Package evaluation to test SimpleBio on Julia 1.14.0-DEV.30 (073666df8b*) started at 2025-11-04T20:12:25.108 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.38s ################################################################################ # Installation # Installing SimpleBio... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [d9eea77d] + SimpleBio v0.3.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [00701ae9] + BioAlignments v3.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.0 [3c28c6f8] + BioSymbols v5.2.0 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.2 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.5 ⌅ [e30172f5] + Documenter v0.27.25 [35a29f4d] + DocumenterTools v0.1.21 [d7ba0133] + Git v1.5.0 [708ec375] + Gumbo v0.8.3 ⌅ [b5f81e59] + IOCapture v0.2.5 [842dd82b] + InlineStrings v1.4.5 [524e6230] + IntervalTrees v1.1.0 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [189a3867] + Reexport v1.2.2 [322a6be2] + Sass v0.2.0 [91c51154] + SentinelArrays v1.4.8 [d9eea77d] + SimpleBio v0.3.0 [a2af1166] + SortingAlgorithms v1.2.2 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [2e619515] + Expat_jll v2.7.3+0 [020c3dae] + Git_LFS_jll v3.7.0+0 [f8c6e375] + Git_jll v2.51.3+0 [528830af] + Gumbo_jll v0.10.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [9bd350c2] + OpenSSH_jll v10.2.1+0 [47bcb7c8] + libsass_jll v3.6.6+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.67.1+0 [3f19e933] + p7zip_jll v17.6.0+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 5.09s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4763.3 ms ✓ DocumenterTools 10103.1 ms ✓ SimpleBio 2 dependencies successfully precompiled in 22 seconds. 84 already precompiled. 1 dependency had output during precompilation: ┌ SimpleBio │ Generated 10 random DNA sequences: │ sequences (5'-3"): │ CGAACCTGAG │ AAAAGTGTCA │ TCACTACGCT │ CGGTATGCTG │ TCAGATTATG │ GTACTCTCTT │ GATGGCCATA │ AAGCGTCTCC │ GGCGAGAAAC │ TACTACAATA └ Precompilation completed after 28.2s ################################################################################ # Testing # Testing SimpleBio Status `/tmp/jl_IvwpFL/Project.toml` [00701ae9] BioAlignments v3.1.0 ⌃ [7e6ae17a] BioSequences v3.1.2 ⌃ [a93c6f00] DataFrames v1.4.4 [d9eea77d] SimpleBio v0.3.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_IvwpFL/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [00701ae9] BioAlignments v3.1.0 ⌃ [47718e42] BioGenerics v0.1.2 ⌃ [7e6ae17a] BioSequences v3.1.2 ⌃ [3c28c6f8] BioSymbols v5.1.2 ⌃ [34da2185] Compat v4.5.0 [a8cc5b0e] Crayons v4.1.1 ⌃ [9a962f9c] DataAPI v1.14.0 ⌃ [a93c6f00] DataFrames v1.4.4 ⌅ [864edb3b] DataStructures v0.18.13 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.5 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.21 ⌃ [59287772] Formatting v0.4.2 [d7ba0133] Git v1.5.0 [708ec375] Gumbo v0.8.3 ⌅ [b5f81e59] IOCapture v0.2.5 ⌃ [524e6230] IntervalTrees v1.0.0 ⌃ [41ab1584] InvertedIndices v1.2.