Package evaluation of MolecularGraphKernels on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T21:03:33.901


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 6.55s


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

Installing MolecularGraphKernels...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [bf3818bd] + MolecularGraphKernels v0.11.0
    Updating `~/.julia/environments/v1.12/Manifest.toml`
⌅ [ec485272] + ArnoldiMethod v0.2.0
  [159f3aea] + Cairo v1.1.1
⌅ [3da002f7] + ColorTypes v0.11.5
⌅ [5ae59095] + Colors v0.12.11
  [861a8166] + Combinatorics v1.0.3
  [34da2185] + Compat v4.17.0
  [a81c6b42] + Compose v0.9.6
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.18.22
  [8bb1440f] + DelimitedFiles v1.9.1
  [5789e2e9] + FileIO v1.17.0
  [53c48c17] + FixedPointNumbers v0.8.5
⌅ [a2cc645c] + GraphPlot v0.5.2
  [a2bd30eb] + Graphics v1.1.3
⌃ [86223c79] + Graphs v1.9.0
  [d25df0c9] + Inflate v0.1.5
  [c8e1da08] + IterTools v1.10.0
⌅ [033835bb] + JLD2 v0.4.54
  [692b3bcd] + JLLWrappers v1.7.0
  [682c06a0] + JSON v0.21.4
  [fc18253b] + LazyJSON v0.2.2
  [1914dd2f] + MacroTools v0.5.16
  [442fdcdd] + Measures v0.3.2
  [6fafb56a] + Memoization v0.2.2
⌅ [626554b9] + MetaGraphs v0.7.2
  [e1d29d7a] + Missings v1.2.0
⌅ [6c89ec66] + MolecularGraph v0.13.0
  [bf3818bd] + MolecularGraphKernels v0.11.0
  [77ba4419] + NaNMath v1.1.3
  [4d1e1d77] + Nullables v1.0.0
  [bac558e1] + OrderedCollections v1.8.1
  [69de0a69] + Parsers v2.8.3
  [7b2266bf] + PeriodicTable v1.2.1
  [91cefc8d] + PrecompileSignatures v3.0.3
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [92933f4c] + ProgressMeter v1.10.4
⌅ [f8a19df8] + PropertyDicts v0.1.2
  [44044271] + RDKitMinimalLib v1.2.0
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [699a6c99] + SimpleTraits v0.9.4
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [69024149] + StringEncodings v0.3.7
  [3bb67fe8] + TranscodingStreams v0.11.3
  [1986cc42] + Unitful v1.23.1
  [cbff2730] + Unmarshal v0.4.4
  [ddb6d928] + YAML v0.4.14
  [6e34b625] + Bzip2_jll v1.0.9+0
  [83423d85] + Cairo_jll v1.18.5+0
  [2e619515] + Expat_jll v2.6.5+0
  [a3f928ae] + Fontconfig_jll v2.16.0+0
  [d7e528f0] + FreeType2_jll v2.13.4+0
  [559328eb] + FriBidi_jll v1.0.17+0
  [b0724c58] + GettextRuntime_jll v0.22.4+0
  [7746bdde] + Glib_jll v2.84.3+0
  [3b182d85] + Graphite2_jll v1.3.15+0
  [2e76f6c2] + HarfBuzz_jll v8.5.1+0
  [1d63c593] + LLVMOpenMP_jll v18.1.8+0
  [dd4b983a] + LZO_jll v2.10.3+0
  [e9f186c6] + Libffi_jll v3.4.7+0
  [94ce4f54] + Libiconv_jll v1.18.0+0
  [4b2f31a3] + Libmount_jll v2.41.0+0
  [38a345b3] + Libuuid_jll v2.41.0+0
  [36c8627f] + Pango_jll v1.56.3+0
⌅ [30392449] + Pixman_jll v0.44.2+0
  [03d1d220] + RDKit_jll v2022.9.5+0
  [4f6342f7] + Xorg_libX11_jll v1.8.12+0
  [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0
  [a3789734] + Xorg_libXdmcp_jll v1.1.6+0
  [1082639a] + Xorg_libXext_jll v1.3.7+0
  [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0
  [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0
  [c5fb5394] + Xorg_xtrans_jll v1.6.0+0
⌅ [28df3c45] + boost_jll v1.76.0+1
  [f6050b86] + coordgenlibs_jll v3.0.2+0
  [172afb32] + libinchi_jll v1.6.0+0
  [b53b4c65] + libpng_jll v1.6.50+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
  [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
  [1a1011a3] + SharedArrays v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.12.0
  [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
  [05823500] + OpenLibm_jll v0.8.5+0
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [efcefdf7] + PCRE2_jll v10.44.0+1
  [bea87d4a] + SuiteSparse_jll v7.8.3+2
  [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 ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

