Package evaluation to test BioRecordsProcessing on Julia 1.10.10 (c8be17dcfd*) started at 2026-02-02T16:42:37.425 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.10` Set-up completed after 4.69s ################################################################################ # Installation # Installing BioRecordsProcessing... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [321bc2d7] + BioRecordsProcessing v0.2.3 Updating `~/.julia/environments/v1.10/Manifest.toml` [67c07d97] + Automa v1.1.0 [28d598bf] + BGZFStreams v0.3.2 [00701ae9] + BioAlignments v3.1.0 [47718e42] + BioGenerics v0.1.5 [321bc2d7] + BioRecordsProcessing v0.2.3 [7e6ae17a] + BioSequences v3.5.1 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 ⌅ [899a7d2d] + GenomicFeatures v2.1.0 [c27321d9] + Glob v1.4.0 ⌅ [4ffb77ac] + Indexes v0.1.3 [524e6230] + IntervalTrees v1.1.0 [bac558e1] + OrderedCollections v1.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [fdea26ae] + SIMD v3.7.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [7200193e] + Twiddle v1.1.2 [d759349c] + XAM v0.4.2 [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+5 [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 To see why use `status --outdated -m` Installation completed after 9.38s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 10333.1 ms ✓ VariantCallFormat 12712.3 ms ✓ FASTX 2903.8 ms ✓ BioRecordsProcessing 2544.8 ms ✓ FASTX → BioSequencesExt 4 dependencies successfully precompiled in 33 seconds. 26 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 40.17s ################################################################################ # Testing # Testing BioRecordsProcessing Status `/tmp/jl_kjJpOz/Project.toml` [321bc2d7] BioRecordsProcessing v0.2.3 [7e6ae17a] BioSequences v3.5.1 [c2308a5c] FASTX v2.1.7 [3372ea36] FormatSpecimens v1.4.0 [28eba6e3] VariantCallFormat v0.5.9 [d759349c] XAM v0.4.2 [8dfed614] Test Status `/tmp/jl_kjJpOz/Manifest.toml` [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [00701ae9] BioAlignments v3.1.0 [47718e42] BioGenerics v0.1.5 [321bc2d7] BioRecordsProcessing v0.2.3 [7e6ae17a] BioSequences v3.5.1 [3c28c6f8] BioSymbols v5.2.0 [e1450e63] BufferedStreams v1.2.2 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 ⌅ [864edb3b] DataStructures v0.18.22 [c2308a5c] FASTX v2.1.7 [3372ea36] FormatSpecimens v1.4.0 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [c27321d9] Glob v1.4.0 ⌅ [4ffb77ac] Indexes v0.1.3 [524e6230] IntervalTrees v1.1.0 [bac558e1] OrderedCollections v1.8.1 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [fdea26ae] SIMD v3.7.2 [354b36f9] StringViews v1.3.7 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [28eba6e3] VariantCallFormat v0.5.9 [d759349c] XAM v0.4.2 [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+5 [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... Test Summary: | Pass Total Time Internals | 2 2 1.3s Test Summary: | Pass Total Time ExternalTool + File | 1 1 0.3s Test Summary: | Pass Total Time ExternalTool + Paired File | 1 1 0.1s [ Info: Processing files: /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/SAM/xx#blank.sam /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/SAM/xx#minimal.sam Test Summary: | Pass Total Time ExternalTool + Directory | 1 1 2.3s p = Pipeline: Reader{File}(FASTX.FASTA, File("/tmp/jl_R4Da6J/test.fa")) ↓ Collect{Int64} p = Pipeline: Reader{File}(FASTX.FASTQ, File("/home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data/illumina_full_range_as_illumina.fastq.gz")) ↓ Writer(FASTX.FASTQ, "/tmp/jl_1ve46b") p = Pipeline: Reader{Directory}(FASTX.FASTQ, Directory("/home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data")"*.fastq") ↓ Writer(FASTX.FASTQ, "/tmp/jl_Qb3Bqo") [ Info: Processing files: /home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data/illumina_full_range_as_illumina.fastq /home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data/illumina_full_range_as_illumina.processed.fastq p = Pipeline: Reader{Directory}(FASTX.FASTQ, Directory("/home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTQ")"solexa*.fastq") ↓ Collect{String} [ Info: Processing files: /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTQ/solexa_example.fastq /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTQ/solexa_faked.fastq /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTQ/solexa_full_range_as_illumina.fastq /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTQ/solexa_full_range_as_sanger.fastq /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTQ/solexa_full_range_as_solexa.fastq /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTQ/solexa_full_range_original_solexa.fastq p = Pipeline: Reader{File}(VariantCallFormat.VCF, File("/home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/VCF/adeno_virus.vcf")) ↓ Collect{VariantCallFormat.Record} p = Pipeline: Reader{File}(VariantCallFormat.VCF, File("/home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/VCF/adeno_virus.vcf")) ↓ Writer(VariantCallFormat.VCF, "/home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/VCF") p = Pipeline: Buffer{Float64}(; filename = "") ↓ Collect{Float64} [ Info: Processing files: /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/FASTA/multi_1.fasta p = Pipeline: Reader{File}(XAM.BAM, File("/home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/BAM/bam1.bam")) ↓ Collect{Bool} ┌ Warning: Index file not found : /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/BAM/bam1.bam.bai └ @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Source.jl:119 BAM + Collect + Group by read name: Error During Test at /home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:265 Got exception outside of a @test UndefVarError: `isprimary` not defined Stacktrace: [1] (::BioRecordsProcessing.var"#20#23")(r::XAM.BAM.Record) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:60 [2] group_record!