Package evaluation to test BioRecordsProcessing on Julia 1.11.7 (58327cce5e*) started at 2025-10-28T18:41:23.875 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.86s ################################################################################ # Installation # Installing BioRecordsProcessing... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [321bc2d7] + BioRecordsProcessing v0.2.3 Updating `~/.julia/environments/v1.11/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 v3.5.0 [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 v1.3.1 ⌅ [4ffb77ac] + Indexes v0.1.3 [524e6230] + IntervalTrees v1.1.0 [bac558e1] + OrderedCollections v1.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.0 [fdea26ae] + SIMD v3.7.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [7200193e] + Twiddle v1.1.2 [d759349c] + XAM v0.4.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates 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 [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. To see why use `status --outdated -m` Installation completed after 5.58s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 57.15s ################################################################################ # Testing # Testing BioRecordsProcessing Status `/tmp/jl_RcsP92/Project.toml` [321bc2d7] BioRecordsProcessing v0.2.3 [7e6ae17a] BioSequences v3.5.0 [c2308a5c] FASTX v2.1.7 [3372ea36] FormatSpecimens v1.3.1 [28eba6e3] VariantCallFormat v0.5.9 [d759349c] XAM v0.4.2 [8dfed614] Test v1.11.0 Status `/tmp/jl_RcsP92/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 v3.5.0 [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 v1.3.1 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [c27321d9] Glob v1.3.1 ⌅ [4ffb77ac] Indexes v0.1.3 [524e6230] IntervalTrees v1.1.0 [bac558e1] OrderedCollections v1.8.1 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.0 [fdea26ae] SIMD v3.7.2 [354b36f9] StringViews v1.3.5 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [28eba6e3] VariantCallFormat v0.5.9 [d759349c] XAM v0.4.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates 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 [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... Test Summary: | Pass Total Time Internals | 2 2 0.2s Test Summary: | Pass Total Time ExternalTool + File | 1 1 5.7s Test Summary: | Pass Total Time ExternalTool + Paired File | 1 1 0.1s [ Info: Processing files: /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/SAM/xx#blank.sam /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/SAM/xx#minimal.sam Test Summary: | Pass Total Time ExternalTool + Directory | 1 1 4.4s p = Pipeline: Reader{File}(FASTX.FASTA, File("/tmp/jl_ug2LUs/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_MImlkd") p = Pipeline: Reader{Directory}(FASTX.FASTQ, Directory("/home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data")"*.fastq") ↓ Writer(FASTX.FASTQ, "/tmp/jl_5JbOcR") [ 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/cmrLJ/FASTQ")"solexa*.fastq") ↓ Collect{String} [ Info: Processing files: /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/FASTQ/solexa_example.fastq /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/FASTQ/solexa_faked.fastq /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/FASTQ/solexa_full_range_as_illumina.fastq /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/FASTQ/solexa_full_range_as_sanger.fastq /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/FASTQ/solexa_full_range_as_solexa.fastq /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/FASTQ/solexa_full_range_original_solexa.fastq p = Pipeline: Reader{File}(VariantCallFormat.VCF, File("/home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/VCF/adeno_virus.vcf")) ↓ Collect{VariantCallFormat.Record} p = Pipeline: Reader{File}(VariantCallFormat.VCF, File("/home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/VCF/adeno_virus.vcf")) ↓ Writer(VariantCallFormat.VCF, "/home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/VCF") p = Pipeline: Buffer{Float64}(; filename = "") ↓ Collect{Float64} [ Info: Processing files: /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/FASTA/multi_1.fasta p = Pipeline: Reader{File}(XAM.BAM, File("/home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/BAM/bam1.bam")) ↓ Collect{Bool} ┌ Warning: Index file not found : /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/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 in `XAM.BAM` 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:819 [9] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:815 [10] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:266 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [12] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:266 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [14] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:8 [15] include(fname::String) @ Main ./sysimg.jl:38 [16] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/runtests.jl:10 [17] include(fname::String) @ Main ./sysimg.jl:38 [18] top-level scope @ none:6 ┌ Warning: Index file not found : /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/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 in `XAM.BAM` 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:819 [9] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:815 [10] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:285 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [12] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:285 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [14] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:8 [15] include(fname::String) @ Main ./sysimg.jl:38 [16] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/runtests.jl:10 [17] include(fname::String) @ Main ./sysimg.jl:38 [18] top-level scope @ none:6 Test Summary: | Pass Error Total Time Pipeline | 21 2 23 35.4s FASTA Collect | 1 1 6.1s FASTQ.gz Writer | 2 2 3.0s FASTA + Directory | 3 3 3.4s Directory + Collect | 1 1 1.2s VCF | 1 1 5.9s VCF overwrite | 1 1 0.4s Buffer + Collect | 1 1 1.5s Buffer + Writer | 1 1 0.9s Paired FASTA + Collect | 5 5 2.1s Paired FASTA + Paired Writer | 1 1 0.3s Paired FASTA + Single Writer | 2 2 0.8s BAM + Collect | 2 2 4.0s BAM + Collect + Group by read name | 1 1 4.7s BAM to paired FASTQ | 1 1 1.0s 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 54.9s ERROR: LoadError: Package BioRecordsProcessing 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:2128 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [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 145.65s: package tests unexpectedly errored