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 ⌃ [b964fa9f] LaTeXStrings v1.3.0 ⌃ [e1d29d7a] Missings v1.1.0 ⌃ [bac558e1] OrderedCollections v1.4.1 [69de0a69] Parsers v2.8.3 ⌃ [2dfb63ee] PooledArrays v1.4.2 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 ⌅ [08abe8d2] PrettyTables v2.2.2 [189a3867] Reexport v1.2.2 [322a6be2] Sass v0.2.0 [d9eea77d] SimpleBio v0.3.0 ⌃ [66db9d55] SnoopPrecompile v1.0.1 ⌃ [a2af1166] SortingAlgorithms v1.1.0 [10745b16] Statistics v1.11.1 ⌅ [892a3eda] StringManipulation v0.3.0 [3783bdb8] TableTraits v1.0.1 ⌃ [bd369af6] Tables v1.10.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.10 [7200193e] Twiddle v1.1.2 [2e619515] Expat_jll v2.7.3+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.51.3+0 [528830af] Gumbo_jll v0.10.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+0 [47bcb7c8] libsass_jll v3.6.6+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+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... Generated one random RNA sequence: sequence: 5'-GGCCTGCAGC-3' Generated one random RNA sequence: sequence: 5'-GGTTCATTGC-3' Generated one random RNA sequence: sequence: 5'-GTTACCTGTT-3' Generated one random RNA sequence: sequence: 5'-GTATTCCATA-3' Generated one random RNA sequence: sequence: 5'-TTGTATGTGA-3' Generated one random RNA sequence: sequence: 5'-TCAAGCGGGT-3' Generated one random RNA sequence: sequence: 5'-CTTAACAATG-3' Generated one random RNA sequence: sequence: 5'-TGGCGCGTAG-3' Generated one random DNA sequence: sequence: 5'-GGCCUGCAGC-3' Generated one random DNA sequence: sequence: 5'-GGUUCAUUGC-3' Generated one random DNA sequence: sequence: 5'-GUUACCUGUU-3' Generated one random DNA sequence: sequence: 5'-GUAUUCCAUA-3' Generated one random DNA sequence: sequence: 5'-UUGUAUGUGA-3' Generated one random DNA sequence: sequence: 5'-UCAAGCGGGU-3' Generated one random DNA sequence: sequence: 5'-CUUAACAAUG-3' Generated one random DNA sequence: sequence: 5'-UGGCGCGUAG-3' Generated one random amino acid peptide chain sequence: sequence: 5'-YTLPITPATP-3' Generated one random amino acid peptide chain sequence: sequence: 5'-YYEEFCIIWF-3' Generated one random amino acid peptide chain sequence: sequence: 5'-YEQAPKHWQH-3' Generated one random amino acid peptide chain sequence: sequence: 5'-TQAEIFKNHA-3' Generated one random amino acid peptide chain sequence: sequence: 5'-QETHCESGTA-3' Generated one random amino acid peptide chain sequence: sequence: 5'-GFDRVKTTWG-3' Generated one random RNA sequence: sequence: 5'-GGCCTGCAGC-3' Generated one random RNA sequence: sequence: 5'-GGTTCATTGC-3' Generated one random RNA sequence: sequence: 5'-GTTACCTGTT-3' Generated one random RNA sequence: sequence: 5'-GTATTCCATA-3' Generated one random RNA