Installation completed after 3.98s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...
ERROR: LoadError: The following 2 direct dependencies failed to precompile:

MetaGraphs 

Failed to precompile MetaGraphs [626554b9-1ddb-594c-aa3c-2596fe9399a5] to "/home/pkgeval/.julia/compiled/v1.12/MetaGraphs/jl_MuYHJ9".
Error encountered while load FileIO.File{FileIO.DataFormat{:JLD2}, String}("/tmp/jl_NxCDNO").

Fatal error:
ERROR: LoadError: ConcurrencyViolationError("deadlock detected in loading JLD2 using JLD2")
Stacktrace:
  [1] canstart_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2178
  [2] start_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2186
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2456
  [4] _require_prelocked
    @ ./loading.jl:2455 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:2453
  [7] require
    @ ./loading.jl:2451 [inlined]
  [8] #37
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203 [inlined]
  [9] lock(f::FileIO.var"#37#38"{Base.PkgId}, l::ReentrantLock)
    @ Base ./lock.jl:335
 [10] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203
 [11] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
 [12] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
 [13] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
 [14] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
 [15] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
 [16] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [17] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [18] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [19] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [20] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [22] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
Stacktrace:
  [1] handle_error(e::ConcurrencyViolationError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:71
  [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:66
  [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:228
  [4] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
  [5] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
  [6] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
  [7] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
  [8] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
  [9] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [10] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [11] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [12] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [13] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [14] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [15] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
 [16] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:306
 [17] IncludeInto
    @ ./Base.jl:307 [inlined]
 [18] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/JLD2.jl:518
 [19] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [20] 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::String)
    @ Base ./loading.jl:2991
 [21] top-level scope
    @ stdin:5
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [24] include_string
    @ ./loading.jl:2847 [inlined]
 [25] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [26] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/precompile.jl:3
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/JLD2.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to "/home/pkgeval/.julia/compiled/v1.12/JLD2/jl_R9DIau".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3278
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2647
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3849
 [10] maybe_cachefile_lock
    @ ./loading.jl:3846 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2633
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [13] macro expansion
    @ ./loading.jl:2389 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [17] top-level scope
    @ ~/.julia/packages/MetaGraphs/qq8oz/src/MetaGraphs.jl:3
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [19] 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
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [23] include_string
    @ ./loading.jl:2847 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [25] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/MetaGraphs/qq8oz/src/MetaGraphs.jl:1
in expression starting at stdin:5
MolecularGraphKernels 

Failed to precompile MolecularGraphKernels [bf3818bd-b6bb-4954-8baa-32c32282e633] to "/home/pkgeval/.julia/compiled/v1.12/MolecularGraphKernels/jl_0DPJkW".
Error encountered while load FileIO.File{FileIO.DataFormat{:JLD2}, String}("/tmp/jl_dRPfCK").

