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BLD: Nix builds are not idempotent #19

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HaoZeke opened this issue Mar 26, 2023 · 4 comments
Open

BLD: Nix builds are not idempotent #19

HaoZeke opened this issue Mar 26, 2023 · 4 comments

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@HaoZeke
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HaoZeke commented Mar 26, 2023 

    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

Originally posted by @Clarkszw in #12 (comment)

This seems to be happening in PR runs as well. Hints towards a deeper issue with the dependency pinning. Looks like a linker issue for fmt and yaml-cpp.
@Clarkszw
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I have tried today, still failed..

20.04.1-Ubuntu
x86_64

-- Build files have been written to: /build/source/build
building
build flags: -j2 -l2 SHELL=/nix/store/2jysm3dfsgby5sw5jgj43qjrb5v79ms9-bash-4.4-p23/bin/bash
Scanning dependencies of target yodaLib
[  2%] Building CXX object src/CMakeFiles/yodaLib.dir/mol_sys.cpp.o
[  4%] Building CXX object src/CMakeFiles/yodaLib.dir/seams_input.cpp.o
[  7%] Building CXX object src/CMakeFiles/yodaLib.dir/seams_output.cpp.o
[  9%] Building CXX object src/CMakeFiles/yodaLib.dir/ring.cpp.o
[ 11%] Building CXX object src/CMakeFiles/yodaLib.dir/bond.cpp.o
[ 14%] Building CXX object src/CMakeFiles/yodaLib.dir/generic.cpp.o
[ 16%] Building CXX object src/CMakeFiles/yodaLib.dir/bop.cpp.o
[ 19%] Building CXX object src/CMakeFiles/yodaLib.dir/neighbours.cpp.o
[ 21%] Building CXX object src/CMakeFiles/yodaLib.dir/opt_parser.cpp.o
[ 23%] Building CXX object src/CMakeFiles/yodaLib.dir/backward.cpp.o
[ 26%] Building CXX object src/CMakeFiles/yodaLib.dir/franzblau.cpp.o
[ 28%] Building CXX object src/CMakeFiles/yodaLib.dir/topo_one_dim.cpp.o
[ 30%] Building CXX object src/CMakeFiles/yodaLib.dir/topo_two_dim.cpp.o
[ 33%] Building CXX object src/CMakeFiles/yodaLib.dir/topo_bulk.cpp.o
[ 35%] Building CXX object src/CMakeFiles/yodaLib.dir/order_parameter.cpp.o
[ 38%] Building CXX object src/CMakeFiles/yodaLib.dir/cluster.cpp.o
[ 40%] Building CXX object src/CMakeFiles/yodaLib.dir/rdf2d.cpp.o
[ 42%] Building CXX object src/CMakeFiles/yodaLib.dir/absOrientation.cpp.o
[ 45%] Building CXX object src/CMakeFiles/yodaLib.dir/pntCorrespondence.cpp.o
[ 47%] Building CXX object src/CMakeFiles/yodaLib.dir/bulkTUM.cpp.o
[ 50%] Building CXX object src/CMakeFiles/yodaLib.dir/shapeMatch.cpp.o
[ 52%] Building CXX object src/CMakeFiles/yodaLib.dir/selection.cpp.o
[ 54%] Linking CXX shared library ../libyodaLib.so
[ 54%] Built target yodaLib
Scanning dependencies of target yodaStruct
Scanning dependencies of target yodaStruct_test
[ 57%] Building CXX object src/CMakeFiles/yodaStruct.dir/main.cpp.o
[ 59%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/main.cpp.o
In file included from /build/source/src/main.cpp:48:
/build/source/src/include/external/sol/sol.hpp:14541:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
/build/source/src/include/external/sol/sol.hpp:17294:32: warning: unknown warning group '-Wmaybe-uninitialized', ignored [-Wunknown-warning-option]
#pragma GCC diagnostic ignored "-Wmaybe-uninitialized"
                               ^
2 warnings generated.
[ 61%] 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+0x3052): 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+0x310e): 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+0x31b8): 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+0x3262): 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....
[ 64%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/franzblau-test.cpp.o
[ 66%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/topo_one_dim-test.cpp.o
[ 69%] Building CXX object tests/CMakeFiles/yodaStruct_test.dir/topo_bulk-test.cpp.o
[ 71%] 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
[ 76%] 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
[ 83%] 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
[ 88%] 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/skqga9i257cnpn8zzxg06wrphn0innks-yodaStruct.drv' failed with exit code 2

@HaoZeke
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HaoZeke commented Mar 27, 2023 via email

@Clarkszw
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yes, I tried as well. it gives me a weird response as

(base) clarkszw@aiida:~/seams-core$ micromamba create -f environment.yml 

Command ' ' not found, but can be installed with:

sudo apt install mailutils-mh  # version 1:3.7-2.1, or
sudo apt install meshio-tools  # version 4.0.4-1
sudo apt install mmh           # version 0.4-2
sudo apt install nmh           # version 1.7.1-6
sudo apt install termtris      # version 1.3-1

is this due to yaml file?

@HaoZeke
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HaoZeke commented Mar 30, 2023 via email

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@HaoZeke @Clarkszw