Package evaluation to test Spglib on Julia 1.14.0-DEV.1384 (b34261b5d0*) started at 2025-12-18T13:51:39.417 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.93s ################################################################################ # Installation # Installing Spglib... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [f761d5c5] + Spglib v1.0.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [34da2185] + Compat v4.18.1 ⌅ [80545937] + CrystallographyCore v0.3.3 [692b3bcd] + JLLWrappers v1.7.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [f761d5c5] + Spglib v1.0.1 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [6ec83bb0] + StructEquality v2.1.0 [ac4a9f1e] + spglib_jll v2.6.0+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.9s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 13.63s ################################################################################ # Testing # Testing Spglib Status `/tmp/jl_DBVlRV/Project.toml` ⌅ [80545937] CrystallographyCore v0.3.3 [f761d5c5] Spglib v1.0.1 [1e83bf80] StaticArraysCore v1.4.4 [6ec83bb0] StructEquality v2.1.0 [ac4a9f1e] spglib_jll v2.6.0+0 [8dfed614] Test v1.11.0 Status `/tmp/jl_DBVlRV/Manifest.toml` [34da2185] Compat v4.18.1 ⌅ [80545937] CrystallographyCore v0.3.3 [692b3bcd] JLLWrappers v1.7.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [f761d5c5] Spglib v1.0.1 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [6ec83bb0] StructEquality v2.1.0 [ac4a9f1e] spglib_jll v2.6.0+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [8e850b90] libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Spglib.jl: Test Failed at /home/pkgeval/.julia/packages/Spglib/daKTm/test/misc.jl:1 Expression: get_version() == v"2.5.0" Evaluated: v"2.6.0" == v"2.5.0" Stacktrace: [1] top-level scope @ ~/.julia/packages/Spglib/daKTm/test/misc.jl:539 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] [3] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [4] top-level scope @ ~/.julia/packages/Spglib/daKTm/test/runtests.jl:6 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/Spglib/daKTm/test/runtests.jl:6 [inlined] [9] signal 11 (1): Segmentation fault in expression starting at /home/pkgeval/.julia/packages/Spglib/daKTm/test/standardize.jl:92 isassigned at ./genericmemory.jl:124 [inlined] unsafe_copyto! at ./genericmemory.jl:171 unsafe_copyto! at ./genericmemory.jl:151 [inlined] _copyto_impl! at ./array.jl:300 [inlined] copyto! at ./array.jl:286 [inlined] _copyto2arg! at ./array.jl:311 [inlined] copyto! at ./array.jl:313 [inlined] copyto_axcheck! at ./abstractarray.jl:1186 [inlined] Array at ./array.jl:652 [inlined] convert at ./array.jl:645 [inlined] SpglibCell at /home/pkgeval/.julia/packages/Spglib/daKTm/src/core.jl:99 [inlined] SpglibCell at /home/pkgeval/.julia/packages/Spglib/daKTm/src/core.jl:135 SpglibCell at /home/pkgeval/.julia/packages/Spglib/daKTm/src/core.jl:105 unknown function (ip: 0x71be171475d2) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_body at /source/src/interpreter.c:581 eval_body at /source/src/interpreter.c:550 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:550 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:757 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 include_string at ./loading.jl:3124 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3184 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_65787.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 eval_body at /source/src/interpreter.c:550 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:757 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 include_string at ./loading.jl:3124 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3184 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_65787.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:757 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_62300.