Fatal error:
ERROR: LoadError: ConcurrencyViolationError("deadlock detected in loading JLD2 using JLD2")
Stacktrace:
  [1] canstart_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2178
  [2] start_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2186
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2456
  [4] _require_prelocked
    @ ./loading.jl:2455 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:2453
  [7] require
    @ ./loading.jl:2451 [inlined]
  [8] #37
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203 [inlined]
  [9] lock(f::FileIO.var"#37#38"{Base.PkgId}, l::ReentrantLock)
    @ Base ./lock.jl:335
 [10] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203
 [11] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
 [12] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
 [13] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
 [14] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
 [15] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
 [16] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [17] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [18] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [19] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [20] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [22] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
Stacktrace:
  [1] handle_error(e::ConcurrencyViolationError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:71
  [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:66
  [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:228
  [4] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
  [5] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
  [6] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
  [7] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
  [8] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
  [9] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [10] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [11] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [12] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [13] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [14] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [15] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
 [16] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:306
 [17] IncludeInto
    @ ./Base.jl:307 [inlined]
 [18] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/JLD2.jl:518
 [19] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [20] 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::String)
    @ Base ./loading.jl:2991
 [21] top-level scope
    @ stdin:5
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [24] include_string
    @ ./loading.jl:2847 [inlined]
 [25] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [26] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/precompile.jl:3
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/JLD2.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to "/home/pkgeval/.julia/compiled/v1.12/JLD2/jl_82cd1C".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3278
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2647
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3849
 [10] maybe_cachefile_lock
    @ ./loading.jl:3846 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2633
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [13] macro expansion
    @ ./loading.jl:2389 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [17] top-level scope
    @ ~/.julia/packages/MolecularGraphKernels/YLyTg/src/MolecularGraphKernels.jl:3
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [19] 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
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [23] include_string
    @ ./loading.jl:2847 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [25] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/MolecularGraphKernels/YLyTg/src/MolecularGraphKernels.jl:1
in expression starting at stdin:5
in expression starting at /PkgEval.jl/scripts/precompile.jl:37

