Package evaluation of BioRecordsProcessing on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T14:13:52.135


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.96s


################################################################################
# Installation
#

Installing BioRecordsProcessing...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [321bc2d7] + BioRecordsProcessing v0.2.3
    Updating `~/.julia/environments/v1.12/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 v3.4.2
  [3c28c6f8] + BioSymbols v5.2.0
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.17.0
  [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 v1.3.2
  [21216c6a] + Preferences v1.4.3
  [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 v1.12.0
  [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 To see why use `status --outdated -m`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 3.75s


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

Precompiling PkgEval dependencies...

┌ Warning: Could not use exact versions of packages in manifest, re-resolving
└ @ TestEnv ~/.julia/packages/TestEnv/iS95e/src/julia-1.11/activate_set.jl:75
Precompiling package dependencies...

Precompilation completed after 72.87s


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

     Testing BioRecordsProcessing
        Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function.
    Updating `/tmp/jl_bVPfiE/Project.toml`
  [321bc2d7] + BioRecordsProcessing v0.2.3
⌃ [c2308a5c] + FASTX v2.1.2
  [3372ea36] + FormatSpecimens v1.3.1
  [28eba6e3] + VariantCallFormat v0.5.6
⌃ [d759349c] ↓ XAM v0.4.2 ⇒ v0.3.1
    Updating `/tmp/jl_bVPfiE/Manifest.toml`
⌅ [67c07d97] ↓ Automa v1.1.0 ⇒ v0.8.4
  [321bc2d7] + BioRecordsProcessing v0.2.3
  [e1450e63] + BufferedStreams v1.2.2
⌃ [c2308a5c] + FASTX v2.1.2
  [3372ea36] + FormatSpecimens v1.3.1
  [c27321d9] + Glob v1.3.1
  [7b38b023] + ScanByte v0.4.0
  [354b36f9] + StringViews v1.3.4
  [28eba6e3] + VariantCallFormat v0.5.6
⌃ [d759349c] ↓ XAM v0.4.2 ⇒ v0.3.1
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
        Test Successfully re-resolved
      Status `/tmp/jl_bVPfiE/Project.toml`
  [321bc2d7] BioRecordsProcessing v0.2.3
  [7e6ae17a] BioSequences v3.4.2
⌃ [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_bVPfiE/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 v3.4.2
  [3c28c6f8] BioSymbols v5.2.0
  [e1450e63] BufferedStreams v1.2.2
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.17.0
  [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 v1.8.1
  [aea7be01] PrecompileTools v1.3.2
  [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
  [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.12.0
  [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 ⌃ 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  1.4s
Test Summary:       | Pass  Total  Time
ExternalTool + File |    1      1  5.0s
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  2.9s
p = Pipeline:
  Reader{File}(FASTX.FASTA, File("/tmp/jl_vZW6s7/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_f0Cthf")

p = Pipeline:
  Reader{Directory}(FASTX.FASTQ, Directory("/home/pkgeval/.julia/packages/BioRecordsProcessing/Dw0CY/test/data")"*.fastq")
     ↓ 
  Writer(FASTX.FASTQ, "/tmp/jl_e7l8l8")

[ 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  29.3s
     Testing BioRecordsProcessing tests passed 

Testing completed after 54.39s

PkgEval succeeded after 168.73s