(rg::RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#18#21", BioRecordsProcessing.var"#19#22", BioRecordsProcessing.var"#20#23"}, r::XAM.BAM.Record, idx::Int64) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:45 [3] run_single(p::Pipeline{Reader{File}, RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#18#21", BioRecordsProcessing.var"#19#22", BioRecordsProcessing.var"#20#23"}, BioRecordsProcessing.Processor, Collect{Bool}}; max_records::Float64, verbose::Bool) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:133 [4] run_single @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:110 [inlined] [5] #run#24 @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:67 [inlined] [6] run @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:63 [inlined] [7] (::var"#37#68")(dir::String) @ Main ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:277 [8] mktempdir(fn::var"#37#68", parent::String; prefix::String) @ Base.Filesystem ./file.jl:766 [9] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:762 [10] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:266 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [12] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:266 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [14] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:8 [15] include(fname::String) @ Base.MainInclude ./client.jl:487 [16] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/runtests.jl:10 [17] include(fname::String) @ Base.MainInclude ./client.jl:487 [18] top-level scope @ none:6 ┌ Warning: Index file not found : /home/pkgeval/.julia/packages/FormatSpecimens/x7QK7/BAM/bam1.bam.bai └ @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Source.jl:119 BAM to paired FASTQ: Error During Test at /home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:284 Got exception outside of a @test UndefVarError: `isprimary` not defined Stacktrace: [1] (::BioRecordsProcessing.var"#20#23")(r::XAM.BAM.Record) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:60 [2] group_record!(rg::RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#18#21", BioRecordsProcessing.var"#19#22", BioRecordsProcessing.var"#20#23"}, r::XAM.BAM.Record, idx::Int64) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:45 [3] run_single(p::Pipeline{Reader{File}, RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#18#21", BioRecordsProcessing.var"#19#22", BioRecordsProcessing.var"#20#23"}, BioRecordsProcessing.Processor, Writer}; max_records::Float64, verbose::Bool) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:133 [4] run_single @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:110 [inlined] [5] #run#24 @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:67 [inlined] [6] run @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:63 [inlined] [7] (::var"#39#70")(dir::String) @ Main ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:304 [8] mktempdir(fn::var"#39#70", parent::String; prefix::String) @ Base.Filesystem ./file.jl:766 [9] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:762 [10] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:285 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [12] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:285 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1582 [inlined] [14] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:8 [15] include(fname::String) @ Base.MainInclude ./client.jl:487 [16] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/runtests.jl:10 [17] include(fname::String) @ Base.MainInclude ./client.jl:487 [18] top-level scope @ none:6 Test Summary: | Pass Error Total Time Pipeline | 21 2 23 22.7s FASTA Collect | 1 1 3.9s FASTQ.gz Writer | 2 2 2.2s FASTA + Directory | 3 3 2.1s Directory + Collect | 1 1 0.7s VCF | 1 1 3.6s VCF overwrite | 1 1 0.2s Buffer + Collect | 1 1 1.2s Buffer + Writer | 1 1 0.5s Paired FASTA + Collect | 5 5 1.3s Paired FASTA + Paired Writer | 1 1 0.3s Paired FASTA + Single Writer | 2 2 0.4s BAM + Collect | 2 2 2.6s BAM + Collect + Group by read name | 1 1 3.0s BAM to paired FASTQ | 1 1 0.7s ERROR: LoadError: Some tests did not pass: 21 passed, 0 failed, 2 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:5 in expression starting at /home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/runtests.jl:10 Testing failed after 36.11s ERROR: LoadError: Package BioRecordsProcessing 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:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 137.25s: package tests unexpectedly errored