Package evaluation to test ReadDatastores on Julia 1.14.0-DEV.1893 (b4aba01002*) started at 2026-03-15T14:09:41.279 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.17s ################################################################################ # Installation # Installing ReadDatastores... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [70a005b8] + ReadDatastores v0.4.0 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [67c07d97] + Automa v0.8.4 [47718e42] + BioGenerics v0.1.5 ⌅ [7e6ae17a] + BioSequences v2.0.6 ⌅ [3c28c6f8] + BioSymbols v4.0.4 [861a8166] + Combinatorics v1.1.0 ⌅ [c2308a5c] + FASTX v1.2.0 [1cb3b9ac] + IndexableBitVectors v1.0.0 [70a005b8] + ReadDatastores v0.4.0 ⌅ [860ef19b] + StableRNGs v0.1.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [7200193e] + Twiddle v1.1.2 [2a0f44e3] + Base64 v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting 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 v1.0.0 [9e88b42a] + Serialization v1.11.0 [f489334b] + StyledStrings v1.13.0 [8dfed614] + Test v1.11.0 [4ec0a83e] + Unicode v1.11.0 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 To see why use `status --outdated -m` Installation completed after 4.54s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 1664.8 ms ✓ BioGenerics WARNING: Constructor for type "Char" was extended in `BioSymbols` without explicit qualification or import.  NOTE: Assumed "Char" refers to `Base.Char`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function Char end`.  Hint: To silence the warning, qualify `Char` as `Base.Char` in the method signature or explicitly `import Base: Char`. 14281.2 ms ✓ BioSymbols [ Info: Compiling bit-parallel GC counter for LongSequence{<:NucleicAcidAlphabet} [ Info: Compiling bit-parallel mismatch counter for LongSequence{<:NucleicAcidAlphabet} [ Info: Compiling bit-parallel match counter for LongSequence{<:NucleicAcidAlphabet} [ Info: Compiling bit-parallel ambiguity counter... [ Info: For a single LongSequence{<:NucleicAcidAlphabet} [ Info: For a pair of LongSequence{<:NucleicAcidAlphabet}s [ Info: Compiling bit-parallel certainty counter for LongSequence{<:NucleicAcidAlphabet} [ Info: Compiling bit-parallel gap counter for LongSequence{<:NucleicAcidAlphabet} 5574.2 ms ✓ BioSequences 15462.2 ms ✓ FASTX 3864.4 ms ✓ ReadDatastores 5 dependencies successfully precompiled in 41 seconds. 16 already precompiled. 6 dependencies precompiled but different versions are currently loaded (Base64, JuliaSyntaxHighlighting, Logging, Markdown, Printf and StyledStrings). Restart julia to access the new versions. Otherwise, 11 dependents of these packages may trigger further precompilation to work with the unexpected versions. 2 dependencies had output during precompilation: ┌ BioSequences │ [ Info: Compiling bit-parallel GC counter for LongSequence{<:NucleicAcidAlphabet} │ [ Info: Compiling bit-parallel mismatch counter for LongSequence{<:NucleicAcidAlphabet} │ [ Info: Compiling bit-parallel match counter for LongSequence{<:NucleicAcidAlphabet} │ [ Info: Compiling bit-parallel ambiguity counter... │ [ Info: For a single LongSequence{<:NucleicAcidAlphabet} │ [ Info: For a pair of LongSequence{<:NucleicAcidAlphabet}s │ [ Info: Compiling bit-parallel certainty counter for LongSequence{<:NucleicAcidAlphabet} │ [ Info: Compiling bit-parallel gap counter for LongSequence{<:NucleicAcidAlphabet} └ ┌ BioSymbols │ WARNING: Constructor for type "Char" was extended in `BioSymbols` without explicit qualification or import. │ NOTE: Assumed "Char" refers to `Base.Char`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Char end`. │ Hint: To silence the warning, qualify `Char` as `Base.Char` in the method signature or explicitly `import Base: Char`. └ Precompilation completed after 63.07s ################################################################################ # Testing # Testing ReadDatastores Status `/tmp/jl_UwYyoo/Project.toml` ⌅ [7e6ae17a] BioSequences v2.0.6 ⌅ [c2308a5c] FASTX v1.2.0 [70a005b8] ReadDatastores v0.4.