commit: 9acdbbd4c8debd771ac4a6e39c1073551f7ce43f Author: Sam James <sam <AT> gentoo <DOT> org> AuthorDate: Tue May 3 02:27:07 2022 +0000 Commit: Sam James <sam <AT> gentoo <DOT> org> CommitDate: Tue May 3 02:27:28 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9acdbbd4
sci-libs/hdf5: add 1.12.2 Lots of correctness and sanitizer fixes in .2 so possibly helps with the sparc bug (although we've applied a workaround now anyway). Bug: https://bugs.gentoo.org/686620 Signed-off-by: Sam James <sam <AT> gentoo.org> sci-libs/hdf5/Manifest | 1 + .../hdf5/files/hdf5-1.12.2-cmake_installdirs.patch | 163 +++++++++++++++++++++ sci-libs/hdf5/hdf5-1.12.2.ebuild | 119 +++++++++++++++ 3 files changed, 283 insertions(+) diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest index bd0243d24944..54270f9e0c89 100644 --- a/sci-libs/hdf5/Manifest +++ b/sci-libs/hdf5/Manifest @@ -1,2 +1,3 @@ DIST hdf5-1.10.5.tar.bz2 8706317 BLAKE2B ac326be8fe4ccc4b0153f15bc7d65aa8f1adc2ae279d3980f57ed46722b754d3f36ecf1d6273c75e80ed1afd4bbf10c6b1c5d9408e1f83a4b2e397e7902a7d3c SHA512 769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4 DIST hdf5-1.12.1.tar.bz2 9724309 BLAKE2B cc75ba497188b33972218d02a7601acad1a0443bdb934ecd1641ef5996076fe120e3b72dba3a99d99f919fb4e478d1e531414448de9a7b97a0afde58a4c7c23f SHA512 158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd +DIST hdf5-1.12.2.tar.bz2 10494264 BLAKE2B 99ca5b57f6f54fa044c909f0773de62b218c1f0ec3c011f88f3c227536dd719e77ddbe42d562b1214e8843e41d8fc56db499d7f122876fdd36ef31b235229cb7 SHA512 cbb4663570de76b11adb6bf62cfdb754371d31eeab04691479a5764a45207a9c1309665ab80f51c63a4b9b87354f9cbe6835cef506a9fd554d142c6d2bec21e5 diff --git a/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch b/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch new file mode 100644 index 000000000000..8218f31aea66 --- /dev/null +++ b/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch @@ -0,0 +1,163 @@ +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -46,6 +46,13 @@ if (CMAKE_VERSION VERSION_LESS "3.14.0") + endif() + endif () + ++include (GNUInstallDirs) ++set (HDF5_INSTALL_BIN_DIR "${CMAKE_INSTALL_FULL_BINDIR}") ++set (HDF5_INSTALL_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}") ++set (HDF5_INSTALL_DOC_DIR "${CMAKE_INSTALL_FULL_DOCDIR}") ++set (HDF5_INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_FULL_INCLUDEDIR}") ++set (HDF5_INSTALL_LIB_DIR "${CMAKE_INSTALL_FULL_LIBDIR}") ++ + #----------------------------------------------------------------------------- + # Instructions for use : Sub-Project Build + # +--- a/c++/src/CMakeLists.txt ++++ b/c++/src/CMakeLists.txt +@@ -173,8 +173,8 @@ endif () + #----------------------------------------------------------------------------- + set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX}) + set (_PKG_CONFIG_EXEC_PREFIX \${prefix}) +-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib) +-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include) ++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR}) ++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR}) + set (_PKG_CONFIG_LIBNAME "${HDF5_CPP_LIB_CORENAME}") + set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}") + +--- a/doxygen/CMakeLists.txt ++++ b/doxygen/CMakeLists.txt +@@ -36,7 +36,7 @@ if (DOXYGEN_FOUND) + + install ( + DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html +- DESTINATION ${HDF5_INSTALL_DATA_DIR} ++ DESTINATION ${HDF5_INSTALL_DOC_DIR} + COMPONENT Documents + ) + +--- a/fortran/src/CMakeLists.txt ++++ b/fortran/src/CMakeLists.txt +@@ -537,8 +537,8 @@ endif () + #----------------------------------------------------------------------------- + set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX}) + set (_PKG_CONFIG_EXEC_PREFIX \${prefix}) +-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib) +-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include) ++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR}) ++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR}) + set (_PKG_CONFIG_LIBNAME "${HDF5_F90_LIB_CORENAME}") + set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}") + +--- a/hl/c++/src/CMakeLists.txt ++++ b/hl/c++/src/CMakeLists.txt +@@ -91,8 +91,8 @@ endif () + #----------------------------------------------------------------------------- + set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX}) + set (_PKG_CONFIG_EXEC_PREFIX \${prefix}) +-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib) +-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include) ++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR}) ++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR}) + set (_PKG_CONFIG_LIBNAME "${HDF5_HL_CPP_LIB_CORENAME}") + set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}") + +--- a/hl/fortran/src/CMakeLists.txt ++++ b/hl/fortran/src/CMakeLists.txt +@@ -324,8 +324,8 @@ endif () + #----------------------------------------------------------------------------- + set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX}) + set (_PKG_CONFIG_EXEC_PREFIX \${prefix}) +-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib) +-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include) ++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR}) ++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR}) + set (_PKG_CONFIG_LIBNAME "${HDF5_HL_F90_LIB_CORENAME}") + set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}") + +--- a/hl/src/CMakeLists.txt ++++ b/hl/src/CMakeLists.txt +@@ -123,8 +123,8 @@ endif () + #----------------------------------------------------------------------------- + set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX}) + set (_PKG_CONFIG_EXEC_PREFIX \${prefix}) +-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib) +-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include) ++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR}) ++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR}) + set (_PKG_CONFIG_LIBNAME "${HDF5_HL_LIB_CORENAME}") + set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}") + +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -1288,8 +1288,8 @@ endif () + #----------------------------------------------------------------------------- + set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX}) + set (_PKG_CONFIG_EXEC_PREFIX \${prefix}) +-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib) +-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include) ++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR}) ++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR}) + set (_PKG_CONFIG_LIBNAME "${HDF5_LIB_CORENAME}") + set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}") + +--- a/CMakeInstallation.cmake ++++ b/CMakeInstallation.cmake +@@ -31,7 +31,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED) + if (HDF5_EXPORTED_TARGETS) + install ( + EXPORT ${HDF5_EXPORTED_TARGETS} +- DESTINATION ${HDF5_INSTALL_CMAKE_DIR} ++ DESTINATION ${HDF5_INSTALL_LIB_DIR}/cmake + FILE ${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-targets.cmake + NAMESPACE ${HDF_PACKAGE_NAMESPACE} + COMPONENT configinstall +@@ -67,12 +67,12 @@ set (HDF5_VERSION_MINOR ${HDF5_PACKAGE_VERSION_MINOR}) + # Configure the hdf5-config.cmake file for the build directory + #----------------------------------------------------------------------------- + set (INCLUDE_INSTALL_DIR ${HDF5_INSTALL_INCLUDE_DIR}) +-set (SHARE_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/${HDF5_INSTALL_CMAKE_DIR}" ) ++set (SHARE_INSTALL_DIR "${CMAKE_CURRENT_BINARY_DIR}/${HDF5_INSTALL_LIB_DIR}/cmake" ) + set (CURRENT_BUILD_DIR "${CMAKE_CURRENT_BINARY_DIR}" ) + configure_package_config_file ( + ${HDF_RESOURCES_DIR}/hdf5-config.cmake.in + "${HDF5_BINARY_DIR}/${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-config.cmake" +- INSTALL_DESTINATION "${HDF5_INSTALL_CMAKE_DIR}" ++ INSTALL_DESTINATION "${HDF5_INSTALL_LIB_DIR}/cmake" + PATH_VARS INCLUDE_INSTALL_DIR SHARE_INSTALL_DIR CURRENT_BUILD_DIR + INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}" + ) +@@ -81,19 +81,19 @@ configure_package_config_file ( + # Configure the hdf5-config.cmake file for the install directory + #----------------------------------------------------------------------------- + set (INCLUDE_INSTALL_DIR ${HDF5_INSTALL_INCLUDE_DIR}) +-set (SHARE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${HDF5_INSTALL_CMAKE_DIR}" ) ++set (SHARE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${HDF5_INSTALL_LIB_DIR}/cmake" ) + set (CURRENT_BUILD_DIR "${CMAKE_INSTALL_PREFIX}" ) + configure_package_config_file ( + ${HDF_RESOURCES_DIR}/hdf5-config.cmake.in + "${HDF5_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-config.cmake" +- INSTALL_DESTINATION "${HDF5_INSTALL_CMAKE_DIR}" ++ INSTALL_DESTINATION "${HDF5_INSTALL_LIB_DIR}/cmake" + PATH_VARS INCLUDE_INSTALL_DIR SHARE_INSTALL_DIR CURRENT_BUILD_DIR + ) + + if (NOT HDF5_EXTERNALLY_CONFIGURED) + install ( + FILES ${HDF5_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-config.cmake +- DESTINATION ${HDF5_INSTALL_CMAKE_DIR} ++ DESTINATION ${HDF5_INSTALL_LIB_DIR}/cmake + COMPONENT configinstall + ) + endif () +@@ -109,7 +109,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED) + ) + install ( + FILES ${HDF5_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${HDF5_PACKAGE}${HDF_PACKAGE_EXT}-config-version.cmake +- DESTINATION ${HDF5_INSTALL_CMAKE_DIR} ++ DESTINATION ${HDF5_INSTALL_LIB_DIR}/cmake + COMPONENT configinstall + ) + endif () diff --git a/sci-libs/hdf5/hdf5-1.12.2.ebuild b/sci-libs/hdf5/hdf5-1.12.2.ebuild new file mode 100644 index 000000000000..76d54a46d435 --- /dev/null +++ b/sci-libs/hdf5/hdf5-1.12.2.ebuild @@ -0,0 +1,119 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +FORTRAN_NEEDED="fortran" + +inherit cmake flag-o-matic fortran-2 toolchain-funcs + +MY_P="${PN}-${PV/_p/-patch}" +MAJOR_P="${PN}-$(ver_cut 1-2)" + +DESCRIPTION="General purpose library and file format for storing scientific data" +HOMEPAGE="https://www.hdfgroup.org/HDF5/"; +SRC_URI="https://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2"; + +LICENSE="NCSA-HDF" +SLOT="0/${PV%%_p*}" +KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux" +IUSE="cxx debug doc examples fortran +hl mpi szip test threads unsupported zlib" + +REQUIRED_USE=" + !unsupported? ( + mpi? ( !cxx !threads ) + threads? ( !cxx !fortran !hl ) + )" + +RESTRICT="!test? ( test )" + +RDEPEND=" + mpi? ( virtual/mpi[romio] ) + szip? ( virtual/szip ) + zlib? ( sys-libs/zlib:0= ) +" +DEPEND="${RDEPEND}" +BDEPEND="doc? ( + app-doc/doxygen + virtual/latex-base +)" + +PATCHES=( + "${FILESDIR}"/${PN}-1.12.2-cmake_installdirs.patch +) + +S="${WORKDIR}/${MY_P}" + +pkg_setup() { + use fortran && fortran-2_pkg_setup + + if use mpi; then + if has_version 'sci-libs/hdf5[-mpi]'; then + ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail." + ewarn "Try to uninstall the current hdf5 prior to enabling mpi support." + fi + export CC="mpicc" + use fortran && export FC="mpif90" + append-libs -lmpi + elif has_version 'sci-libs/hdf5[mpi]'; then + ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail." + ewarn "Try to uninstall the current hdf5 prior to disabling mpi support." + fi +} + +src_configure() { + use sparc && tc-is-gcc && append-flags -fno-tree-ccp # bug 686620 + local mycmakeargs=( + -DBUILD_STATIC_LIBS=OFF + -DFETCHCONTENT_FULLY_DISCONNECTED=ON + -DHDF5_BUILD_EXAMPLES=OFF + -DALLOW_UNSUPPORTED=$(usex unsupported) + -DBUILD_TESTING=$(usex test) + -DHDF5_BUILD_CPP_LIB=$(usex cxx) + -DHDF5_BUILD_DOC=$(usex doc) + -DHDF5_BUILD_FORTRAN=$(usex fortran) + -DHDF5_BUILD_HL_LIB=$(usex hl) + -DHDF5_ENABLE_CODESTACK=$(usex debug) + -DHDF5_ENABLE_PARALLEL=$(usex mpi) + -DHDF5_ENABLE_SZIP_ENCODING=$(usex szip) + -DHDF5_ENABLE_SZIP_SUPPORT=$(usex szip) + -DHDF5_ENABLE_THREADSAFE=$(usex threads) + -DHDF5_ENABLE_Z_LIB_SUPPORT=$(usex zlib) + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + + # TODO: generate functioning example runners from their respective + # .in files - as of version 1.12.1 upstream only has it implemented + # for autoconf. + if use examples; then + # These are all useless outside the source tree + rm -f {examples,c++/examples,fortran/examples}/{Makefile*,CMake*} + rm -f hl/{examples,c++/examples,fortran/examples}/{Makefile*,CMake*} + + dodoc -r examples + if use cxx; then + docinto c++ + dodoc -r c++/examples + fi + if use fortran; then + docinto fortran + dodoc -r fortran/examples + fi + if use hl; then + docinto hl + dodoc -r hl/examples + if use cxx; then + docinto hl/c++ + dodoc -r hl/c++/examples + fi + if use fortran; then + docinto hl/fortran + dodoc -r hl/fortran/examples + fi + fi + fi +}