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2285 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x71be185ec249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S Allocations: 27140060 (Pool: 27139615; Big: 445); GC: 16 Testing failed after 53.84s ERROR: LoadError: Package Spglib errored during testing (received signal: 11) Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:237 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval crashed after 98.25s: a segmentation fault happened ################################################################################ # Bug reporting # The package crashed during testing (reason=segfault), but PkgEval was unable to reproduce the crash under rr (status=fail, reason=test_errors). For debugging, here is the tail end of the rr log: > [15] top-level scope > @ none:6 > [16] eval(m::Module, e::Any) > @ Core ./boot.jl:489 > [17] exec_options(opts::Base.JLOptions) > @ Base ./client.jl:310 > [18] _start() > @ Base ./client.jl:577 > Test Summary: | Pass Fail Error Total Time > Spglib.jl | 781 1 1 783 1m04.4s > Test constructors | 8 8 2.6s > Get symmetry operations | 24 24 6.4s > Test LaMnO₃ | 9 9 4.0s > Test example given by Jae-Mo Lihm (@jaemolihm) | 19 19 3.0s > Test type I | 19 19 2.9s > Test type III | 19 19 0.9s > Test monoclinic | 19 19 0.2s > Test centered monoclinic | 19 19 0.2s > Test trigonal | 19 19 0.1s > Test conventional | 19 19 0.0s > Test type IV | 19 19 0.0s > Test nonstandard setting | 19 19 0.0s > Test nonstandard setting 2 | 19 19 0.0s > Test nonstandard setting 3 | 19 19 0.0s > Test nonstandard type 4 | 19 19 0.0s > Test primitive lattice | 17 17 0.0s > Test site tensors for rutile (type III) | 23 23 1.4s > Test site tensors for Cr (type IV) | 23 23 0.4s > Test site tensors non-collinear | 22 22 0.7s > Test `get_magnetic_symmetry_from_database` | 6 6 0.6s > Test `get_magnetic_spacegroup_type` | 9 9 0.1s > Test CrCl₂ | 40 40 2.4s > Test type-IV MSG | 9 9 1.3s > Transformation to a primitive cell | 3 3 2.0s > Rotate the basis vectors rigidly in the above example | 6 6 0.5s > Cell reduce standardize | 3 1 4 4.1s > Test `find_primitive` | 1 1 2.8s > Test `refine_cell` | 3 3 1.3s > A test that will cause an error | 4 4 0.2s > Test reciprocal mesh using the example from `LibSymspg.jl` | 1 1 0.9s > Python example | 14 14 3.1s > Test rutile structure | 13 13 2.5s > Test distorted silicon structure | 4 4 3.7s > Test the primitive cell of silicon | 1 1 0.0s > Test MgB₂ structure | 8 8 0.3s > Test examples from Python | 4 4 0.4s > Test examples from `LibSymspg.jl` | 4 4 2.9s > Test an example from C | 2 2 0.4s > Test `get_spacegroup_type` | 9 9 0.2s > Computing rigid rotation introduced by idealization | 35 35 4.3s > Test rutile structure | 34 34 1.0s > Test distorted rutile structure | 35 35 0.1s > Test on P-3m1 space group | 36 36 0.2s > Test silicon structure | 34 34 0.1s > Test primitive silicon structure | 33 33 0.2s > Test MgB₂ structure | 33 33 0.2s > Test wurtzite structure (P6_3mc) | 33 33 0.1s > Test issue 176 | 1 1 0.2s > Test zincblende | 2 2 0.0s > Test when no error occurs | 1 1 0.0s > Test error types | 10 10 0.1s > RNG of the outermost testset: Random.Xoshiro(0xaf6500bb37c82098, 0x911a53342d66c8e1, 0x38e5162b6b0f71fc, 0x33b4e76c23b3bf10, 0xe91fbd25d133ee97) > ERROR: LoadError: Some tests did not pass: 781 passed, 1 failed, 1 errored, 0 broken. > in expression starting at /home/pkgeval/.julia/packages/Spglib/daKTm/test/runtests.jl:4 > > Testing failed after 96.0s > > ERROR: LoadError: Package Spglib errored during testing > Stacktrace: > [1] pkgerror(msg::String) > @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 > [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) > @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3067 > [3] test > @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [inlined] > [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 > [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 > [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 > [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 > [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 > [9] test > @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] > [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) > @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 > [11] top-level scope > @ /PkgEval.jl/scripts/evaluate.jl:235 > [12] include(mod::Module, _path::String) > @ Base ./Base.jl:309 > [13] exec_options(opts::Base.JLOptions) > @ Base ./client.jl:344 > [14] _start() > @ Base ./client.jl:577 > in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 > > PkgEval failed after 147.62s: package tests unexpectedly errored