Package evaluation of GeneticVariation on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T13:47:31.526 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.34s ################################################################################ # Installation # Installing GeneticVariation... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [9bc6ac9d] + GeneticVariation v0.4.1 Updating `~/.julia/environments/v1.10/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 v4.16.0 [864edb3b] + DataStructures v0.18.22 [9bc6ac9d] + GeneticVariation v0.4.1 [1cb3b9ac] + IndexableBitVectors v1.0.0 [524e6230] + IntervalTrees v1.1.0 [692b3bcd] + JLLWrappers v1.7.0 [bac558e1] + OrderedCollections v1.8.1 ⌅ [f27b6e38] + Polynomials v0.6.1 [21216c6a] + Preferences v1.4.3 ⌅ [3cdcf5f2] + RecipesBase v0.8.0 [69024149] + StringEncodings v0.3.7 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [7200193e] + Twiddle v1.1.2 [ddb6d928] + YAML v0.4.14 [94ce4f54] + Libiconv_jll v1.18.0+0 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [b77e0a4c] + InteractiveUtils [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [de0858da] + Printf [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [fa267f1f] + TOML v1.0.3 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.23+4 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+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 To see why use `status --outdated -m` Installation completed after 8.33s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 52.84s ################################################################################ # Testing # Testing GeneticVariation Status `/tmp/jl_pbTthj/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 v0.4.14 [8dfed614] Test Status `/tmp/jl_pbTthj/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 v4.16.0 [864edb3b] DataStructures v0.18.22 [9bc6ac9d] GeneticVariation v0.4.1 [1cb3b9ac] IndexableBitVectors v1.0.0 [524e6230] IntervalTrees v1.1.0 [692b3bcd] JLLWrappers v1.7.0 [bac558e1] OrderedCollections v1.8.1 ⌅ [f27b6e38] Polynomials v0.6.1 [21216c6a] Preferences v1.4.3 ⌅ [3cdcf5f2] RecipesBase v0.8.0 [69024149] StringEncodings v0.3.7 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [ddb6d928] YAML v0.4.14 [94ce4f54] Libiconv_jll v1.18.0+0 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [b77e0a4c] InteractiveUtils [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [de0858da] Printf [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [fa267f1f] TOML v1.0.3 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [4536629a] OpenBLAS_jll v0.3.23+4 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+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 Test Summary: | Pass Total Time VCF | 165 165 17.8s Test Summary: | Pass Total Time BCF | 39 39 3.1s ┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead │ caller = bp_chunk_count at site_counting.jl:96 [inlined] └ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96 ┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead │ caller = bp_chunk_count at site_counting.jl:96 [inlined] └ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96 ┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead │ caller = bp_chunk_count at site_counting.jl:96 [inlined] └ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96 ┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead │ caller = bp_chunk_count at site_counting.jl:96 [inlined] └ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96 ┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead │ caller = bp_chunk_count at site_counting.jl:96 [inlined] └ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96 ┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead │ caller = bp_chunk_count at site_counting.jl:96 [inlined] └ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96 ┌ Warning: count_zero_bitpairs is deprecated, use count_00_bitpairs instead │ caller = bp_chunk_count at site_counting.jl:96 [inlined] └ @ Core ~/.julia/packages/BioSequences/7i86L/src/bioseq/site_counting/site_counting.jl:96 Test Summary: | Pass Total Time Site counting | 348 348 13.9s MASH distances: Test Failed at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/minhash.jl:4 Expression: ≈(mash(a, b), 0.2745, atol = 0.001) Evaluated: 0.10136627702704111 ≈ 0.2745 (atol=0.001) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:672 [inlined] [2] macro expansion @ ~/.julia/packages/GeneticVariation/1wh3b/test/minhash.jl:4 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [4] top-level scope @ ~/.julia/packages/GeneticVariation/1wh3b/test/minhash.jl:2 Test Summary: | Pass Fail Total Time MASH distances | 2 1 3 4.5s ERROR: LoadError: Some tests did not pass: 2 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/minhash.jl:1 in expression starting at /home/pkgeval/.julia/packages/GeneticVariation/1wh3b/test/runtests.jl:1 Testing failed after 77.83s ERROR: LoadError: Package GeneticVariation errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 150.99s: package has test failures