Precompilation failed after 234.44s



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

     Testing MolecularGraphKernels
      Status `/tmp/jl_kkc21p/Project.toml`
  [4c88cf16] Aqua v0.8.13
⌅ [5ae59095] Colors v0.12.11
  [861a8166] Combinatorics v1.0.3
  [a2441757] Coverage v1.6.1
  [e30172f5] Documenter v1.14.1
⌃ [86223c79] Graphs v1.9.0
  [b5f81e59] IOCapture v0.2.5
⌅ [626554b9] MetaGraphs v0.7.2
⌅ [6c89ec66] MolecularGraph v0.13.0
  [bf3818bd] MolecularGraphKernels v0.11.0
  [44044271] RDKitMinimalLib v1.2.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [37e2e46d] LinearAlgebra v1.12.0
  [2f01184e] SparseArrays v1.12.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_kkc21p/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [1520ce14] AbstractTrees v0.4.5
  [4c88cf16] Aqua v0.8.13
⌅ [ec485272] ArnoldiMethod v0.2.0
  [d1d4a3ce] BitFlags v0.1.9
  [159f3aea] Cairo v1.1.1
  [944b1d66] CodecZlib v0.7.8
⌅ [3da002f7] ColorTypes v0.11.5
⌅ [5ae59095] Colors v0.12.11
  [861a8166] Combinatorics v1.0.3
  [34da2185] Compat v4.17.0
  [a81c6b42] Compose v0.9.6
  [f0e56b4a] ConcurrentUtilities v2.5.0
  [a2441757] Coverage v1.6.1
  [c36e975a] CoverageTools v1.3.2
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.22
  [8bb1440f] DelimitedFiles v1.9.1
  [ffbed154] DocStringExtensions v0.9.5
  [e30172f5] Documenter v1.14.1
  [460bff9d] ExceptionUnwrapping v0.1.11
  [5789e2e9] FileIO v1.17.0
  [53c48c17] FixedPointNumbers v0.8.5
  [d7ba0133] Git v1.4.0
⌅ [a2cc645c] GraphPlot v0.5.2
  [a2bd30eb] Graphics v1.1.3
⌃ [86223c79] Graphs v1.9.0
  [cd3eb016] HTTP v1.10.17
  [b5f81e59] IOCapture v0.2.5
  [d25df0c9] Inflate v0.1.5
  [c8e1da08] IterTools v1.10.0
⌅ [033835bb] JLD2 v0.4.54
  [692b3bcd] JLLWrappers v1.7.0
  [682c06a0] JSON v0.21.4
  [0e77f7df] LazilyInitializedFields v1.3.0
  [fc18253b] LazyJSON v0.2.2
  [e6f89c97] LoggingExtras v1.1.0
  [1914dd2f] MacroTools v0.5.16
  [d0879d2d] MarkdownAST v0.1.2
  [739be429] MbedTLS v1.1.9
  [442fdcdd] Measures v0.3.2
  [6fafb56a] Memoization v0.2.2
⌅ [626554b9] MetaGraphs v0.7.2
  [e1d29d7a] Missings v1.2.0
⌅ [6c89ec66] MolecularGraph v0.13.0
  [bf3818bd] MolecularGraphKernels v0.11.0
  [77ba4419] NaNMath v1.1.3
  [4d1e1d77] Nullables v1.0.0
  [4d8831e6] OpenSSL v1.5.0
  [bac558e1] OrderedCollections v1.8.1
  [69de0a69] Parsers v2.8.3
  [7b2266bf] PeriodicTable v1.2.1
  [91cefc8d] PrecompileSignatures v3.0.3
  [aea7be01] PrecompileTools v1.3.2
  [21216c6a] Preferences v1.4.3
  [92933f4c] ProgressMeter v1.10.4
⌅ [f8a19df8] PropertyDicts v0.1.2
  [44044271] RDKitMinimalLib v1.2.0
  [189a3867] Reexport v1.2.2
  [2792f1a3] RegistryInstances v0.1.0
  [ae029012] Requires v1.3.1
  [777ac1f9] SimpleBufferStream v1.2.0
  [699a6c99] SimpleTraits v0.9.4
  [90137ffa] StaticArrays v1.9.13
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [69024149] StringEncodings v0.3.7
  [3bb67fe8] TranscodingStreams v0.11.3
  [5c2747f8] URIs v1.6.1
  [1986cc42] Unitful v1.23.1
  [cbff2730] Unmarshal v0.4.4
  [ddb6d928] YAML v0.4.14
  [6e34b625] Bzip2_jll v1.0.9+0
  [83423d85] Cairo_jll v1.18.5+0
  [2e619515] Expat_jll v2.6.5+0
  [a3f928ae] Fontconfig_jll v2.16.0+0
  [d7e528f0] FreeType2_jll v2.13.4+0
  [559328eb] FriBidi_jll v1.0.17+0
  [b0724c58] GettextRuntime_jll v0.22.4+0
  [f8c6e375] Git_jll v2.50.0+0
  [7746bdde] Glib_jll v2.84.3+0
  [3b182d85] Graphite2_jll v1.3.15+0
  [2e76f6c2] HarfBuzz_jll v8.5.1+0
  [1d63c593] LLVMOpenMP_jll v18.1.8+0
  [dd4b983a] LZO_jll v2.10.3+0
  [e9f186c6] Libffi_jll v3.4.7+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [4b2f31a3] Libmount_jll v2.41.0+0
  [38a345b3] Libuuid_jll v2.41.0+0
  [c8ffd9c3] MbedTLS_jll v2.28.6+2
  [9bd350c2] OpenSSH_jll v10.0.1+0
  [36c8627f] Pango_jll v1.56.3+0
⌅ [30392449] Pixman_jll v0.44.2+0
  [03d1d220] RDKit_jll v2022.9.5+0
  [4f6342f7] Xorg_libX11_jll v1.8.12+0
  [0c0b7dd1] Xorg_libXau_jll v1.0.13+0
  [a3789734] Xorg_libXdmcp_jll v1.1.6+0
  [1082639a] Xorg_libXext_jll v1.3.7+0
  [ea2f1a96] Xorg_libXrender_jll v0.9.12+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.1+0
  [c5fb5394] Xorg_xtrans_jll v1.6.0+0
⌅ [28df3c45] boost_jll v1.76.0+1
  [f6050b86] coordgenlibs_jll v3.0.2+0
  [172afb32] libinchi_jll v1.6.0+0
  [b53b4c65] libpng_jll v1.6.50+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
  [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
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.12.0
  [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
  [05823500] OpenLibm_jll v0.8.5+0
  [458c3c95] OpenSSL_jll v3.5.1+0
  [efcefdf7] PCRE2_jll v10.44.0+1
  [bea87d4a] SuiteSparse_jll v7.8.3+2
  [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 ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading.
     Testing Running tests...
Precompiling packages...
           ✗ JLD2
           ✗ MetaGraphs
Info Given MolecularGraphKernels was explicitly requested, output will be shown live 
Error encountered while load FileIO.File{FileIO.DataFormat{:JLD2}, String}("/tmp/jl_E3AmKl").

