Package evaluation of CHMMAIRRa on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T12:19:55.567 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.95s ################################################################################ # Installation # Installing CHMMAIRRa... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [d8677c85] + CHMMAIRRa v0.0.2 Updating `~/.julia/environments/v1.11/Manifest.toml` [c7e460c6] + ArgParse v1.2.0 [d8677c85] + CHMMAIRRa v0.0.2 [4c20a592] + CHMMera v0.1.2 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.16.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [48062228] + FilePathsBase v0.9.24 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.0 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.1 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [b718987f] + TextWrap v1.0.2 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.27+1 [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 To see why use `status --outdated -m` Installation completed after 4.07s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 23.33s ################################################################################ # Testing # Testing CHMMAIRRa Status `/tmp/jl_QhzOjb/Project.toml` [c7e460c6] ArgParse v1.2.0 [d8677c85] CHMMAIRRa v0.0.2 [4c20a592] CHMMera v0.1.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_QhzOjb/Manifest.toml` [c7e460c6] ArgParse v1.2.0 [d8677c85] CHMMAIRRa v0.0.2 [4c20a592] CHMMera v0.1.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.16.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [48062228] FilePathsBase v0.9.24 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [189a3867] Reexport v1.2.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [b718987f] TextWrap v1.0.2 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [4536629a] OpenBLAS_jll v0.3.27+1 [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... utils.jl: Error During Test at /home/pkgeval/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:22 Got exception outside of a @test Could not find mafft executable. Please ensure mafft is installed and in your PATH, or provide the path using --mafft Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] #mafft_wrapper#23 @ ~/.julia/packages/CHMMAIRRa/ahDZ6/src/utils.jl:103 [inlined] [3] mafft_wrapper(seqs::Vector{String}, seqnames::Vector{String}) @ CHMMAIRRa ~/.julia/packages/CHMMAIRRa/ahDZ6/src/utils.jl:94 [4] macro expansion @ ~/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:71 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [6] macro expansion @ ~/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:24 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [8] top-level scope @ ~/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:22 [9] include(fname::String) @ Main ./sysimg.jl:38 [10] top-level scope @ none:6 [11] eval @ ./boot.jl:430 [inlined] [12] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [13] _start() @ Base ./client.jl:531 Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment Threading alignment Running forward algorithm to get chimerism probabilities Running viterbi to get chimeric paths Number of chimeric sequences: 1 (50.0%) Counting chimeric segments Finding chimeric alignments Done. ------------------------------ Processing chunk 1 ------------------------------ Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment Threading alignment Running forward algorithm to get chimerism probabilities Running viterbi to get chimeric paths Number of chimeric sequences: 1 (100.0%) Finding chimeric alignments ------------------------------ Processing chunk 2 ------------------------------ Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment Threading alignment Running forward algorithm to get chimerism probabilities Running viterbi to get chimeric paths Number of chimeric sequences: 0 (0.0%) Finding chimeric alignments ------------------------------ Processing chunk 3 ------------------------------ Removing 0 rows with missing values in required columns sequence_id, v_call, v_sequence_alignment, v_germline_alignment Threading alignment Running forward algorithm to get chimerism probabilities Running viterbi to get chimeric paths Number of chimeric sequences: false (NaN%) Finding chimeric alignments Done. Test Summary: | Pass Error Total Time CHMMAIRRa.jl | 39 1 40 2m55.2s utils.jl | 17 1 18 1m04.3s CHMMAIRRa.jl | 22 22 1m50.9s ERROR: LoadError: Some tests did not pass: 39 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/CHMMAIRRa/ahDZ6/test/runtests.jl:21 Testing failed after 187.52s ERROR: LoadError: Package CHMMAIRRa errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/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 237.59s: package tests unexpectedly errored