sequence: sequence: 5'-TTGTATGTGA-3' Generated one random RNA sequence: sequence: 5'-TCAAGCGGGT-3' Generated one random RNA sequence: sequence: 5'-CTTAACAATG-3' Generated one random RNA sequence: sequence: 5'-TGGCGCGTAG-3' Generated one random DNA sequence: sequence: 5'-AAUUCAAUAG-3' Generated one random DNA sequence: sequence: 5'-CGUCGUCGAG-3' Generated one random DNA sequence: sequence: 5'-UGUCCUUCUG-3' Generated one random DNA sequence: sequence: 5'-UGAAAAGUGA-3' Generated one random DNA sequence: sequence: 5'-ACGAUCAGAA-3' Generated one random DNA sequence: sequence: 5'-CACAGAGUAU-3' Generated one random DNA sequence: sequence: 5'-CUUCCAACUG-3' Generated one random DNA sequence: sequence: 5'-UAAUGCGGAC-3' Generated one random amino acid peptide chain sequence: sequence: 5'-HCLYAEDNNP-3' Generated one random amino acid peptide chain sequence: sequence: 5'-CNAHDLIAQE-3' Generated one random amino acid peptide chain sequence: sequence: 5'-GYSGPWIRET-3' Generated one random amino acid peptide chain sequence: sequence: 5'-NEQPIVDDKT-3' Generated one random amino acid peptide chain sequence: sequence: 5'-HYHCVHHRES-3' Generated one random amino acid peptide chain sequence: sequence: 5'-GHSASMFCNM-3' Generated 10 random DNA sequences: sequences (5'-3"): GGCCTGCAGC GGTTCATTGC GTTACCTGTT GTATTCCATA TTGTATGTGA TCAAGCGGGT CTTAACAATG TGGCGCGTAG AATTCAATAG CGTCGTCGAG Generated 10 random DNAs sequences: sequences (5'-3"): TGTCCTTCTG TGAAAAGTGA ACGATCAGAA CACAGAGTAT CTTCCAACTG TAATGCGGAC TACGATAAAC AAATACTATT TGGTCGTATG ATTCTGAACG Generated 10 random DNA nucleotides sequences: sequences (5'-3"): TGTAGTTATG TTGAGCCAAC GAACCGTCAG GGTACTCGAA TCTGATCTCT AATATGAGCA GAAACGGCTA CGCAGCCTTA TATTCTTGCG GTACTTCGTA Generated 10 random DNA chain sequences: sequences (5'-3"): AGTGCTTGAA TGTGGCATAG CTATTGAAAT GGTGACGTAC CAAGAACGAT CTCTTAGTCA AATAGGGAGA GGTCTTGCGG TCTGAATATT CTGGGGTAAG Generated 10 random dna sequences: sequences (5'-3"): CTTAGGCGCT GACCACCCCC TTACGTATAT ACCAATTGGA ACCTGGGGAC CGGCGTGTCT AAGGCTTGTG ACGTTACGCG GCCACTTGAA CAGTGGTATT Generated 10 random dnas sequences: sequences (5'-3"): GGCAGCGGCG CAGGGGTTTT CTAAACGCAT GGAACCTCTC GTGGGTGGTA GGTTCAGCTA TGGGTACTAA CCTAACGCAG TATGACAGAT ATCCACGCAC Generated 10 random dna nucleotides sequences: sequences (5'-3"): TCAATAAGCG GTCGAGCACA GTGTCGAGAC AAAAATCTGC TCACGAGCAC GAACGGGCGG GCGGCAGAAT CACAACGTGT TAACCATATT GTAATCTCGT Generated 10 random dna chain sequences: sequences (5'-3"): TTAAAGCCAA GTGACCACTG ACATACATGT GTCGTCACAC TCGCGAGGCC ATATGAGCCA ATCTGCTCTT GTTTACCCTG ACTGCACCCT AATCTACCGT Generated 10 random RNA sequences: sequences (5'-3"): GGCCUGCAGC GGUUCAUUGC GUUACCUGUU GUAUUCCAUA UUGUAUGUGA UCAAGCGGGU CUUAACAAUG UGGCGCGUAG AAUUCAAUAG CGUCGUCGAG Generated 10 random RNAs sequences: sequences (5'-3"): UGUCCUUCUG UGAAAAGUGA ACGAUCAGAA CACAGAGUAU CUUCCAACUG UAAUGCGGAC