Bug 862222 – sci-chemistry/gromacs-2022.2 - /.../x86_64-pc-linux-gnu-ld: lib/libgromacs.so.7.0.0: undefined reference to mu::ParserError::GetMs

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2022-07-30 07:52:35 UTC]

too long lines were shrinked:

[1143/1147] /usr/bin/cmake -E cmake_symlink_library lib/libnblib_gmx.so.0.1.0  lib/libnblib_gmx.so.0 lib/libnblib_gmx.so && :
[1144/1147] : && /usr/lib/llvm/14/bin/x86_64-pc-linux-gnu-clang++ -pipe -march=native -fno-diagnostics-color -O2 -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/usr/lib64 -Wl,--enable-new-dtags -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o
FAILED: bin/gmx 
: && /usr/lib/llvm/14/bin/x86_64-pc-linux-gnu-clang++ -pipe -march=native -fno-diagnostics-color -O2 -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/usr/lib64 -Wl,--enable-new-dtags -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 src/programs/CMakeFiles/gmx_objlib.dir/gmx.cpp.o src/program
/usr/bin/x86_64-pc-linux-gnu-ld: lib/libgromacs.so.7.0.0: undefined reference to `mu::ParserError::GetMsg() const'
/usr/bin/x86_64-pc-linux-gnu-ld: lib/libgromacs.so.7.0.0: undefined reference to `mu::ParserBase::SetExpr(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)'
/usr/bin/x86_64-pc-linux-gnu-ld: lib/libgromacs.so.7.0.0: undefined reference to `mu::ParserBase::DefineVar(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, double*)'

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 17.1_desktop_plasma_systemd-j4-20220727-190004

  -------------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-12.1.1 *
clang/llvm (if any):
clang version 14.0.6
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/lib/llvm/14/bin
/usr/lib/llvm/14
14.0.6
Python 3.10.5
Available Ruby profiles:
  [1]   ruby27 (with Rubygems)
  [2]   ruby31 (with Rubygems) *
Available Rust versions:
  [1]   rust-bin-1.62.1 *
The following VMs are available for generation-2:
1)	IcedTea JDK 3.16.0 [icedtea-bin-8]
2)	Eclipse Temurin JDK 11.0.15_p10 [openjdk-bin-11]
*)	Eclipse Temurin JDK 17.0.3_p7 [openjdk-bin-17]
4)	Eclipse Temurin JDK 8.332_p09 [openjdk-bin-8]
5)	Eclipse Temurin JRE 17.0.3_p7 [openjdk-jre-bin-17]
Available Java Virtual Machines:
  [1]   icedtea-bin-8 
  [2]   openjdk-bin-8 
  [3]   openjdk-bin-11 
  [4]   openjdk-bin-17  system-vm
  [5]   openjdk-jre-bin-17 

The Glorious Glasgow Haskell Compilation System, version 9.0.2
php cli:

  HEAD of ::gentoo
commit d00b06af4340441f460626fe1f000ebbeb1fe293
Author: Repository mirror & CI <[e-mail]>
Date:   Sat Jul 30 00:16:38 2022 +0000

    2022-07-30 00:16:38 UTC

emerge -qpvO sci-chemistry/gromacs
[ebuild  N    ] sci-chemistry/gromacs-2022.2  USE="clang custom-cflags doc fftw gmxapi gmxapi-legacy hwloc offensive openmp single-precision threads tng -blas -build-manual -clang-cuda (-cuda) -double-precision -lapack -mkl -mpi -opencl (-python) -test" CPU_FLAGS_X86="avx avx2 sse2 sse4_1 -avx512f -fma4" PYTHON_SINGLE_TARGET="python3_10 -python3_8 -python3_9 -python3_11"

[Comment 1 Toralf Förster 2022-07-30 07:52:36 UTC]

Created attachment 795628 [details]
emerge-info.txt

[Comment 2 Toralf Förster 2022-07-30 07:52:37 UTC]

Created attachment 795631 [details]
emerge-history.txt

[Comment 3 Toralf Förster 2022-07-30 07:52:39 UTC]

Created attachment 795634 [details]
environment

[Comment 4 Toralf Förster 2022-07-30 07:52:40 UTC]

Created attachment 795637 [details]
etc.portage.tar.bz2

[Comment 5 Toralf Förster 2022-07-30 07:52:41 UTC]

Created attachment 795640 [details]
logs.tar.bz2

[Comment 6 Toralf Förster 2022-07-30 07:52:43 UTC]

Created attachment 795643 [details]
sci-chemistry:gromacs-2022.2:20220730-025812.log.bz2

[Comment 7 Toralf Förster 2022-07-30 07:52:44 UTC]

Created attachment 795646 [details]
temp.tar.bz2

[Comment 8 Alexey Shvetsov 2022-12-20 21:10:48 UTC]

Should be fixed with recent versions