Fatal error:
ERROR: LoadError: ConcurrencyViolationError("deadlock detected in loading JLD2 using JLD2")
Stacktrace:
  [1] canstart_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2178
  [2] start_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2186
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2456
  [4] _require_prelocked
    @ ./loading.jl:2455 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:2453
  [7] require
    @ ./loading.jl:2451 [inlined]
  [8] #37
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203 [inlined]
  [9] lock(f::FileIO.var"#37#38"{Base.PkgId}, l::ReentrantLock)
    @ Base ./lock.jl:335
 [10] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203
 [11] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
 [12] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
 [13] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
 [14] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
 [15] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
 [16] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [17] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [18] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [19] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [20] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [22] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
Stacktrace:
  [1] handle_error(e::ConcurrencyViolationError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:71
  [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:66
  [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:228
  [4] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
  [5] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
  [6] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
  [7] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
  [8] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
  [9] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [10] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [11] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [12] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [13] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [14] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [15] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
 [16] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:306
 [17] IncludeInto
    @ ./Base.jl:307 [inlined]
 [18] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/JLD2.jl:518
 [19] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [20] 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::String)
    @ Base ./loading.jl:2991
 [21] top-level scope
    @ stdin:5
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [24] include_string
    @ ./loading.jl:2847 [inlined]
 [25] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [26] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/precompile.jl:3
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/JLD2.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to "/home/pkgeval/.julia/compiled/v1.12/JLD2/jl_L2Ayre".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3278
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2647
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3849
 [10] maybe_cachefile_lock
    @ ./loading.jl:3846 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2633
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [13] macro expansion
    @ ./loading.jl:2389 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [17] top-level scope
    @ ~/.julia/packages/MolecularGraphKernels/YLyTg/src/MolecularGraphKernels.jl:3
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [19] 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
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [23] include_string
    @ ./loading.jl:2847 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [25] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/MolecularGraphKernels/YLyTg/src/MolecularGraphKernels.jl:1
in expression starting at stdin:5
           ✗ MolecularGraphKernels
  0 dependencies successfully precompiled in 184 seconds. 116 already precompiled.

ERROR: LoadError: The following 2 direct dependencies failed to precompile:

MetaGraphs 

Failed to precompile MetaGraphs [626554b9-1ddb-594c-aa3c-2596fe9399a5] to "/home/pkgeval/.julia/compiled/v1.12/MetaGraphs/jl_CiTVG4".
Error encountered while load FileIO.File{FileIO.DataFormat{:JLD2}, String}("/tmp/jl_mZpnGe").

Fatal error:
ERROR: LoadError: ConcurrencyViolationError("deadlock detected in loading JLD2 using JLD2")
Stacktrace:
  [1] canstart_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2178
  [2] start_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2186
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2456
  [4] _require_prelocked
    @ ./loading.jl:2455 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:2453
  [7] require
    @ ./loading.jl:2451 [inlined]
  [8] #37
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203 [inlined]
  [9] lock(f::FileIO.var"#37#38"{Base.PkgId}, l::ReentrantLock)
    @ Base ./lock.jl:335
 [10] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203
 [11] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
 [12] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
 [13] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
 [14] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
 [15] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
 [16] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [17] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [18] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [19] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [20] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [22] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
Stacktrace:
  [1] handle_error(e::ConcurrencyViolationError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:71
  [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:66
  [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:228
  [4] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
  [5] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
  [6] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
  [7] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
  [8] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
  [9] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [10] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [11] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [12] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [13] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [14] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [15] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
 [16] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:306
 [17] IncludeInto
    @ ./Base.jl:307 [inlined]
 [18] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/JLD2.jl:518
 [19] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [20] 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::String)
    @ Base ./loading.jl:2991
 [21] top-level scope
    @ stdin:5
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [24] include_string
    @ ./loading.jl:2847 [inlined]
 [25] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [26] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/precompile.jl:3
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/JLD2.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to "/home/pkgeval/.julia/compiled/v1.12/JLD2/jl_WtK5AW".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3278
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2647
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3849
 [10] maybe_cachefile_lock
    @ ./loading.jl:3846 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2633
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [13] macro expansion
    @ ./loading.jl:2389 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [17] top-level scope
    @ ~/.julia/packages/MetaGraphs/qq8oz/src/MetaGraphs.jl:3
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [19] 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
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [23] include_string
    @ ./loading.jl:2847 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [25] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/MetaGraphs/qq8oz/src/MetaGraphs.jl:1
in expression starting at stdin:5
MolecularGraphKernels 

