Package evaluation to test MassSpecBioChemicals on Julia 1.14.0-DEV.1851 (d64c0da64c*) started at 2026-03-05T20:40:08.084 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv, BugReporting)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 19.33s ################################################################################ # Installation # Installing MassSpecBioChemicals... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [f4388e49] + MassSpecBioChemicals v0.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [79e6a3ab] + Adapt v4.5.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [31f734f8] + ArrowTypes v2.3.0 [6309b1aa] + CodecInflate64 v0.1.3 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [34da2185] + Compat v4.18.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [85a47980] + Dictionaries v0.4.6 [ffbed154] + DocStringExtensions v0.9.5 [e2ba6199] + ExprTools v0.1.10 [313cdc1a] + Indexing v1.1.1 [842dd82b] + InlineStrings v1.4.5 [0c81fc1b] + InputBuffers v1.1.1 [d8418881] + Intervals v1.11.0 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [d8e11817] + MLStyle v0.4.17 [f4388e49] + MassSpecBioChemicals v0.2.0 [a0caa3fb] + MassSpecChemicals v0.3.5 [e1d29d7a] + Missings v1.2.0 [78c3b35d] + Mocking v0.8.1 [bac558e1] + OrderedCollections v1.8.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [43287f4e] + PtrArrays v1.4.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.9 [a2af1166] + SortingAlgorithms v1.2.2 [03a91e81] + SplitApplyCombine v1.2.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [dc5dba14] + TZJData v1.5.0+2025b [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [f269a46b] + TimeZones v1.22.2 [3bb67fe8] + TranscodingStreams v0.11.3 [9d95f2ec] + TypedTables v1.4.6 [1986cc42] + Unitful v1.28.0 [999f2bd7] + UnitfulMoles v0.1.1 [49080126] + ZipArchives v2.6.0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b27032c2] + LibCURL v1.0.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.18.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Installation completed after 4.71s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 27.25s ################################################################################ # Testing # Testing MassSpecBioChemicals Status `/tmp/jl_Gf6HLT/Project.toml` [0f8b85d8] JSON3 v1.14.3 [f4388e49] MassSpecBioChemicals v0.2.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Gf6HLT/Manifest.toml` [79e6a3ab] Adapt v4.5.0 [66dad0bd] AliasTables v1.1.3 [dce04be8] ArgCheck v2.5.0 [31f734f8] ArrowTypes v2.3.0 [6309b1aa] CodecInflate64 v0.1.3 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [34da2185] Compat v4.18.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [85a47980] Dictionaries v0.4.6 [ffbed154] DocStringExtensions v0.9.5 [e2ba6199] ExprTools v0.1.10 [313cdc1a] Indexing v1.1.1 [842dd82b] InlineStrings v1.4.5 [0c81fc1b] InputBuffers v1.1.1 [d8418881] Intervals v1.11.0 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [0f8b85d8] JSON3 v1.14.3 [2ab3a3ac] LogExpFunctions v0.3.29 [d8e11817] MLStyle v0.4.17 [f4388e49] MassSpecBioChemicals v0.2.0 [a0caa3fb] MassSpecChemicals v0.3.5 [e1d29d7a] Missings v1.2.0 [78c3b35d] Mocking v0.8.1 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [aea7be01] PrecompileTools v1.3.3 ⌃ [21216c6a] Preferences v1.5.0 [43287f4e] PtrArrays v1.4.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [03a91e81] SplitApplyCombine v1.2.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [856f2bd8] StructTypes v1.11.0 [dc5dba14] TZJData v1.5.0+2025b [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [f269a46b] TimeZones v1.22.2 [3bb67fe8] TranscodingStreams v0.11.3 [9d95f2ec] TypedTables v1.4.6 [1986cc42] Unitful v1.28.0 [999f2bd7] UnitfulMoles v0.1.1 [49080126] ZipArchives v2.6.0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [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 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [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 [deac9b47] LibCURL_jll v8.18.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [458c3c95] OpenSSL_jll v3.5.5+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ have new versions available and may be upgradable. Testing Running tests... Activating project at `~/.julia/environments/pkgeval` Activating project at `/tmp/jl_Gf6HLT` Switching execution to under rr [29] signal 11 (1): Segmentation fault in expression starting at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/test/runtests.jl:24 ncodeunits at ./strings/string.jl:158 [inlined] checkbounds at ./strings/basic.jl:204 [inlined] checkbounds at ./strings/basic.jl:212 [inlined] codeunit at ./strings/string.jl:163 [inlined] codeunit at ./strings/substring.jl:87 [inlined] _thisind_str at ./strings/string.jl:202 [inlined] thisind at ./strings/substring.jl:112 [inlined] lastindex at ./strings/basic.jl:180 [inlined] split_class_chain at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/input.jl:67 #parse_lipid#275 at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/input.jl:15 parse_lipid at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/input.jl:5 [inlined] parse_singleheadgroup at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_group.jl:119 unknown function (ip: 0x7b801800a7dc) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 parse_headgroup at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_group.jl:103 #parse_tailsubstituent#285 at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_group.jl:311 parse_tailsubstituent at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_group.jl:275 unknown function (ip: 0x7b80188cc93b) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2295 [inlined] jl_f__apply_iterate at /source/src/builtins.c:897 #parse_definedmodification#339 at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_chainmodification.jl:194 parse_definedmodification at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_chainmodification.jl:172 [inlined] #parse_chainmodification##2 at ./none (unknown line) [inlined] iterate at ./generator.jl:48 unknown function (ip: 0x7b804bfee032) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_f__apply_iterate at /source/src/builtins.c:870 parse_chainmodification at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_chainmodification.jl:71 parse_carbonchainbody at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:422 [inlined] #make_carbonchain#325 at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:382 make_carbonchain at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:379 unknown function (ip: 0x7b8019212f8f) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 #make_carbonchain#312 at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:342 make_carbonchain at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:341 [inlined] #make_carbonchain#311 at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:340 [inlined] make_carbonchain at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:340 unknown function (ip: 0x7b8019212c58) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 parse_carbonchain at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/parse_carbonchain.jl:15 unknown function (ip: 0x7b801800054d) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 #parse_lipid#275 at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/input.jl:31 parse_lipid at /home/pkgeval/.julia/packages/MassSpecBioChemicals/Wli0j/src/lipid/input/input.jl:5 unknown function (ip: 0x7b804bf6d852) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2295 [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 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 ijl_eval_thunk at /source/src/toplevel.c:766 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 include_string at ./loading.jl:3130 _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 _include at ./loading.jl:3190 include at ./Base.jl:324 IncludeInto at ./Base.jl:325 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2295 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:766 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2295 [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: 0x7b806698c249) 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: 75830805 (Pool: 75830000; Big: 805); GC: 26 Testing failed after 64.35s ERROR: LoadError: Package MassSpecBioChemicals 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:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [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:586 [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:562 [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:221 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval crashed after 345.64s: a segmentation fault happened ################################################################################ # Bug reporting # Finalizing trace... BugReporting completed after 37.44s Uploaded rr trace to https://s3.amazonaws.com/julialang-reports/nanosoldier/pkgeval/rr/MassSpecBioChemicals-1772725596.tar.zst