Package evaluation of SIRIUS on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T15:31:26.712


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.27s


################################################################################
# Installation
#

Installing SIRIUS...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [3581e6f0] + SIRIUS v0.1.0
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [ffbed154] + DocStringExtensions v0.9.5
  [692b3bcd] + JLLWrappers v1.7.0
  [0f8b85d8] + JSON3 v1.14.3
  [da04e1cc] + MPI v0.20.22
  [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 v1.4.3
  [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 v1.6.0
  [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 v1.12.0
  [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 v8.11.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.13.1+0
  [8e850ede] + nghttp2_jll v1.64.0+1
  [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 11.28s


################################################################################
# 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/v1.12/SIRIUS/jl_f7JujD".
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/GfYNv/src/products/library_generators.jl:63 [inlined]
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1411
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1399
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool)
    @ Base ./loading.jl:1287
  [8] _include_from_serialized
    @ ./loading.jl:1246 [inlined]
  [9] _tryrequire_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing)
    @ Base ./loading.jl:1971
 [10] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2662
 [11] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [12] macro expansion
    @ ./loading.jl:2389 [inlined]
 [13] macro expansion
    @ ./lock.jl:376 [inlined]
 [14] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [15] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [16] top-level scope
    @ ~/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:5
 [17] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [18] 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:2991
 [19] top-level scope
    @ stdin:5
 [20] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [21] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [22] include_string
    @ ./loading.jl:2847 [inlined]
 [23] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [24] _start()
    @ Base ./client.jl:554
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 101.96s



################################################################################
# Testing
#

     Testing SIRIUS
      Status `/tmp/jl_tT3erG/Project.toml`
  [0f8b85d8] JSON3 v1.14.3
  [da04e1cc] MPI v0.20.22
  [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_tT3erG/Manifest.toml`
  [ffbed154] DocStringExtensions v0.9.5
  [692b3bcd] JLLWrappers v1.7.0
  [0f8b85d8] JSON3 v1.14.3
  [da04e1cc] MPI v0.20.22
  [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 v1.4.3
  [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 v1.6.0
  [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 v1.12.0
  [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 v8.11.1+1
  [e37daf67] LibGit2_jll v1.9.0+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.5.20
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.5.1+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.13.1+0
  [8e850ede] nghttp2_jll v1.64.0+1
  [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/GfYNv/src/products/library_generators.jl:63 [inlined]
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1411
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1399
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool)
    @ Base ./loading.jl:1287
  [8] _include_from_serialized
    @ ./loading.jl:1246 [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:2083
 [10] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2595
 [11] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [12] macro expansion
    @ ./loading.jl:2389 [inlined]
 [13] macro expansion
    @ ./lock.jl:376 [inlined]
 [14] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [15] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [16] top-level scope
    @ ~/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:5
 [17] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [18] 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:2991
 [19] top-level scope
    @ stdin:5
 [20] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [21] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [22] include_string
    @ ./loading.jl:2847 [inlined]
 [23] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [24] _start()
    @ Base ./client.jl:554
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. 60 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/v1.12/SIRIUS/jl_Lfv3mf".
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/GfYNv/src/products/library_generators.jl:63 [inlined]
  [5] run_module_init(mod::Module, i::Int64)
    @ Base ./loading.jl:1411
  [6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
    @ Base ./loading.jl:1399
  [7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool)
    @ Base ./loading.jl:1287
  [8] _include_from_serialized
    @ ./loading.jl:1246 [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:2083
 [10] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2595
 [11] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [12] macro expansion
    @ ./loading.jl:2389 [inlined]
 [13] macro expansion
    @ ./lock.jl:376 [inlined]
 [14] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [15] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [16] top-level scope
    @ ~/.julia/packages/SIRIUS/ebgHq/src/SIRIUS.jl:5
 [17] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [18] 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:2991
 [19] top-level scope
    @ stdin:5
 [20] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [21] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [22] include_string
    @ ./loading.jl:2847 [inlined]
 [23] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [24] _start()
    @ Base ./client.jl:554
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:598 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base ./process.jl:513
 [3] run(::Cmd)
   @ Base ./process.jl:510
 [4] top-level scope
   @ ~/.julia/packages/SIRIUS/ebgHq/test/runtests.jl:36
 [5] include(mapexpr::Function, mod::Module, _path::String)
   @ Base ./Base.jl:306
 [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:287
 [9] _start()
   @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/SIRIUS/ebgHq/test/runtests.jl:33

Testing failed after 87.75s

ERROR: LoadError: Package SIRIUS errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2458
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [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/v1.12/Pkg/src/API.jl:511
  [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:321
 [12] _start()
    @ Base ./client.jl:554
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 231.64s: package requires a missing binary dependency