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# Contributor: Isaac Dunham <ibid.ag@gmail.com>
# Maintainer: Holger Jaekel <holger.jaekel@gmx.de>
#
# HDF5 depends on zlib and provides a C interface by default.
# Optionally, it can be built with szip (which has limitations on
# commercial use and thus is non-free), MPI, and C++ and Fortran bindings.
# C++ and Fortran bindings may not be thread-safe:
# building either and passing --enable-threadsafe is unsupported.
# Additionally, the 'high-level' bindings are incompatible with threadsafe
# builds, due to inadequate locking.
pkgname=hdf5
pkgver=1.12.1
pkgrel=2
pkgdesc="HDF5 is a data model, library, and file format for storing and managing data"
url="https://www.hdfgroup.org/solutions/hdf5/"
arch="all"
license="custom"
options="!check" # test suite takes a very long time
depends_dev="zlib-dev"
makedepends="cmake $depends_dev gfortran libaec-dev perl"
subpackages="$pkgname-fortran $pkgname-static $pkgname-doc $pkgname-dev"
source="https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${pkgver%.*}/hdf5-$pkgver/src/hdf5-$pkgver.tar.bz2"
# Optional dependency java-jdk is not available on riscv64
_with_java=""
_enable_java=""
case "$CARCH" in
riscv64) ;;
*)
makedepends="$makedepends java-jdk"
subpackages="$subpackages java-$pkgname:java"
_with_java="-DHDF5_BUILD_JAVA=ON -DJAVA_HOME=/usr/lib/jvm/default-jvm"
_enable_java="--enable-java"
;;
esac
# secfixes:
# 1.12.1-r0:
# - CVE-2018-11206
# - CVE-2018-13869
# - CVE-2018-13870
# - CVE-2018-14033
# - CVE-2018-14460
# - CVE-2018-17435
# - CVE-2019-9151
# - CVE-2020-10811
prepare() {
default_prepare
update_config_sub
update_config_guess
}
build() {
if [ "$CBUILD" != "$CHOST" ]; then
CMAKE_CROSSOPTS="-DCMAKE_SYSTEM_NAME=Linux -DCMAKE_HOST_SYSTEM_NAME=Linux"
fi
export PATH=/usr/lib/jvm/default-jvm/bin:$PATH
# Crazy workaround: run CMake to generate pkg-config file
# 2nd workaround: cmake creates the file pac_Cconftest.out in the current
# directory, but checks if it is successfully created in the build dir.
# So the current directory must be build.
mkdir build && cd build
cmake \
-DCMAKE_INSTALL_PREFIX=/usr \
-DBUILD_SHARED_LIBS=True \
-DCMAKE_BUILD_TYPE=None \
-DCMAKE_CXX_FLAGS="$CXXFLAGS" \
-DCMAKE_C_FLAGS="$CFLAGS" \
-DHDF5_BUILD_HL_LIB=ON \
-DHDF5_BUILD_CPP_LIB=ON \
-DHDF5_BUILD_FORTRAN=ON \
$_with_java \
-DHDF5_ENABLE_Z_LIB_SUPPORT=ON \
-DHDF5_ENABLE_SZIP_SUPPORT=OFF \
-DHDF5_ENABLE_SZIP_ENCODING=OFF \
-DDEFAULT_API_VERSION=v18 \
${CMAKE_CROSSOPTS} ..
cd $builddir
# But don’t build with it, it’s quite broken
./configure \
--prefix=/usr \
--docdir=/usr/share/doc/hdf5/ \
--with-examplesdir='${prefix}/share/doc/hdf5/examples' \
--enable-static \
--disable-sharedlib-rpath \
--enable-build-mode=production \
--enable-hl \
--enable-cxx \
--enable-fortran \
$_enable_java \
--with-pic \
--with-zlib \
--without-szlib \
--with-default-api-version=v18
make
}
check() {
# Without this, checks are failing with messages like
# "error while loading shared libraries: libhdf5.so.101: cannot open shared object file: No such file or directory"
export LD_LIBRARY_PATH="$srcdir"/$pkgname-${pkgver/_/-}/src/.libs/
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$srcdir"/$pkgname-${pkgver/_/-}/c++/src/.libs/
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$srcdir"/$pkgname-${pkgver/_/-}/fortran/src/.libs/
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$srcdir"/$pkgname-${pkgver/_/-}/hl/src/.libs/
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$srcdir"/$pkgname-${pkgver/_/-}/hl/c++/src/.libs/
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH":"$srcdir"/$pkgname-${pkgver/_/-}/hl/fortran/src/.libs/
make check
}
package() {
make DESTDIR="$pkgdir" install
install -Dm0644 COPYING "$pkgdir"/usr/share/licenses/"$pkgname"/COPYING
# Install pkg-config files from CMake tree
install -Dm644 build/CMakeFiles/hdf5*.pc -t "${pkgdir}"/usr/lib/pkgconfig/
}
fortran() {
pkgdesc="Fortran bindings for HDF5 library"
amove usr/lib/libhdf5*fortran.so.*
}
java() {
pkgdesc="Java bindings for HDF5 library"
mkdir -p "$subpkgdir"/usr/share/java/
mkdir -p "$subpkgdir"/usr/lib/jni/
mv "$pkgdir"/usr/lib/jarhdf5-$pkgver.jar "$subpkgdir"/usr/share/java/
ln -s jarhdf5-$pkgver.jar "$subpkgdir"/usr/share/java/jarhdf5.jar
mv "$pkgdir"/usr/lib/libhdf5_java.so "$subpkgdir"/usr/lib/jni/
}
sha512sums="
158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd hdf5-1.12.1.tar.bz2
"
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