Package evaluation to test BioDemuX on Julia 1.14.0-DEV.2212 (062a90bc8c*) started at 2026-05-22T03:51:10.031 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.99s ################################################################################ # Installation # Installing BioDemuX... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [ac87d701] + BioDemuX v1.6.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [c7e460c6] + ArgParse v1.2.0 [ac87d701] + BioDemuX v1.6.0 [e1450e63] + BufferedStreams v1.2.2 [336ed68f] + CSV v0.10.16 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.4 [e2d170a0] + DataValueInterfaces v1.0.0 [48062228] + FilePathsBase v0.9.24 [c27321d9] + Glob v1.5.0 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [9b87118b] + PackageCompiler v2.3.0 [69de0a69] + Parsers v2.8.4 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.3.2 [189a3867] + Reexport v1.2.2 [05181044] + RelocatableFolders v1.0.1 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.10 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [b718987f] + TextWrap v1.0.2 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [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 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [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 v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.1+0 [deac9b47] + LibCURL_jll v8.20.0+1 [e37daf67] + LibGit2_jll v1.9.3+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+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 v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Installation completed after 6.0s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 9.8 s ✓ BioDemuX 1 dependency successfully precompiled in 11 seconds. 77 already precompiled. Precompilation completed after 37.09s ################################################################################ # Testing # Testing BioDemuX Status `/tmp/jl_wZJ9UR/Project.toml` [c7e460c6] ArgParse v1.2.0 [ac87d701] BioDemuX v1.6.0 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [9b87118b] PackageCompiler v2.3.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_wZJ9UR/Manifest.toml` [c7e460c6] ArgParse v1.2.0 [ac87d701] BioDemuX v1.6.0 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.4 [e2d170a0] DataValueInterfaces v1.0.0 [48062228] FilePathsBase v0.9.24 [c27321d9] Glob v1.5.0 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [9b87118b] PackageCompiler v2.3.0 [69de0a69] Parsers v2.8.4 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [189a3867] Reexport v1.2.2 [05181044] RelocatableFolders v1.0.1 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.10 [a2af1166] SortingAlgorithms v1.2.2 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [b718987f] TextWrap v1.0.2 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [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 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v1.0.0 [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 v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.13.0 [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 v1.5.1+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.3+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+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 v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Testing Running tests... Test Summary: | Pass Total Time Unit Tests | 61 61 4.5s Running tests with 1 threads Test Summary: | Pass Total Time Integration Tests (Current Process) | 444 444 1m21.5s Running multi-threaded tests in a subprocess... Program aborted due to an unhandled Error: Unexpected definitions in module match_barcode_pass-jitted-173: [ julia__throw_boundserror_indices_2#2 ] [19] signal 6 (-6): Aborted in expression starting at /home/pkgeval/.julia/packages/BioDemuX/wwaOp/test/integration/single_barcode.jl:1 unknown function (ip: 0x7c036628cebc) at /lib/x86_64-linux-gnu/libc.so.6 gsignal at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) abort at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) _ZNK4llvm5Error19fatalUncheckedErrorEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm6detail18UniqueFunctionBaseIvJNS_5ErrorEEE11DestroyImplIZNS_7jitlink13JITLinkerBase22abandonAllocAndBailOutESt10unique_ptrIS6_St14default_deleteIS6_EES2_EUlS2_E_EEvPv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm7jitlink13JITLinkerBase22abandonAllocAndBailOutESt10unique_ptrIS1_St14default_deleteIS1_EENS_5ErrorE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm7jitlink13JITLinkerBase10linkPhase2ESt10unique_ptrIS1_St14default_deleteIS1_EENS_8ExpectedIS2_INS0_20JITLinkMemoryManager13InFlightAllocES3_IS8_EEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm6detail18UniqueFunctionBaseIvJNS_8ExpectedISt10unique_ptrINS_7jitlink20JITLinkMemoryManager13InFlightAllocESt14default_deleteIS6_EEEEEE8CallImplIZNS4_13JITLinkerBase10linkPhase1ES3_ISD_S7_ISD_EEEUlSA_E0_EEvPvRSA_ at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) operator() at /source/usr/include/llvm/ADT/FunctionExtras.h:389:30 [inlined] allocate at /source/src/cgmemmgr.cpp:1072:16 _ZN4llvm7jitlink13JITLinkerBase10linkPhase1ESt10unique_ptrIS1_St14default_deleteIS1_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm7jitlink15link_ELF_x86_64ESt10unique_ptrINS0_9LinkGraphESt14default_deleteIS2_EES1_INS0_14JITLinkContextES3_IS6_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm7jitlink8link_ELFESt10unique_ptrINS0_9LinkGraphESt14default_deleteIS2_EES1_INS0_14JITLinkContextES3_IS6_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm7jitlink4linkESt10unique_ptrINS0_9LinkGraphESt14default_deleteIS2_EES1_INS0_14JITLinkContextES3_IS6_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc21LinkGraphLinkingLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EES2_INS_7jitlink9LinkGraphES4_IS8_EES2_INS_12MemoryBufferES4_ISB_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) materialize at /source/src/jitlayers.cpp:944:16 _ZN4llvm3orc19MaterializationTask3runEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) dispatch at /source/src/julia-task-dispatcher.h:353:11 _ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_vEEEENSG_ISD_vEENS_6detail12DenseMapPairISD_SI_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc25InProgressFullLookupState8completeESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) _ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS0_17ExecutorSymbolDefENS_12DenseMapInfoISI_vEENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_vEENSN_IS6_SV_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM.so.21.1jl (unknown line) publishCIs at /source/src/jitlayers.cpp:2085:14 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:510:39 jl_compile_method_internal at /source/src/gf.c:3666:27 _jl_invoke at /source/src/gf.c:4119:16 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 jl_apply at /source/src/julia.h:2328:12 [inlined] start_task at /source/src/task.c:1275:19 Allocations: 17447540 (Pool: 17447361; Big: 179); GC: 10 Integration Tests (Subprocess: 4 threads): Error During Test at /home/pkgeval/.julia/packages/BioDemuX/wwaOp/test/runtests.jl:34 Test threw exception Expression: success(run(cmd)) 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 --project=/tmp/jl_wZJ9UR/Project.toml -t 4 run_subprocess.jl`, ProcessSignaled(6)) [0] Stacktrace: [1] spawn_opts_inherit() @ Base ./process.jl:612 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:525 [3] run(::Cmd) @ Base ./process.jl:522 [4] top-level scope @ ~/.julia/packages/BioDemuX/wwaOp/test/runtests.jl:33 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [6] macro expansion @ ~/.julia/packages/BioDemuX/wwaOp/test/runtests.jl:34 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] Test Summary: | Error Total Time Integration Tests (Subprocess: 4 threads) | 1 1 1m25.3s RNG of the outermost testset: Random.Xoshiro(0x35920f7f316426da, 0xff0a2e207582fb5c, 0xc8f37f045260b2fd, 0xc9659ec549efc460, 0xa1396c5b335ef67f) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BioDemuX/wwaOp/test/runtests.jl:30 Testing failed after 199.28s ERROR: LoadError: Package BioDemuX errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:355 [12] _start() @ Base ./client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 277.56s: package tests unexpectedly errored