Package evaluation of SIRIUS on Julia 1.13.0-DEV.974 (7bbb213719*) started at 2025-08-12T16:06:26.561 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.88s ################################################################################ # Installation # Installing SIRIUS... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [3581e6f0] + SIRIUS v0.1.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [ffbed154] + DocStringExtensions v0.9.5 [692b3bcd] + JLLWrappers v1.7.1 [0f8b85d8] + JSON3 v1.14.3 [da04e1cc] + MPI v0.20.23 [3da0fdf6] + MPIPreferences v0.1.11 [51095b67] + OpenBLAS32 v0.1.0 [69de0a69] + Parsers v2.8.3 [eebad327] + PkgVersion v0.3.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.5.0 [ae029012] + Requires v1.3.1 [3581e6f0] + SIRIUS v0.1.0 [856f2bd8] + StructTypes v1.11.0 [5f6e5a8a] + COSTA_jll v2.2.2+0 [f5851436] + FFTW_jll v3.3.11+0 ⌅ [1b77fbbe] + GSL_jll v2.7.2+0 ⌅ [0234f1f7] + HDF5_jll v1.14.3+3 [e33a78d0] + Hwloc_jll v2.12.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [a56a6d9d] + Libxc_jll v7.0.0+2 [7cb0a576] + MPICH_jll v4.3.1+0 [f1f71cc9] + MPItrampoline_jll v5.5.4+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [656ef2d0] + OpenBLAS32_jll v0.3.29+0 ⌅ [fe0851c0] + OpenMPI_jll v4.1.8+1 [6b659922] + SIRIUS_jll v7.6.1+0 [8be71ea8] + SpFFT_jll v1.1.0+0 [477f73a3] + libaec_jll v1.1.3+0 [ef860afa] + pugixml_jll v1.14.1+0 [ac4a9f1e] + spglib_jll v2.4.0+0 [c0b6e1fa] + spla_jll v1.6.1+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.2+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 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 12.41s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... ERROR: LoadError: The following 1 direct dependency failed to precompile: SIRIUS Failed to precompile SIRIUS [3581e6f0-5a2a-4fbf-9499-336905df69aa] to "/home/pkgeval/.julia/compiled/v1.13/SIRIUS/jl_AHeFUQ" (ProcessExited(1)). ERROR: LoadError: InitError: could not load library "/home/pkgeval/.julia/artifacts/a8272b4931ee4a7857ac2e4d53ee5152370930a8/lib/libsirius.so" libxc.so.12: cannot open shared object file: No such file or directory Stacktrace: [1] #dlopen#3 @ ./libdl.jl:120 [inlined] [2] dlopen(s::String, flags::UInt32) @ Base.Libc.Libdl ./libdl.jl:119 [3] top-level scope @ ~/.julia/packages/SIRIUS_jll/dM808/src/wrappers/x86_64-linux-gnu-libgfortran5-cxx11-mpi+mpich.jl:19 [4] macro expansion @ ~/.julia/packages/JLLWrappers/m2Pjh/src/products/library_generators.jl:63 [inlined] [5] run_module_init(mod::Module, i::Int64) @ Base ./loading.jl:1417 [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1405 [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool) @ Base ./loading.jl:1293 [8] _include_from_serialized @ ./loading.jl:1247 [inlined] [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String}) @ Base ./loading.jl:2089 [10] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2602 [11] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2468 [12] macro expansion @ ./loading.jl:2396 [inlined] [13] macro expansion @ ./lock.jl:376 [inlined] [14] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2360 [15] require @ ./loading.jl:2336 [inlined] [16] eval_import_path @ ./module.jl:36 [inlined] [17] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [18] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [19] top-level scope @ ~/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:5 [20] include(mod::Module, _path::String) @ Base ./Base.jl:311 [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3001 [22] top-level scope @ stdin:5 [23] eval(m::Module, e::Any) @ Core ./boot.jl:489 [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2847 [25] include_string @ ./loading.jl:2857 [inlined] [26] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [27] _start() @ Base ./client.jl:553 during initialization of module SIRIUS_jll in expression starting at /home/pkgeval/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:1 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 75.17s ################################################################################ # Testing # Testing SIRIUS Status `/tmp/jl_3VC9fy/Project.toml` [0f8b85d8] JSON3 v1.14.3 [da04e1cc] MPI v0.20.23 [51095b67] OpenBLAS32 v0.1.0 [3581e6f0] SIRIUS v0.1.0 [f8b46487] TestItemRunner v1.1.0 [6b659922] SIRIUS_jll v7.6.1+0 [8f399da3] Libdl v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_3VC9fy/Manifest.toml` [ffbed154] DocStringExtensions v0.9.5 [692b3bcd] JLLWrappers v1.7.1 [0f8b85d8] JSON3 v1.14.3 [da04e1cc] MPI v0.20.23 [3da0fdf6] MPIPreferences v0.1.11 [51095b67] OpenBLAS32 v0.1.0 [69de0a69] Parsers v2.8.3 [eebad327] PkgVersion v0.3.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.5.0 [ae029012] Requires v1.3.1 [3581e6f0] SIRIUS v0.1.0 [856f2bd8] StructTypes v1.11.0 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [5f6e5a8a] COSTA_jll v2.2.2+0 [f5851436] FFTW_jll v3.3.11+0 ⌅ [1b77fbbe] GSL_jll v2.7.2+0 ⌅ [0234f1f7] HDF5_jll v1.14.3+3 [e33a78d0] Hwloc_jll v2.12.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [a56a6d9d] Libxc_jll v7.0.0+2 [7cb0a576] MPICH_jll v4.3.1+0 [f1f71cc9] MPItrampoline_jll v5.5.4+0 [9237b28f] MicrosoftMPI_jll v10.1.4+3 [656ef2d0] OpenBLAS32_jll v0.3.29+0 ⌅ [fe0851c0] OpenMPI_jll v4.1.8+1 [6b659922] SIRIUS_jll v7.6.1+0 [8be71ea8] SpFFT_jll v1.1.0+0 [477f73a3] libaec_jll v1.1.3+0 [ef860afa] pugixml_jll v1.14.1+0 [ac4a9f1e] spglib_jll v2.4.0+0 [c0b6e1fa] spla_jll v1.6.