) + + IF(WIN32) + IF(QT_DEPLOY_EXECUTABLE) +- INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/pluginBALLaxy.dll)" ++ INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/pluginBALLaxy.dll)" + COMPONENT "Unspecified") + ENDIF() + ENDIF() +diff --git a/source/EXTENSIONS/JUPYTER/CMakeLists.txt b/source/EXTENSIONS/JUPYTER/CMakeLists.txt +index bb7e91921..24a459fbf 100644 +--- a/source/EXTENSIONS/JUPYTER/CMakeLists.txt ++++ b/source/EXTENSIONS/JUPYTER/CMakeLists.txt +@@ -78,7 +78,7 @@ IF(NOT APPLE) + + IF(WIN32) + IF(QT_DEPLOY_EXECUTABLE) +- INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/pluginJupyter.dll)" ++ INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/pluginJupyter.dll)" + COMPONENT "Unspecified") + ENDIF() + ENDIF() +diff --git a/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt b/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt +index 8606f2f26..ad027fd03 100644 +--- a/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt ++++ b/source/EXTENSIONS/PRESENTABALL/CMakeLists.txt +@@ -66,7 +66,7 @@ IF(NOT APPLE) + + IF(WIN32) + IF(QT_DEPLOY_EXECUTABLE) +- INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${BALL_RUNTIME_INSTALL_DIRECTORY}/pluginPresentaBALL.dll)" ++ INSTALL(CODE "EXECUTE_PROCESS(COMMAND ${QT_DEPLOY_EXECUTABLE} \$\{CMAKE_INSTALL_PREFIX\}/${CMAKE_INSTALL_BINDIR}/pluginPresentaBALL.dll)" + COMPONENT "Unspecified") + ENDIF() + ENDIF() +diff --git a/source/PYTHON/EXTENSIONS/CMakeLists.txt b/source/PYTHON/EXTENSIONS/CMakeLists.txt +index 590e1de3a..374732519 100644 +--- a/source/PYTHON/EXTENSIONS/CMakeLists.txt ++++ b/source/PYTHON/EXTENSIONS/CMakeLists.txt +@@ -49,15 +49,15 @@ IF(BALL_PYTHON_SUPPORT) + IF(NOT APPLE) + INSTALL(TARGETS BALLCoremodule + COMPONENT "${COMPONENT_PYTHON_BINDINGS_BALL}" +- RUNTIME DESTINATION ${BALL_RUNTIME_INSTALL_DIRECTORY} +- LIBRARY DESTINATION ${BALL_LIBRARY_INSTALL_DIRECTORY} ++ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ) + + IF(BALL_HAS_VIEW) + INSTALL(TARGETS VIEWmodule + COMPONENT "${COMPONENT_PYTHON_BINDINGS_VIEW}" +- RUNTIME DESTINATION ${BALL_RUNTIME_INSTALL_DIRECTORY} +- LIBRARY DESTINATION ${BALL_LIBRARY_INSTALL_DIRECTORY} ++ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} ++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ) + ENDIF() + +@@ -69,7 +69,7 @@ IF(BALL_PYTHON_SUPPORT) + IF (WIN32) + # INSTALL(FILES ${PYTHON_EXECUTABLE} + # COMPONENT "${COMPONENT_PYTHON_BINDINGS_BALL}" +- # DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}" ++ # DESTINATION "${CMAKE_INSTALL_BINDIR}" + #) + + +@@ -78,7 +78,7 @@ IF(BALL_PYTHON_SUPPORT) + + INSTALL(DIRECTORY "${PYTHON_SITE_PACKAGES_DIR}" + COMPONENT "${COMPONENT_PYTHON_BINDINGS_BALL}" +- DESTINATION "${BALL_RUNTIME_INSTALL_DIRECTORY}" ++ DESTINATION "${CMAKE_INSTALL_BINDIR}" + ) + ENDIF () + ENDIF() +-- +2.17.0 + + +From 666ca19b00b14752e69c05600725724fb4f6d488 Mon Sep 17 00:00:00 2001 +From: Andreas Sturmlechner +Date: Sat, 21 Apr 2018 22:02:14 +0200 +Subject: [PATCH 3/3] Install html doc into "html" dir + +--- + cmake/BALLDoc.cmake | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/cmake/BALLDoc.cmake b/cmake/BALLDoc.cmake +index 2d7c17466..a070613c8 100644 +--- a/cmake/BALLDoc.cmake ++++ b/cmake/BALLDoc.cmake +@@ -53,7 +53,7 @@ IF (DOXYGEN_FOUND) + + IF(NOT APPLE) + INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/doc/html/" +- DESTINATION "${CMAKE_INSTALL_DOCDIR}/BALL" ++ DESTINATION "${CMAKE_INSTALL_DOCDIR}/html" + COMPONENT "${COMPONENT_DOCUMENTATION_HTML}" + ) + ENDIF() +-- +2.17.0 + diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml index 72d683b18460..6f18011f2e04 100644 --- a/sci-chemistry/ball/metadata.xml +++ b/sci-chemistry/ball/metadata.xml @@ -1,11 +1,11 @@ - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + Rapid Software Prototyping can significantly reduce development times in the field of Computational Molecular Biology and Molecular Modeling. BALL (Biochemical Algorithms Library) is an application framework in C++ that @@ -23,9 +23,14 @@ structures and algorithms. Based on BALL we have developed a stand-alone tool for molecular visualization, BALLView . BALLView makes the broad functionality available through an integrated user-friendly GUI. - - - Include SQL database support - Include cuda support - + + + Include cuda support + Build with sci-libs/fftw (switching BALL to GPL3) + Build VIEW library required for visualization and graphical user interfaces + Enable support for the Mixed Integer Linear Programming solver + Enable support for sci-chemistry/openbabel (switching BALL to GPL3) + Enable support for the Support Vector Machine module + Enable QtWebEngine support with Qt5 (requires gui) + -- cgit v1.2.3