Package evaluation of BioRecordsProcessing on Julia 1.13.0-DEV.1072 (de815ed1fa*) started at 2025-09-03T13:09:29.956 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.73s ################################################################################ # Installation # Installing BioRecordsProcessing... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [321bc2d7] + BioRecordsProcessing v0.2.3 Updating `~/.julia/environments/v1.13/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 v4.18.0 ⌅ [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 v1.3.3 [21216c6a] + Preferences v1.5.0 [fdea26ae] + SIMD v3.7.1 ⌅ [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 [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 v0.7.0 [9e88b42a] + Serialization v1.11.0 [f489334b] + StyledStrings 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 v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+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 To see why use `status --outdated -m` Installation completed after 3.58s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 70.93s ################################################################################ # Testing # Testing BioRecordsProcessing Status `/tmp/jl_oR12wz/Project.toml` [321bc2d7] BioRecordsProcessing v0.2.3 [7e6ae17a] BioSequences v3.5.0 [c2308a5c] FASTX v2.1.7 [3372ea36] FormatSpecimens v1.3.1 [28eba6e3] VariantCallFormat v0.5.7 [d759349c] XAM v0.4.2 [8dfed614] Test v1.11.0 Status `/tmp/jl_oR12wz/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 v4.18.0 ⌅ [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 v1.3.3 [21216c6a] Preferences v1.5.0 [fdea26ae] SIMD v3.7.1 [354b36f9] StringViews v1.3.5 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [28eba6e3] VariantCallFormat v0.5.7 [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 [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 v0.7.0 [9e88b42a] Serialization v1.11.0 [f489334b] StyledStrings 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 v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+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 0.9s Test Summary: | Pass Total Time ExternalTool + File | 1 1 0.8s 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 3.2s p = Pipeline: Reader{File}(FASTX.FASTA, File("/tmp/jl_iWD8AD/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_b49Vo4") p = Pipeline: Reader{Directory}(FASTX.FASTQ, Directory("/home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data")"*.fastq") ↓ Writer(FASTX.FASTQ, "/tmp/jl_EIJgeD") [ 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` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] getproperty @ ./Base_compiler.jl:50 [inlined] [2] (::BioRecordsProcessing.var"#BAMPairedReadGrouper##4#BAMPairedReadGrouper##5")(r::XAM.BAM.Record) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:60 [3] group_record!(rg::RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#BAMPairedReadGrouper##0#BAMPairedReadGrouper##1", BioRecordsProcessing.var"#BAMPairedReadGrouper##2#BAMPairedReadGrouper##3", BioRecordsProcessing.var"#BAMPairedReadGrouper##4#BAMPairedReadGrouper##5"}, r::XAM.BAM.Record, idx::Int64) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:45 [4] run_single(p::Pipeline{Reader{File}, RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#BAMPairedReadGrouper##0#BAMPairedReadGrouper##1", BioRecordsProcessing.var"#BAMPairedReadGrouper##2#BAMPairedReadGrouper##3", BioRecordsProcessing.var"#BAMPairedReadGrouper##4#BAMPairedReadGrouper##5"}, BioRecordsProcessing.Processor, Collect{Bool}}; max_records::Float64, verbose::Bool) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:133 [5] run_single @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:110 [inlined] [6] #run#21 @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:67 [inlined] [7] run @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:63 [inlined] [8] (::var"#98#99")(dir::String) @ Main ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:277 [9] mktempdir(fn::var"#98#99", parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [10] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:895 [11] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:8 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1945 [inlined] [13] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:266 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1945 [inlined] [15] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:266 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:309 [17] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/runtests.jl:10 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:309 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [22] _start() @ Base ./client.jl:563 ┌ 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` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] getproperty @ ./Base_compiler.jl:50 [inlined] [2] (::BioRecordsProcessing.var"#BAMPairedReadGrouper##4#BAMPairedReadGrouper##5")(r::XAM.BAM.Record) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:60 [3] group_record!(rg::RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#BAMPairedReadGrouper##0#BAMPairedReadGrouper##1", BioRecordsProcessing.var"#BAMPairedReadGrouper##2#BAMPairedReadGrouper##3", BioRecordsProcessing.var"#BAMPairedReadGrouper##4#BAMPairedReadGrouper##5"}, r::XAM.BAM.Record, idx::Int64) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/RecordGrouper.jl:45 [4] run_single(p::Pipeline{Reader{File}, RecordGrouper{XAM.BAM.Record, String, BioRecordsProcessing.var"#BAMPairedReadGrouper##0#BAMPairedReadGrouper##1", BioRecordsProcessing.var"#BAMPairedReadGrouper##2#BAMPairedReadGrouper##3", BioRecordsProcessing.var"#BAMPairedReadGrouper##4#BAMPairedReadGrouper##5"}, BioRecordsProcessing.Processor, Writer}; max_records::Float64, verbose::Bool) @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:133 [5] run_single @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:110 [inlined] [6] #run#21 @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:67 [inlined] [7] run @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Pipeline.jl:63 [inlined] [8] (::var"#102#103")(dir::String) @ Main ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:304 [9] mktempdir(fn::var"#102#103", parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [10] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:895 [11] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:8 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1945 [inlined] [13] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:285 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1945 [inlined] [15] macro expansion @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/test_pipeline.jl:285 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:309 [17] top-level scope @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/test/runtests.jl:10 [18] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:309 [19] top-level scope @ none:6 [20] eval(m::Module, e::Any) @ Core ./boot.jl:489 [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [22] _start() @ Base ./client.jl:563 Test Summary: | Pass Error Total Time Pipeline | 21 2 23 38.1s FASTA Collect | 1 1 6.4s FASTQ.gz Writer | 2 2 3.5s FASTA + Directory | 3 3 3.2s Directory + Collect | 1 1 1.2s VCF | 1 1 6.1s VCF overwrite | 1 1 1.1s Buffer + Collect | 1 1 1.3s Buffer + Writer | 1 1 1.3s Paired FASTA + Collect | 5 5 1.9s Paired FASTA + Paired Writer | 1 1 0.6s Paired FASTA + Single Writer | 2 2 0.7s BAM + Collect | 2 2 4.1s BAM + Collect + Group by read name | 1 1 5.6s BAM to paired FASTQ | 1 1 0.9s RNG of the outermost testset: Random.Xoshiro(0x7b9f393ec7dd3f75, 0xdae504be87701c8f, 0x6ca9bbef4b9d5d43, 0x1b9f508d6616a9a0, 0xecfa2704a2df0ad1) 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 62.73s ERROR: LoadError: Package BioRecordsProcessing errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2673 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2522 [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/v1.13/Pkg/src/API.jl:538 [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/v1.13/Pkg/src/API.jl:515 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:308 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:330 [14] _start() @ Base ./client.jl:563 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 168.43s: package tests unexpectedly errored