build with nix link does not work

[Clarkszw]

Hi HaoZeKe,

In the README.md, build with nix link does not work.

Could you send a link for installation and get started for the software?

Thanks in advance
Clark

[Clarkszw]

ah, I found the installation in the compilation section. I will check it.

[Clarkszw]

Here is the error message from build via nix-build .
builder for '/nix/store/vb245y6zalkacd779w8yd6h00f2fhs7d-yodaStruct.drv' failed with exit code 2

It gives the same output when I use nix-env if . to install.

Could anyone give me some hint to fix it?

Thanks in advance.

Scanning dependencies of target yodaStruct
Scanning dependencies of target yodaStruct_test
[ 56%] Building CXX object src/CMakeFiles/yodaStruct.dir/main.cpp.o
[ 58%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/main.cpp.o
[ 60%] Linking CXX executable ../yodaStruct
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: CMakeFiles/yodaStruct.dir/main.cpp.o: in function `main':
main.cpp:(.text+0x2f28): undefined reference to `fmt::v9::vformat[abi:cxx11](fmt::v9::basic_string_view<char>, fmt::v9::basic_format_args<fmt::v9::basic_format_context<fmt::v9::appender, char> >)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: main.cpp:(.text+0x2fe4): undefined reference to `fmt::v9::vformat[abi:cxx11](fmt::v9::basic_string_view<char>, fmt::v9::basic_format_args<fmt::v9::basic_format_context<fmt::v9::appender, char> >)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: main.cpp:(.text+0x308e): undefined reference to `fmt::v9::vformat[abi:cxx11](fmt::v9::basic_string_view<char>, fmt::v9::basic_format_args<fmt::v9::basic_format_context<fmt::v9::appender, char> >)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: main.cpp:(.text+0x3138): undefined reference to `fmt::v9::vformat[abi:cxx11](fmt::v9::basic_string_view<char>, fmt::v9::basic_format_args<fmt::v9::basic_format_context<fmt::v9::appender, char> >)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: CMakeFiles/yodaStruct.dir/main.cpp.o: in function `YAML::detail::node& YAML::detail::node_data::get<char [11]>(char const (&) [11], std::shared_ptr<YAML::detail::memory_holder>)':
main.cpp:(.text._ZN4YAML6detail9node_data3getIA11_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE[_ZN4YAML6detail9node_data3getIA11_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE]+0x102): undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder> const&)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: CMakeFiles/yodaStruct.dir/main.cpp.o: in function `YAML::detail::node& YAML::detail::node_data::get<char [10]>(char const (&) [10], std::shared_ptr<YAML::detail::memory_holder>)':
main.cpp:(.text._ZN4YAML6detail9node_data3getIA10_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE[_ZN4YAML6detail9node_data3getIA10_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE]+0x102): undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder> const&)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: CMakeFiles/yodaStruct.dir/main.cpp.o: in function `YAML::detail::node& YAML::detail::node_data::get<char [4]>(char const (&) [4], std::shared_ptr<YAML::detail::memory_holder>)':
main.cpp:(.text._ZN4YAML6detail9node_data3getIA4_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE[_ZN4YAML6detail9node_data3getIA4_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE]+0x102): undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder> const&)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: CMakeFiles/yodaStruct.dir/main.cpp.o: in function `YAML::detail::node& YAML::detail::node_data::get<char [5]>(char const (&) [5], std::shared_ptr<YAML::detail::memory_holder>)':
main.cpp:(.text._ZN4YAML6detail9node_data3getIA5_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE[_ZN4YAML6detail9node_data3getIA5_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE]+0x102): undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder> const&)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: CMakeFiles/yodaStruct.dir/main.cpp.o: in function `YAML::detail::node& YAML::detail::node_data::get<char [20]>(char const (&) [20], std::shared_ptr<YAML::detail::memory_holder>)':
main.cpp:(.text._ZN4YAML6detail9node_data3getIA20_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE[_ZN4YAML6detail9node_data3getIA20_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE]+0x102): undefined reference to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder> const&)'
/nix/store/p792j5f44l3f0xi7ai5jllwnxqwnka88-binutils-2.31.1/bin/ld: CMakeFiles/yodaStruct.dir/main.cpp.o:main.cpp:(.text._ZN4YAML6detail9node_data3getIA28_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE[_ZN4YAML6detail9node_data3getIA28_cEERNS0_4nodeERKT_St10shared_ptrINS0_13memory_holderEE]+0x102): more undefined references to `YAML::detail::node_data::convert_to_map(std::shared_ptr<YAML::detail::memory_holder> const&)' follow
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [src/CMakeFiles/yodaStruct.dir/build.make:106: yodaStruct] Error 1
make[1]: *** [CMakeFiles/Makefile2:191: src/CMakeFiles/yodaStruct.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 63%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/franzblau-test.cpp.o
[ 65%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/topo_one_dim-test.cpp.o
[ 68%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/topo_bulk-test.cpp.o
[ 70%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/absor-test.cpp.o
[ 73%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/franzblau.cpp.o
[ 75%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/topo_one_dim.cpp.o
[ 78%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/topo_bulk.cpp.o
[ 80%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/ring.cpp.o
[ 82%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/neighbours.cpp.o
[ 85%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/mol_sys.cpp.o
[ 87%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/absOrientation.cpp.o
[ 90%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/seams_input.cpp.o
[ 92%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/seams_output.cpp.o
[ 95%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/pntCorrespondence.cpp.o
[ 97%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/__/src/bulkTUM.cpp.o
[100%] Linking CXX executable ../yodaStruct_test
[100%] Built target yodaStruct_test
make: *** [Makefile:160: all] Error 2
error: builder for '/nix/store/vb245y6zalkacd779w8yd6h00f2fhs7d-yodaStruct.drv' failed with exit code 2