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.2+0 [efcefdf7] PCRE2_jll v10.45.0+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... Info Given SIRIUS was explicitly requested, output will be shown live  ERROR: LoadError: InitError: could not load library "/home/pkgeval/.julia/artifacts/a8272b4931ee4a7857ac2e4d53ee5152370930a8/lib/libsirius.so" libxc.so.12: cannot open shared object file: No such file or directory Stacktrace:  [1] #dlopen#3  @ ./libdl.jl:120 [inlined]  [2] dlopen(s::String, flags::UInt32)  @ Base.Libc.Libdl ./libdl.jl:119  [3] top-level scope  @ ~/.julia/packages/SIRIUS_jll/dM808/src/wrappers/x86_64-linux-gnu-libgfortran5-cxx11-mpi+mpich.jl:19  [4] macro expansion  @ ~/.julia/packages/JLLWrappers/m2Pjh/src/products/library_generators.jl:63 [inlined]  [5] run_module_init(mod::Module, i::Int64)  @ Base ./loading.jl:1417  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)  @ Base ./loading.jl:1405  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool)  @ Base ./loading.jl:1293  [8] _include_from_serialized  @ ./loading.jl:1247 [inlined]  [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String})  @ Base ./loading.jl:2089  [10] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2602  [11] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2468  [12] macro expansion  @ ./loading.jl:2396 [inlined]  [13] macro expansion  @ ./lock.jl:376 [inlined]  [14] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2360  [15] require  @ ./loading.jl:2336 [inlined]  [16] eval_import_path  @ ./module.jl:36 [inlined]  [17] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [18] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [19] top-level scope  @ ~/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:5  [20] include(mod::Module, _path::String)  @ Base ./Base.jl:311  [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3001  [22] top-level scope  @ stdin:5  [23] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2847  [25] include_string  @ ./loading.jl:2857 [inlined]  [26] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:318  [27] _start()  @ Base ./client.jl:553 during initialization of module SIRIUS_jll in expression starting at /home/pkgeval/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:1 in expression starting at stdin:5 ✗ SIRIUS 0 dependencies successfully precompiled in 9 seconds. 61 already precompiled. ERROR: LoadError: The following 1 direct dependency failed to precompile: SIRIUS Failed to precompile SIRIUS [3581e6f0-5a2a-4fbf-9499-336905df69aa] to "/home/pkgeval/.julia/compiled/v1.13/SIRIUS/jl_OaQ184" (ProcessExited(1)). ERROR: LoadError: InitError: could not load library "/home/pkgeval/.julia/artifacts/a8272b4931ee4a7857ac2e4d53ee5152370930a8/lib/libsirius.so" libxc.so.12: cannot open shared object file: No such file or directory Stacktrace: [1] #dlopen#3 @ ./libdl.jl:120 [inlined] [2] dlopen(s::String, flags::UInt32) @ Base.Libc.Libdl ./libdl.jl:119 [3] top-level scope @ ~/.julia/packages/SIRIUS_jll/dM808/src/wrappers/x86_64-linux-gnu-libgfortran5-cxx11-mpi+mpich.jl:19 [4] macro expansion @ ~/.julia/packages/JLLWrappers/m2Pjh/src/products/library_generators.jl:63 [inlined] [5] run_module_init(mod::Module, i::Int64) @ Base ./loading.jl:1417 [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1405 [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool) @ Base ./loading.jl:1293 [8] _include_from_serialized @ ./loading.jl:1247 [inlined] [9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String}) @ Base ./loading.jl:2089 [10] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2602 [11] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2468 [12] macro expansion @ ./loading.jl:2396 [inlined] [13] macro expansion @ ./lock.jl:376 [inlined] [14] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2360 [15] require @ ./loading.jl:2336 [inlined] [16] eval_import_path @ ./module.jl:36 [inlined] [17] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [18] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [19] top-level scope @ ~/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:5 [20] include(mod::Module, _path::String) @ Base ./Base.jl:311 [21] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3001 [22] top-level scope @ stdin:5 [23] eval(m::Module, e::Any) @ Core ./boot.jl:489 [24] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2847 [25] include_string @ ./loading.jl:2857 [inlined] [26] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [27] _start() @ Base ./client.jl:553 during initialization of module SIRIUS_jll in expression starting at /home/pkgeval/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:1 in expression starting at stdin: in expression starting at /home/pkgeval/.julia/packages/SIRIUS/ebgHq/test/runtests_runner.jl:3 ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so --depwarn=yes --check-bounds=yes --pkgimages=existing -g1 --startup-file=no /home/pkgeval/.julia/packages/SIRIUS/ebgHq/test/runtests_runner.jl`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:602 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:517 [3] run(::Cmd) @ Base ./process.jl:514 [4] top-level scope @ ~/.julia/packages/SIRIUS/ebgHq/test/runtests.jl:36 [5] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [6] top-level scope @ none:6 [7] eval(m::Module, e::Any) @ Core ./boot.jl:489 [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [9] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/SIRIUS/ebgHq/test/runtests.jl:33 Testing failed after 90.96s ERROR: LoadError: Package SIRIUS errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2672 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2521 [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/v1.13/Pkg/src/API.jl:538 [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/v1.13/Pkg/src/API.jl:515 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 207.01s: package requires a missing binary dependency