Package evaluation to test GeneticVariation on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T14:19:00.963 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.83s ################################################################################ # Installation # Installing GeneticVariation... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [9bc6ac9d] + GeneticVariation v0.4.1 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [67c07d97] + Automa v0.7.0 [28d598bf] + BGZFStreams v0.3.2 [37cfa864] + BioCore v2.0.5 ⌅ [7e6ae17a] + BioSequences v1.1.0 ⌅ [3c28c6f8] + BioSymbols v3.1.0 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 ⌅ [861a8166] + Combinatorics v0.7.0 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 [9bc6ac9d] + GeneticVariation v0.4.1 [1cb3b9ac] + IndexableBitVectors v1.0.0 [524e6230] + IntervalTrees v1.1.0 [692b3bcd] + JLLWrappers v1.7.1 [bac558e1] + OrderedCollections v1.8.1 ⌅ [f27b6e38] + Polynomials v0.6.1 [21216c6a] + Preferences v1.5.0 ⌅ [3cdcf5f2] + RecipesBase v0.8.0 [69024149] + StringEncodings v0.3.7 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [7200193e] + Twiddle v1.1.2 [ddb6d928] + YAML v0.4.16 [94ce4f54] + Libiconv_jll v1.18.0+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [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 [4536629a] + OpenBLAS_jll v0.3.29+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 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 To see why use `status --outdated -m` Installation completed after 4.6s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 13.18s ################################################################################ # Testing # Testing GeneticVariation Status `/tmp/jl_96iP8e/Project.toml` ⌅ [67c07d97] Automa v0.7.0 [28d598bf] BGZFStreams v0.3.2 [37cfa864] BioCore v2.0.5 ⌅ [7e6ae17a] BioSequences v1.1.0 [e1450e63] BufferedStreams v1.2.2 ⌅ [861a8166] Combinatorics v0.7.0 [9bc6ac9d] GeneticVariation v0.4.1 [524e6230] IntervalTrees v1.1.0 [7200193e] Twiddle v1.1.2 [ddb6d928] YAML v0.4.16 [8dfed614] Test v1.11.0 Status `/tmp/jl_96iP8e/Manifest.toml` ⌅ [67c07d97] Automa v0.7.0 [28d598bf] BGZFStreams v0.3.2 [37cfa864] BioCore v2.0.5 ⌅ [7e6ae17a] BioSequences v1.1.0 ⌅ [3c28c6f8] BioSymbols v3.1.0 [e1450e63] BufferedStreams v1.2.2 [944b1d66] CodecZlib v0.7.8 ⌅ [861a8166] Combinatorics v0.7.0 [34da2185] Compat v4.18.1 ⌅ [864edb3b] DataStructures v0.18.22 [9bc6ac9d] GeneticVariation v0.4.1 [1cb3b9ac] IndexableBitVectors v1.0.0 [524e6230] IntervalTrees v1.1.0 [692b3bcd] JLLWrappers v1.7.1 [bac558e1] OrderedCollections v1.8.1 ⌅ [f27b6e38] Polynomials v0.6.1 [21216c6a] Preferences v1.5.0 ⌅ [3cdcf5f2] RecipesBase v0.8.0 [69024149] StringEncodings v0.3.7 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [ddb6d928] YAML v0.4.16 [94ce4f54] Libiconv_jll v1.18.0+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [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 [4536629a] OpenBLAS_jll v0.3.29+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... WARNING: Constructor for type "Char" was extended in `BioSymbols` without explicit qualification or import.  NOTE: Assumed "Char" refers to `Base.Char`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function Char end`.  Hint: To silence the warning, qualify `Char` as `Base.Char` in the method signature or explicitly `import Base: Char`. WARNING: Constructor for type "UInt64" was extended in `BioSequences` without explicit qualification or import.  NOTE: Assumed "UInt64" refers to `Base.UInt64`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function UInt64 end`.  Hint: To silence the warning, qualify `UInt64` as `Base.UInt64` in the method signature or explicitly `import Base: UInt64`. WARNING: method definition for BroadcastStyle at /home/pkgeval/.julia/packages/BioSequences/7i86L/src/search/pwm.jl:76 declares type variable T but does not use it. WARNING: method definition for BroadcastStyle at /home/pkgeval/.julia/packages/BioSequences/7i86L/src/search/pwm.jl:76 declares type variable S but does not use it. 2 dependencies had output during precompilation: ┌ BioSequences │ [Output was shown above] └ ┌ BioSymbols │ WARNING: Constructor for type "Char" was extended in `BioSymbols` without explicit qualification or import. │ NOTE: Assumed "Char" refers to `Base.Char`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Char end`. │ Hint: To silence the warning, qualify `Char` as `Base.Char` in the method signature or explicitly `import Base: Char`. └ [ Info: Compiling VCF parser... 1 dependency had output during precompilation: ┌ GeneticVariation │ [Output was shown above] └ Cloning into '/home/pkgeval/.julia/packages/BioCore/YBJvb/BioFmtSpecimens'... Note: switching to 'v1.0.0-9-ga88ddc9'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at a88ddc9 Merge pull request #29 from jgreener64/mmtf VCF: Test Failed at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/vcf.jl:93 Expression: VCF.infokeys(record) == ["DP", "AA", "DB"] Evaluated: ["AA", "DP", "DB"] == ["DP", "AA", "DB"] Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] [2] macro expansion @ ~/.julia/packages/GeneticVariation/1wh3b/test/vcf.jl:93 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [4] top-level scope @ ~/.julia/packages/GeneticVariation/1wh3b/test/vcf.jl:2 Test Summary: | Pass Fail Total Time VCF | 164 1 165 32.0s RNG of the outermost testset: Random.Xoshiro(0xfa796affad1657ed, 0xc86528bd685d7854, 0x708e5ccf4d6ed6f1, 0x1e63afe41a021b35, 0x5b2a84811f67b211) ERROR: LoadError: Some tests did not pass: 164 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/vcf.jl:1 in expression starting at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/runtests.jl:1 Testing failed after 133.97s ERROR: LoadError: Package GeneticVariation 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:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [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:572 [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:548 [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:237 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 177.33s: package has test failures