Package evaluation to test GeneticVariation on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T14:02:50.607 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.34s ################################################################################ # Installation # Installing GeneticVariation... Resolving package versions... Installed CodecZlib ─────────── v0.7.8 Installed Combinatorics ─────── v0.7.0 Installed Compat ────────────── v4.18.1 Installed StringEncodings ───── v0.3.7 Installed RecipesBase ───────── v0.8.0 Installed OrderedCollections ── v1.8.1 Installed TranscodingStreams ── v0.9.13 Installed DataStructures ────── v0.18.22 Installed Twiddle ───────────── v1.1.2 Installed YAML ──────────────── v0.4.16 Installed JLLWrappers ───────── v1.7.1 Installed BufferedStreams ───── v1.2.2 Installed Preferences ───────── v1.5.0 Installed Libiconv_jll ──────── v1.18.0+0 Installed Polynomials ───────── v0.6.1 Installed IndexableBitVectors ─ v1.0.0 Installed BioSymbols ────────── v3.1.0 Installed IntervalTrees ─────── v1.1.0 Installed GeneticVariation ──── v0.4.1 Installed BGZFStreams ───────── v0.3.2 Installed Automa ────────────── v0.7.0 Installed BioCore ───────────── v2.0.5 Installed BioSequences ──────── v1.1.0 Installing 1 artifacts Installed artifact Libiconv 1.9 MiB 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 v1.12.0 [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 7.13s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4333.9 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 889.1 ms ✓ RecipesBase 827.9 ms ✓ Twiddle 1167.5 ms ✓ IntervalTrees 1011.6 ms ✓ BufferedStreams 1246.8 ms ✓ OrderedCollections 1127.8 ms ✓ Preferences 1156.9 ms ✓ Compat 2188.6 ms ✓ TranscodingStreams 1421.4 ms ✓ IndexableBitVectors 1764.5 ms ✓ Polynomials 1195.3 ms ✓ JLLWrappers 868.6 ms ✓ Compat → CompatLinearAlgebraExt 1602.6 ms ✓ CodecZlib 2019.6 ms ✓ Combinatorics 1381.7 ms ✓ Libiconv_jll 3867.5 ms ✓ DataStructures 1633.5 ms ✓ BGZFStreams 1076.4 ms ✓ StringEncodings 2442.8 ms ✓ Automa 2647.4 ms ✓ YAML 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`. 14306.7 ms ✓ BioSymbols 1894.4 ms ✓ BioCore 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. 17768.2 ms ✓ BioSequences [ Info: Compiling VCF parser... 15035.4 ms ✓ GeneticVariation 24 dependencies successfully precompiled in 81 seconds. 14 already precompiled. 3 dependencies had output during precompilation: ┌ 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`. └ ┌ BioSequences │ 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. └ ┌ GeneticVariation │ [ Info: Compiling VCF parser... └ Precompilation completed after 96.93s ################################################################################ # Testing # Testing GeneticVariation Status `/tmp/jl_GTa4ev/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_GTa4ev/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 v1.12.0 [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... 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 35.8s RNG of the outermost testset: Random.Xoshiro(0xbf4a233834c32d23, 0x109189b58a9b1a02, 0xd76276af1d291558, 0xdae0845d55af8e14, 0x220eb051be2ec86d) 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 53.91s 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:219 [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:210 PkgEval failed after 181.11s: package has test failures