Package evaluation of BioRecordsProcessing on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T10:53:13.473


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 7.78s


################################################################################
# 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 v3.4.1
  [3c28c6f8] + BioSymbols v5.1.3
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.16.0
  [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 v1.8.0
⌅ [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [fdea26ae] + SIMD v3.7.1
⌅ [3bb67fe8] + TranscodingStreams v0.9.13
  [7200193e] + Twiddle v1.1.2
  [d759349c] + XAM v0.4.0
  [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 To see why use `status --outdated -m`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 2.79s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

┌ Warning: Could not use exact versions of packages in manifest, re-resolving
└ @ TestEnv ~/.julia/packages/TestEnv/tgnBf/src/julia-1.11/activate_set.jl:63
Precompiling package dependencies...

Precompilation completed after 57.77s


################################################################################
# Testing
#

     Testing BioRecordsProcessing
┌ Warning: Could not use exact versions of packages in manifest, re-resolving
└ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1920
      Status `/tmp/jl_2F9JWd/Project.toml`
  [321bc2d7] BioRecordsProcessing v0.2.3
  [7e6ae17a] BioSequences v3.4.1
⌃ [c2308a5c] FASTX v2.1.2
  [3372ea36] FormatSpecimens v1.3.1
  [28eba6e3] VariantCallFormat v0.5.6
⌃ [d759349c] XAM v0.3.1
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_2F9JWd/Manifest.toml`
⌅ [67c07d97] Automa v0.8.4
  [28d598bf] BGZFStreams v0.3.2
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [321bc2d7] BioRecordsProcessing v0.2.3
  [7e6ae17a] BioSequences v3.4.1
  [3c28c6f8] BioSymbols v5.1.3
  [e1450e63] BufferedStreams v1.2.2
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.16.0
  [864edb3b] DataStructures v0.18.22
⌃ [c2308a5c] FASTX v2.1.2
  [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 v1.8.0
⌅ [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [fdea26ae] SIMD v3.7.1
  [7b38b023] ScanByte v0.4.0
  [354b36f9] StringViews v1.3.4
⌅ [3bb67fe8] TranscodingStreams v0.9.13
  [7200193e] Twiddle v1.1.2
  [28eba6e3] VariantCallFormat v0.5.6
⌃ [d759349c] XAM v0.3.1
  [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 ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading.
     Testing Running tests...
Test Summary: | Pass  Total  Time
Internals     |    2      2  0.1s
Test Summary:       | Pass  Total  Time
ExternalTool + File |    1      1  4.4s
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  3.4s
p = Pipeline:
  Reader{File}(FASTX.FASTA, File("/tmp/jl_ZtU8rG/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_yMJXK1")

p = Pipeline:
  Reader{Directory}(FASTX.FASTQ, Directory("/home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data")"*.fastq")
     ↓ 
  Writer(FASTX.FASTQ, "/tmp/jl_Em9wwc")

[ 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
┌ Warning: Index file not found : /home/pkgeval/.julia/packages/FormatSpecimens/cmrLJ/BAM/bam1.bam.bai
└ @ BioRecordsProcessing ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/Source.jl:119
Test Summary: | Pass  Total   Time
Pipeline      |   29     29  23.3s
     Testing BioRecordsProcessing tests passed 

Testing completed after 37.79s

PkgEval succeeded after 116.82s