Failed to precompile MolecularGraphKernels [bf3818bd-b6bb-4954-8baa-32c32282e633] to "/home/pkgeval/.julia/compiled/v1.12/MolecularGraphKernels/jl_RmqVlp".
Error encountered while load FileIO.File{FileIO.DataFormat{:JLD2}, String}("/tmp/jl_E3AmKl").

Fatal error:
ERROR: LoadError: ConcurrencyViolationError("deadlock detected in loading JLD2 using JLD2")
Stacktrace:
  [1] canstart_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2178
  [2] start_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2186
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2456
  [4] _require_prelocked
    @ ./loading.jl:2455 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:2453
  [7] require
    @ ./loading.jl:2451 [inlined]
  [8] #37
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203 [inlined]
  [9] lock(f::FileIO.var"#37#38"{Base.PkgId}, l::ReentrantLock)
    @ Base ./lock.jl:335
 [10] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:203
 [11] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
 [12] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
 [13] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
 [14] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
 [15] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
 [16] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [17] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [18] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [19] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [20] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [21] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [22] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
Stacktrace:
  [1] handle_error(e::ConcurrencyViolationError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:71
  [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector}}, action::String)
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/error_handling.jl:66
  [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:228
  [4] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:196 [inlined]
  [5] action
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:185 [inlined]
  [6] load(::String; options::@Kwargs{})
    @ FileIO ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:113
  [7] load
    @ ~/.julia/packages/FileIO/ePyCW/src/loadsave.jl:109 [inlined]
  [8] #111
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:26 [inlined]
  [9] mktemp(fn::JLD2.var"#111#112"{Symbol, Vector{Float64}, NTuple{5, Int64}, String, Dict{String, Int64}, Matrix{ComplexF64}, Vector{Float64}, Float64, Int64}, parent::String)
    @ Base.Filesystem ./file.jl:870
 [10] mktemp(fn::Function)
    @ Base.Filesystem ./file.jl:868
 [11] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:15 [inlined]
 [12] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]
 [13] macro expansion
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:14 [inlined]
 [14] macro expansion
    @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]
 [15] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/precompile.jl:118
 [16] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:306
 [17] IncludeInto
    @ ./Base.jl:307 [inlined]
 [18] top-level scope
    @ ~/.julia/packages/JLD2/wLPAN/src/JLD2.jl:518
 [19] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [20] 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::String)
    @ Base ./loading.jl:2991
 [21] top-level scope
    @ stdin:5
 [22] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [24] include_string
    @ ./loading.jl:2847 [inlined]
 [25] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [26] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/precompile.jl:3
in expression starting at /home/pkgeval/.julia/packages/JLD2/wLPAN/src/JLD2.jl:1
in expression starting at stdin:5
ERROR: LoadError: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to "/home/pkgeval/.julia/compiled/v1.12/JLD2/jl_L2Ayre".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3278
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()
    @ Base ./loading.jl:2647
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93
  [5] #mkpidlock#7
    @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1282 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1274 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3849
 [10] maybe_cachefile_lock
    @ ./loading.jl:3846 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2633
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2461
 [13] macro expansion
    @ ./loading.jl:2389 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2354
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2330
 [17] top-level scope
    @ ~/.julia/packages/MolecularGraphKernels/YLyTg/src/MolecularGraphKernels.jl:3
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:305
 [19] 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
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2837
 [23] include_string
    @ ./loading.jl:2847 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:319
 [25] _start()
    @ Base ./client.jl:554
in expression starting at /home/pkgeval/.julia/packages/MolecularGraphKernels/YLyTg/src/MolecularGraphKernels.jl:1
in expression starting at stdin:5
in expression starting at /home/pkgeval/.julia/packages/MolecularGraphKernels/YLyTg/test/runtests.jl:1

Testing failed after 191.72s

ERROR: LoadError: Package MolecularGraphKernels 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 472.78s: package fails to precompile