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_UwYyoo/Manifest.toml` ⌅ [67c07d97] Automa v0.8.4 [47718e42] BioGenerics v0.1.5 ⌅ [7e6ae17a] BioSequences v2.0.6 ⌅ [3c28c6f8] BioSymbols v4.0.4 [861a8166] Combinatorics v1.1.0 ⌅ [c2308a5c] FASTX v1.2.0 [1cb3b9ac] IndexableBitVectors v1.0.0 [70a005b8] ReadDatastores v0.4.0 ⌅ [860ef19b] StableRNGs v0.1.2 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [2a0f44e3] Base64 v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting 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 v1.0.0 [9e88b42a] Serialization v1.11.0 [f489334b] StyledStrings v1.13.0 [8dfed614] Test v1.11.0 [4ec0a83e] Unicode v1.11.0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: Building paired read datastore from FASTQ files [ Info: Writing paired reads to datastore [ Info: Done writing paired read sequences to datastore [ Info: 0 read pairs were discarded due to a too short sequence [ Info: 8 reads were truncated to 300 base pairs [ Info: Created paired sequence datastore with 10 sequence pairs [ Info: Building paired read datastore from FASTQ files [ Info: Writing paired reads to datastore [ Info: Done writing paired read sequences to datastore [ Info: 0 read pairs were discarded due to a too short sequence [ Info: 8 reads were truncated to 300 base pairs [ Info: Created paired sequence datastore with 10 sequence pairs Test Summary: | Pass Total Time Paired read datastores | 38 38 15.2s [ Info: Building long read datastore from FASTQ file [ Info: Writing long reads to datastore [ Info: Done writing long read sequences to datastore [ Info: 0 reads were discarded due to a too short sequence [ Info: Writing index to datastore [ Info: Built long read datastore with 10 reads [ Info: Resizing buffer! [ Info: Resizing buffer! [ Info: Resizing buffer! [ Info: Resizing buffer! [ Info: Building long read datastore from FASTQ file [ Info: Writing long reads to datastore [ Info: Done writing long read sequences to datastore [ Info: 0 reads were discarded due to a too short sequence [ Info: Writing index to datastore [ Info: Built long read datastore with 10 reads [ Info: Resizing buffer! [ Info: Resizing buffer! [ Info: Resizing buffer! [ Info: Resizing buffer! Test Summary: | Pass Total Time Long read datastores | 36 36 4.7s [ Info: Building tag sorted chunks of 10 pairs [ Info: Dumping 10 tag-sorted read pairs to chunk 0 [ Info: Dumped [ Info: Processed 10 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 1 [ Info: Dumped [ Info: Processed 20 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 2 [ Info: Dumped [ Info: Processed 30 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 3 [ Info: Dumped [ Info: Processed 40 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 4 [ Info: Dumped [ Info: Processed 50 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 5 [ Info: Dumped [ Info: Processed 60 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 6 [ Info: Dumped [ Info: Processed 70 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 7 [ Info: Dumped [ Info: Processed 80 read pairs so far [ Info: Dumping 3 tag-sorted read pairs to chunk 8 [ Info: Dumped [ Info: Processed 83 read pairs so far [ Info: Finished building tag sorted chunks [ Info: Performing merge from disk [ Info: Leaving space for 83 read_tag entries [ Info: Chunk 6 is finished [ Info: Chunk 8 is finished [ Info: Chunk 0 is finished [ Info: Chunk 7 is finished [ Info: Chunk 4 is finished [ Info: Chunk 3 is finished [ Info: Chunk 5 is finished [ Info: Chunk 2 is finished [ Info: Chunk 1 is finished [ Info: Finished merge from disk [ Info: Writing 83 read tag entries [ Info: Created linked sequence datastore with 83 sequence pairs [ Info: Building tag sorted chunks of 10 pairs [ Info: Dumping 10 tag-sorted read pairs to chunk 0 [ Info: Dumped [ Info: Processed 10 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 1 [ Info: Dumped [ Info: Processed 20 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 2 [ Info: Dumped [ Info: Processed 30 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 3 [ Info: Dumped [ Info: Processed 40 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 4 [ Info: Dumped [ Info: Processed 50 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 5 [ Info: Dumped [ Info: Processed 60 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 6 [ Info: Dumped [ Info: Processed 70 read pairs so far [ Info: Dumping 10 tag-sorted read pairs to chunk 7 [ Info: Dumped [ Info: Processed 80 read pairs so far [ Info: Dumping 3 tag-sorted read pairs to chunk 8 [ Info: Dumped [ Info: Processed 83 read pairs so far [ Info: Finished building tag sorted chunks [ Info: Performing merge from disk [ Info: Leaving space for 83 read_tag entries [ Info: Chunk 6 is finished [ Info: Chunk 8 is finished [ Info: Chunk 0 is finished [ Info: Chunk 7 is finished [ Info: Chunk 4 is finished [ Info: Chunk 3 is finished [ Info: Chunk 5 is finished [ Info: Chunk 2 is finished [ Info: Chunk 1 is finished [ Info: Finished merge from disk [ Info: Writing 83 read tag entries [ Info: Created linked sequence datastore with 83 sequence pairs Test Summary: | Pass Total Time Linked read datastores | 20 20 10.8s Test Summary: | Pass Total Time Error Messages | 6 6 0.1s Testing ReadDatastores tests passed Testing completed after 41.07s PkgEval succeeded after 132.55s