[HaoZeke]

spack is working, but that is rather slow to work with. It will take a while to install but should be fine. Could you test with that? Should have the nix issue fixed soon.

[Clarkszw]

will do that :)

[Clarkszw]

o

yes, confirmed. The same with CI report.

[HaoZeke]

Awesome, thank you. Instead of spack or nix, it seems that as of #21 the cmake and mamba instructions work? If this works for you as well, could you open a PR updating the documentation about which of the methods is preferred?

[Clarkszw]

Spack took me 5 hours to install the dependencies to a new VM..
I was stopped in the last step of the spack path, here is the report:

$ cmake --build build
[1/42] Building CXX object src/CMakeFiles/yodaLib.dir/seams_input.cpp.o
FAILED: src/CMakeFiles/yodaLib.dir/seams_input.cpp.o 
/usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DyodaLib_EXPORTS -I/home/clarkszw/seams-core/src/include/internal -I/home/clarkszw/seams-core/src/include/external -I/home/clarkszw/spack/opt/spack/linux-ubuntu20.04-x86_64_v4/gcc-9.4.0/boost-1.81.0-mrcd6ui7dmzh3vlv2tmmk2uxhbywq3qs/include -pg -fsanitize=address -O2 -g -DNDEBUG -fPIC -std=gnu++17 -MD -MT src/CMakeFiles/yodaLib.dir/seams_input.cpp.o -MF src/CMakeFiles/yodaLib.dir/seams_input.cpp.o.d -o src/CMakeFiles/yodaLib.dir/seams_input.cpp.o -c /home/clarkszw/seams-core/src/seams_input.cpp
In file included from /home/clarkszw/seams-core/src/seams_input.cpp:15:
/home/clarkszw/seams-core/src/include/internal/generic.hpp:26:10: fatal error: eigen3/Eigen/Core: No such file or directory
   26 | #include <eigen3/Eigen/Core>
      |          ^~~~~~~~~~~~~~~~~~~
compilation terminated.
[2/42] Building CXX object src/CMakeFiles/yodaStruct.dir/main.cpp.o
FAILED: src/CMakeFiles/yodaStruct.dir/main.cpp.o 
/usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -I/home/clarkszw/seams-core/src/include/internal -I/home/clarkszw/seams-core/src/include/external -I/home/clarkszw/spack/opt/spack/linux-ubuntu20.04-x86_64_v4/gcc-9.4.0/boost-1.81.0-mrcd6ui7dmzh3vlv2tmmk2uxhbywq3qs/include -pg -fsanitize=address -O2 -g -DNDEBUG -std=gnu++17 -MD -MT src/CMakeFiles/yodaStruct.dir/main.cpp.o -MF src/CMakeFiles/yodaStruct.dir/main.cpp.o.d -o src/CMakeFiles/yodaStruct.dir/main.cpp.o -c /home/clarkszw/seams-core/src/main.cpp
In file included from /home/clarkszw/seams-core/src/include/internal/seams_output.hpp:21,
                 from /home/clarkszw/seams-core/src/include/internal/ring.hpp:33,
                 from /home/clarkszw/seams-core/src/include/internal/seams_input.hpp:21,
                 from /home/clarkszw/seams-core/src/include/internal/bond.hpp:33,
                 from /home/clarkszw/seams-core/src/main.cpp:28:
/home/clarkszw/seams-core/src/include/internal/generic.hpp:26:10: fatal error: eigen3/Eigen/Core: No such file or directory
   26 | #include <eigen3/Eigen/Core>
      |          ^~~~~~~~~~~~~~~~~~~
compilation terminated.
[3/42] Building CXX object src/CMakeFiles/yodaLib.dir/mol_sys.cpp.o
ninja: build stopped: subcommand failed.

I have clone the latest repository this morning.