UACGAUAAAC AAAUACUAUU UGGUCGUAUG AUUCUGAACG Generated 10 random RNA nucleotides sequences: sequences (5'-3"): UGUAGUUAUG UUGAGCCAAC GAACCGUCAG GGUACUCGAA UCUGAUCUCU AAUAUGAGCA GAAACGGCUA CGCAGCCUUA UAUUCUUGCG GUACUUCGUA Generated 10 random RNA chain sequences: sequences (5'-3"): AGUGCUUGAA UGUGGCAUAG CUAUUGAAAU GGUGACGUAC CAAGAACGAU CUCUUAGUCA AAUAGGGAGA GGUCUUGCGG UCUGAAUAUU CUGGGGUAAG Generated 10 random rna sequences: sequences (5'-3"): CUUAGGCGCU GACCACCCCC UUACGUAUAU ACCAAUUGGA ACCUGGGGAC CGGCGUGUCU AAGGCUUGUG ACGUUACGCG GCCACUUGAA CAGUGGUAUU Generated 10 random rnas sequences: sequences (5'-3"): GGCAGCGGCG CAGGGGUUUU CUAAACGCAU GGAACCUCUC GUGGGUGGUA GGUUCAGCUA UGGGUACUAA CCUAACGCAG UAUGACAGAU AUCCACGCAC Generated 10 random rna nucleotides sequences: sequences (5'-3"): UCAAUAAGCG GUCGAGCACA GUGUCGAGAC AAAAAUCUGC UCACGAGCAC GAACGGGCGG GCGGCAGAAU CACAACGUGU UAACCAUAUU GUAAUCUCGU Generated 10 random rna chain sequences: sequences (5'-3"): UUAAAGCCAA GUGACCACUG ACAUACAUGU GUCGUCACAC UCGCGAGGCC AUAUGAGCCA AUCUGCUCUU GUUUACCCUG ACUGCACCCU AAUCUACCGU Generated 10 random AminoAcid sequences: sequences (5'-3"): YTLPITPATP YYEEFCIIWF YEQAPKHWQH TQAEIFKNHA QETHCESGTA GFDRVKTTWG LGIRCFDAHT QVVMVLYGCW DNEILRRGDS LYEMWELVCT Generated 10 random aminoacid sequences: sequences (5'-3"): ESIFMGIPQV EYDNNAVQSN ALWAEPDTCD FAPAYATIAH PEQFKCCPIW HCDQYKVYRL HCLYAEDNNP CNAHDLIAQE GYSGPWIRET NEQPIVDDKT Generated 10 random amino acid sequences: sequences (5'-3"): HYHCVHHRES GHSASMFCNM YRRMKYGKRS WTHAKQLSND EPGYCIMHKH ADHRGTAVFN WARDFTVPQR LYFNSMFIQD GDGGPIETKV SQDPGGKSER Generated 10 random peptide sequences: sequences (5'-3"): AYEWFQQYRC ISHTSFCEAY LIRGQVCNDG WYQYALTGAL LRNYCALYDH MILEQDSHMC DDGDTWYNWA VSQKGEYLVY HPHYNNHCHH PGWYWVHNDS Generated 10 random aa sequences: sequences (5'-3"): LIQDVTLVME TDKLDFKLMM IHAMVERENH CMLRNHHTTR CMKQSTVVCF PYWLVHWGMI DAVTPEGYEW CPSHECLSPW WFPDLGIYRA KAVQSVQRQE Generated 10 random AA sequences: sequences (5'-3"): TVFNSKTVPW LNTTWSHGEQ KERNDLWMNG SWRRFMEFQL WHTWVGWVID VVQGPNTPGR HVWTGRKGRN FLQDCLVFRY HAIVNPNWNH REKKAMSPRK Test Summary: | Pass Total Time SimpleBio | 161 161 15.1s identify | 6 6 0.8s nucleotidetools | 5 5 0.4s RandSeq-DNA | 22 22 0.4s RandSeq-DNA-1 | 8 8 0.4s RandSeq-DNA-2 | 8 8 0.0s RandSeq-DNA-3 | 6 6 0.0s RandSeq-RNA | 22 22 0.0s 10 rand seqs | 22 22 0.3s 10 rand dna | 8 8 0.3s 10 rand rna | 8 8 0.0s 10 rand aa | 6 6 0.0s 10 rand seqs arr out | 22 22 0.4s 10 rand dna | 8 8 0.4s 10 rand rna | 8 8 0.0s 10 rand aa | 6 6 0.0s 10 rand dna-rna dataframe | 1 1 1.4s alignment | 6 6 0.0s translation to aa | 5 5 0.8s primer design tools | 50 50 1.1s dnatm | 3 3 0.4s step_gen | 5 5 0.1s step_from_end | 4 4 0.1s multidnatm | 2 2 0.2s fwd primers | 18 18 0.2s rev primers | 18 18 0.2s Testing SimpleBio tests passed Testing completed after 144.18s PkgEval succeeded after 222.95s