| Summary: | sci-chemistry/gromacs-2025.0_beta - [ncurses-6.5] [meson] [libtool] ld: lib/libgromacs.so.10.0.0: undefined reference to H5Pclose | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Alexey Shvetsov <alexxy> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | sci-chemistry |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
emerge-info.txt
emerge-history.txt environment etc.clang.tar.xz etc.portage.tar.xz logs.tar.xz qlist-info.txt.xz sci-chemistry:gromacs-2025.0_beta:20241124-041037.log.xz temp.tar.xz |
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Created attachment 911736 [details]
emerge-info.txt
Created attachment 911737 [details]
emerge-history.txt
Created attachment 911738 [details]
environment
Created attachment 911739 [details]
etc.clang.tar.xz
Created attachment 911740 [details]
etc.portage.tar.xz
Created attachment 911741 [details]
logs.tar.xz
Created attachment 911742 [details]
qlist-info.txt.xz
Created attachment 911743 [details]
sci-chemistry:gromacs-2025.0_beta:20241124-041037.log.xz
Created attachment 911744 [details]
temp.tar.xz
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f3c616b80818d6710aad35e42f264987ea391d9c commit f3c616b80818d6710aad35e42f264987ea391d9c Author: Alexey Shvetsov <alexxy@gentoo.org> AuthorDate: 2024-11-25 06:04:07 +0000 Commit: Alexey Shvetsov <alexxy@gentoo.org> CommitDate: 2024-11-25 06:04:07 +0000 sci-chemistry/gromacs: hdf5 support not ready for 2025 Closes: https://bugs.gentoo.org/944796 Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org> sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild | 5 ++--- sci-chemistry/gromacs/gromacs-2025.9999.ebuild | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) |
too long lines were shrinked: [1187/1200] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTMPI_USE_VISIBILITY -Dgmxapi_EXPORTS -I/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta/api/gmxapi/include -I/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0_beta_float/api/ [1188/1200] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -DTMPI_USE_VISIBILITY -I/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta/src -I/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta/api/legacy/include -I/var/tmp/portage/sci-chemistry/gromac [1189/1200] /usr/bin/x86_64-pc-linux-gnu-g++ -DGMX_DOUBLE=0 -I/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta/api/nblib/include -I/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/work/gromacs-2025.0-beta/api/nblib -I/var/tmp/portage/sci-chemistry/gromacs-2025.0_beta/wor [1190/1200] : && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,--dependency-file,share/template/CMakeFiles/template.dir/link.d share/template/CMakeFiles/template.dir/ FAILED: bin/template : && /usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,--defsym=__gentoo_check_ldflags__=0 -Wl,--dependency-file,share/template/CMakeFiles/template.dir/link.d share/template/CMakeFiles/template.dir/template.cpp /usr/lib/gcc/x86_64-pc-linux-gnu/14/../../../../x86_64-pc-linux-gnu/bin/ld: lib/libgromacs.so.10.0.0: undefined reference to `H5Pclose' /usr/lib/gcc/x86_64-pc-linux-gnu/14/../../../../x86_64-pc-linux-gnu/bin/ld: lib/libgromacs.so.10.0.0: undefined reference to `H5Eset_auto2' /usr/lib/gcc/x86_64-pc-linux-gnu/14/../../../../x86_64-pc-linux-gnu/bin/ld: lib/libgromacs.so.10.0.0: undefined reference to `H5Eprint2' ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 23.0_desktop_systemd-20241117-085002 UNMASKED: Please re-assign to ztrawhcse@ if you cannot reproduced it with regular meson. <dev-build/meson-9999 Issues involving opaque types / incomplete typedefs should block bug 930805 >=sys-libs/ncurses-6.5 The attached etc.portage.tar.xz has all details. ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-14 * clang version 19.1.4 llvm-config: 19.1.4 Python 3.12.7 go version go1.23.3 linux/amd64 [1] php8.3 * Available Ruby profiles: [1] ruby32 (with Rubygems) [2] ruby33 (with Rubygems) * Available Rust versions: [1] rust-bin-1.71.1 [2] rust-bin-1.77.1 [3] rust-bin-1.82.0 * The following VMs are available for generation-2: 1) Eclipse Temurin JDK 11.0.25_p9 [openjdk-bin-11] 2) Eclipse Temurin JDK 17.0.13_p11 [openjdk-bin-17] *) Eclipse Temurin JDK 21.0.5_p11 [openjdk-bin-21] 4) Eclipse Temurin JDK 8.432_p06 [openjdk-bin-8] Available Java Virtual Machines: [1] openjdk-bin-8 [2] openjdk-bin-11 [3] openjdk-bin-17 [4] openjdk-bin-21 system-vm HEAD of ::gentoo commit 77d85f448d0db64ce910f286584f281583d90781 Author: Repository mirror & CI <repomirrorci@gentoo.org> Date: Sun Nov 24 00:35:32 2024 +0000 2024-11-24 00:35:31 UTC emerge -qpvO =sci-chemistry/gromacs-2025.0_beta [ebuild U ] sci-chemistry/gromacs-2025.0_beta [2024.4] USE="blas custom-cflags doc fftw gmxapi gmxapi-legacy hdf5%* hwloc offensive openmp single-precision threads tng -build-manual -clang -clang-cuda -cuda -double-precision -lapack -mkl -mpi -nnpot% -opencl (-python) -test" CPU_FLAGS_X86="avx avx2 sse2 sse4_1 -avx512f -fma4" PYTHON_SINGLE_TARGET="python3_12 -python3_10 -python3_11"