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Currently, we get weird CMake errors that actually do not seem to affect the compilation of OpenMS.
-- Unable to determine HDF5 C flags from HDF5 wrapper.
-- Unable to determine HDF5 C version from HDF5 wrapper.
-- Unable to determine HDF5 CXX flags from HDF5 wrapper.
-- Unable to determine HDF5 CXX version from HDF5 wrapper.
or
-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
/Users/runner/work/OpenMS/OpenMS/contribbld/h5c++
dir is /Users/runner/work/OpenMS/OpenMS/contribbld
Package hdf5 was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5.pc'
to the PKG_CONFIG_PATH environment variable
Package 'hdf5', required by 'hdf5_cpp-1.10.5', not found
/Users/runner/work/OpenMS/OpenMS/bld/src/openms/CMakeFiles/hdf5/cmake_hdf5_test.cxx:1:10: fatal error: 'H5Cpp.h' file not found
#include <H5Cpp.h>
^~~~~~~~~
1 error generated.
-- HDF5 CXX compiler wrapper is unable to compile a minimal HDF5 program.
-- Found HDF5: /Users/runner/work/OpenMS/OpenMS/contribbld/lib/libhdf5_cpp.a;/Users/runner/work/OpenMS/OpenMS/contribbld/lib/libhdf5.a (found version "1.10.5") found components: C CXX HL
This is because the FindHDF5.cmake module is used, which tries to infer compile options from the hdf5 compiler wrappers (hdf5c++, etc.).
Those wrappers are not correctly built in our contrib, e.g. on macOS it has stuff like a hardcoded compiler path in it:
#! /bin/sh
##
# Copyright by The HDF Group....
prg=$0
if [ ! -e "$prg" ]; then
case $prg in
(*/*) exit 1;;
(*) prg=$(command -v -- "$prg") || exit;;
esac
fi
dir=$(
cd -P -- "$(dirname -- "$prg")/.." && pwd -P
) || exit
prg=$dir/$(basename -- "$prg") || exit
printf '%s\n' "$prg"
printf 'dir is %s\n' "$dir"
export PKG_CONFIG_PATH=$dir/lib/pkgconfig
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++ `pkg-config --define-variable=prefix=$dir --cflag --libs hdf5_cpp-1.10.5` $@
and probably the try_compile commands of the Find module do not specify the sysroot always correctly.
Therefore I think it is better to rely on an hdf5-config.cmake if present and therefore use find_package(HDF5 ... NO_MODULE) in OpenMS.
The text was updated successfully, but these errors were encountered:
Currently, we get weird CMake errors that actually do not seem to affect the compilation of OpenMS.
or
This is because the FindHDF5.cmake module is used, which tries to infer compile options from the hdf5 compiler wrappers (hdf5c++, etc.).
Those wrappers are not correctly built in our contrib, e.g. on macOS it has stuff like a hardcoded compiler path in it:
and probably the try_compile commands of the Find module do not specify the sysroot always correctly.
Therefore I think it is better to rely on an hdf5-config.cmake if present and therefore use
find_package(HDF5 ... NO_MODULE)
in OpenMS.The text was updated successfully, but these errors were encountered: