Package evaluation of SimpleBio on Julia 1.13.0-DEV.464 (abc56fde89*) started at 2025-05-01T20:57:47.492 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... ┌ Warning: could not download https://pkg.julialang.org/registries │ exception = RequestError: HTTP/2 301 (Connection timed out after 30005 milliseconds) while requesting https://pkg.julialang.org/registries └ @ Pkg.Registry /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Registry/Registry.jl:77 Set-up completed after 7.23s ################################################################################ # Installation # Installing SimpleBio... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [d9eea77d] + SimpleBio v0.3.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [00701ae9] + BioAlignments v3.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.1 [3c28c6f8] + BioSymbols v5.2.0 [34da2185] + Compat v4.16.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.4 ⌅ [e30172f5] + Documenter v0.27.25 [35a29f4d] + DocumenterTools v0.1.20 [d7ba0133] + Git v1.3.1 [708ec375] + Gumbo v0.8.3 [b5f81e59] + IOCapture v0.2.5 [842dd82b] + InlineStrings v1.4.3 [524e6230] + IntervalTrees v1.1.0 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [189a3867] + Reexport v1.2.2 [322a6be2] + Sass v0.2.0 [91c51154] + SentinelArrays v1.4.8 [d9eea77d] + SimpleBio v0.3.0 [a2af1166] + SortingAlgorithms v1.2.1 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [2e619515] + Expat_jll v2.6.5+0 [f8c6e375] + Git_jll v2.49.0+0 [528830af] + Gumbo_jll v0.10.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 ⌅ [9bd350c2] + OpenSSH_jll v9.9.2+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 v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [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 v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 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 3.89s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 20.95s ################################################################################ # Testing # Testing SimpleBio Status `/tmp/jl_Cf4vtb/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_Cf4vtb/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 v0.9.4 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.20 ⌃ [59287772] Formatting v0.4.2 [d7ba0133] Git v1.3.1 [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 v1.7.0 [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 v1.3.2 [21216c6a] Preferences v1.4.3 ⌃ [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 v2.6.5+0 [f8c6e375] Git_jll v2.49.0+0 [528830af] Gumbo_jll v0.10.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 ⌅ [9bd350c2] OpenSSH_jll v9.9.2+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 v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [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 v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2024.12.31 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.0.16+0 [efcefdf7] PCRE2_jll v10.44.0+1 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 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... Precompiling packages... 1066.3 ms ✓ SnoopPrecompile 799.2 ms ✓ InvertedIndices 2000.6 ms ✓ StringManipulation 1086.3 ms ✓ Formatting 1030.1 ms ✓ PooledArrays 1120.6 ms ✓ IntervalTrees 2482.7 ms ✓ TranscodingStreams 2071.1 ms ✓ Tables 2133.4 ms ✓ BioSymbols 1633.4 ms ✓ BioGenerics 8831.8 ms ✓ PrettyTables 8229.2 ms ✓ BioSequences 52310.1 ms ✓ DataFrames 3774.2 ms ✓ BioAlignments Info Given SimpleBio was explicitly requested, output will be shown live  Generated 10 random DNA sequences: sequences (5'-3"): CAGTCACTAA ACTAACCGTG CCGGAATTAT AATCTCAGCT CACATAATAG AGCACAATGG TAGCTAGTCA CTTCAGGGAA GTACGGACCT AAGAGGACAT 6858.1 ms ✓ SimpleBio 15 dependencies successfully precompiled in 96 seconds. 68 already precompiled. 2 dependencies had output during precompilation: ┌ SimpleBio │ [Output was shown above] └ ┌ 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`. └ Generated one random RNA sequence: sequence: 5'-CCGTGCTATT-3' Generated one random RNA sequence: sequence: 5'-ATTGCCTCCC-3' Generated one random RNA sequence: sequence: 5'-GACAGTATCA-3' Generated one random RNA sequence: sequence: 5'-TGTCTTGCTA-3' Generated one random RNA sequence: sequence: 5'-GGCGCTTGAT-3' Generated one random RNA sequence: sequence: 5'-GGCCTCCGCA-3' Generated one random RNA sequence: sequence: 5'-GGCGGGTGTC-3' Generated one random RNA sequence: sequence: 5'-ATATTTTACC-3' Generated one random DNA sequence: sequence: 5'-CCGUGCUAUU-3' Generated one random DNA sequence: sequence: 5'-AUUGCCUCCC-3' Generated one random DNA sequence: sequence: 5'-GACAGUAUCA-3' Generated one random DNA sequence: sequence: 5'-UGUCUUGCUA-3' Generated one random DNA sequence: sequence: 5'-GGCGCUUGAU-3' Generated one random DNA sequence: sequence: 5'-GGCCUCCGCA-3' Generated one random DNA sequence: sequence: 5'-GGCGGGUGUC-3' Generated one random DNA sequence: sequence: 5'-AUAUUUUACC-3' Generated one random amino acid peptide chain sequence: sequence: 5'-MMVHYKHNEI-3' Generated one random amino acid peptide chain sequence: sequence: 5'-AQIYFPGPMF-3' Generated one random amino acid peptide chain sequence: sequence: 5'-SDMRVEDHLD-3' Generated one random amino acid peptide chain sequence: sequence: 5'-QYHLEGYMQA-3' Generated one random amino acid peptide chain sequence: sequence: 5'-SSLYMHIVCH-3' Generated one random amino acid peptide chain sequence: sequence: 5'-WYLFELFVMC-3' Generated one random RNA sequence: sequence: 5'-CCGTGCTATT-3' Generated one random RNA sequence: sequence: 5'-ATTGCCTCCC-3' Generated one random RNA sequence: sequence: 5'-GACAGTATCA-3' Generated one random RNA sequence: sequence: 5'-TGTCTTGCTA-3' Generated one random RNA sequence: sequence: 5'-GGCGCTTGAT-3' Generated one random RNA sequence: sequence: 5'-GGCCTCCGCA-3' Generated one random RNA sequence: sequence: 5'-GGCGGGTGTC-3' Generated one random RNA sequence: sequence: 5'-ATATTTTACC-3' Generated one random DNA sequence: sequence: 5'-CUACAGAGUG-3' Generated one random DNA sequence: sequence: 5'-ACCCCCUGAC-3' Generated one random DNA sequence: sequence: 5'-CUGUAACAGG-3' Generated one random DNA sequence: sequence: 5'-CAUAGUCUUU-3' Generated one random DNA sequence: sequence: 5'-GGGUCUGGCC-3' Generated one random DNA sequence: sequence: 5'-AAUCGAUCUG-3' Generated one random DNA sequence: sequence: 5'-UUAAAUCAUC-3' Generated one random DNA sequence: sequence: 5'-AGAUACGGAG-3' Generated one random amino acid peptide chain sequence: sequence: 5'-PCYNCRIPGW-3' Generated one random amino acid peptide chain sequence: sequence: 5'-QRIWKIEPWS-3' Generated one random amino acid peptide chain sequence: sequence: 5'-APWYLDCEFT-3' Generated one random amino acid peptide chain sequence: sequence: 5'-GLTAHQDMTW-3' Generated one random amino acid peptide chain sequence: sequence: 5'-EDPPMCRWWR-3' Generated one random amino acid peptide chain sequence: sequence: 5'-DTNLMTAWPV-3' Generated 10 random DNA sequences: sequences (5'-3"): CCGTGCTATT ATTGCCTCCC GACAGTATCA TGTCTTGCTA GGCGCTTGAT GGCCTCCGCA GGCGGGTGTC ATATTTTACC CTACAGAGTG ACCCCCTGAC Generated 10 random DNAs sequences: sequences (5'-3"): CTGTAACAGG CATAGTCTTT GGGTCTGGCC AATCGATCTG TTAAATCATC AGATACGGAG CAGAAATCTG TATGCTTCGG ACGGCAATCG TCGATTACGG Generated 10 random DNA nucleotides sequences: sequences (5'-3"): TACCCAAGGA AGACCGAGCG AAGTGAGAAT TACCCGCCTG GGCCACGCTT GGTCCCGGAA CTCTCAGTCT CTATTGGACA ATTCTTAACG GCACCAACAA Generated 10 random DNA chain sequences: sequences (5'-3"): TTCGTGTTGC CGTGTGGCCA GTATGATGGG AAGCGGTTTA TTCGTTTTAA ACACTTGGAG GACTGGCGGT ACGAGGAGAC ATGAGAACAT CCGGTGAGTC Generated 10 random dna sequences: sequences (5'-3"): TCAGACAGAC AGTGAACCGA CTAAAGTGGC GCCAAAACCA GTGCGATGTG ACCAAAACTA ATCTCCTACT TTAGTCGTGG TAGGATTTAA CTCGGGCACG Generated 10 random dnas sequences: sequences (5'-3"): CCACATGGGG TTCATACACG TCATCCACCG TCTGCGGCAA GAAGACTTGA GGGCGTACAT AAAATTGAAT GCGTGTTAGG AACTCTTTTT TAAATTGTGG Generated 10 random dna nucleotides sequences: sequences (5'-3"): GACGATCTAG AGCGTAGGTT CTTCAAAACC CTGAGCGGAC GTTCATTGTC GGGCTAACAC CGGAATGATC TCATGAGGGT TCGAAACGAA ATGCTAATCG Generated 10 random dna chain sequences: sequences (5'-3"): AAATTACAGG GGGTCGGTGA TACTCTCCTA TCAAGCGTTG TGACGACAAT CACAGCCCTT CCAATAATCT AGTTACCGAT TGTCCTGCCG CATCATGGAG Generated 10 random RNA sequences: sequences (5'-3"): CCGUGCUAUU AUUGCCUCCC GACAGUAUCA UGUCUUGCUA GGCGCUUGAU GGCCUCCGCA GGCGGGUGUC AUAUUUUACC CUACAGAGUG ACCCCCUGAC Generated 10 random RNAs sequences: sequences (5'-3"): CUGUAACAGG CAUAGUCUUU GGGUCUGGCC AAUCGAUCUG UUAAAUCAUC AGAUACGGAG CAGAAAUCUG UAUGCUUCGG ACGGCAAUCG UCGAUUACGG Generated 10 random RNA nucleotides sequences: sequences (5'-3"): UACCCAAGGA AGACCGAGCG AAGUGAGAAU UACCCGCCUG GGCCACGCUU GGUCCCGGAA CUCUCAGUCU CUAUUGGACA AUUCUUAACG GCACCAACAA Generated 10 random RNA chain sequences: sequences (5'-3"): UUCGUGUUGC CGUGUGGCCA GUAUGAUGGG AAGCGGUUUA UUCGUUUUAA ACACUUGGAG GACUGGCGGU ACGAGGAGAC AUGAGAACAU CCGGUGAGUC Generated 10 random rna sequences: sequences (5'-3"): UCAGACAGAC AGUGAACCGA CUAAAGUGGC GCCAAAACCA GUGCGAUGUG ACCAAAACUA AUCUCCUACU UUAGUCGUGG UAGGAUUUAA CUCGGGCACG Generated 10 random rnas sequences: sequences (5'-3"): CCACAUGGGG UUCAUACACG UCAUCCACCG UCUGCGGCAA GAAGACUUGA GGGCGUACAU AAAAUUGAAU GCGUGUUAGG AACUCUUUUU UAAAUUGUGG Generated 10 random rna nucleotides sequences: sequences (5'-3"): GACGAUCUAG AGCGUAGGUU CUUCAAAACC CUGAGCGGAC GUUCAUUGUC GGGCUAACAC CGGAAUGAUC UCAUGAGGGU UCGAAACGAA AUGCUAAUCG Generated 10 random rna chain sequences: sequences (5'-3"): AAAUUACAGG GGGUCGGUGA UACUCUCCUA UCAAGCGUUG UGACGACAAU CACAGCCCUU CCAAUAAUCU AGUUACCGAU UGUCCUGCCG CAUCAUGGAG Generated 10 random AminoAcid sequences: sequences (5'-3"): MMVHYKHNEI AQIYFPGPMF SDMRVEDHLD QYHLEGYMQA SSLYMHIVCH WYLFELFVMC YVLSVVITGL DIRHEGERLK MGCFRWDWIT CKKLMLQTAP Generated 10 random aminoacid sequences: sequences (5'-3"): LGYQDRFRWS LRICYHFQEI SYYHKGSWMM DRIKTCGMEV IICNDGMAIF NTNQNMVVAS PCYNCRIPGW QRIWKIEPWS APWYLDCEFT GLTAHQDMTW Generated 10 random amino acid sequences: sequences (5'-3"): EDPPMCRWWR DTNLMTAWPV NDYGSASDDI IALPFTPFQW TTMPNKWPGE WVGKFLSTDA MIKILAVHMI FHCHHVSRFC AGHMIHADPY TLCFLNDMCD Generated 10 random peptide sequences: sequences (5'-3"): GIMTGYQIVK KSGWGWTFFD TGRIWNGVVS RCVKVTHGID EGKTQQGECC AFAPIHTSNV YRKEYYKVSI RKTNTVDVNF RQWCSNNLCI LMVWGWAVIL Generated 10 random aa sequences: sequences (5'-3"): EMRSAKRVRM AWQSRNMMSD KECDRYEYYP YPMRARDMMC SHYMYNQVGT RKMDDADLHA AEFIPKEAME GERYHMYISW IRTWDGQGRR PGMWWSKRPV Generated 10 random AA sequences: sequences (5'-3"): LMRFDITYSV GEFAEAMNMV HPNGMLNKFS HKETMSSLDA WAATRLIHWR YWVMSHALCI ACDNGEVCDI VPWEYHGNYV ARPIMEGHQG GDRDEIWHWV Test Summary: | Pass Total Time SimpleBio | 161 161 14.4s identify | 6 6 1.0s nucleotidetools | 5 5 0.4s RandSeq-DNA | 22 22 0.5s RandSeq-DNA-1 | 8 8 0.5s 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 0.4s 10 rand dna | 8 8 0.4s 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 1.0s alignment | 6 6 0.0s translation to aa | 5 5 0.5s primer design tools | 50 50 0.9s dnatm | 3 3 0.2s 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 128.86s PkgEval succeeded after 294.12s