Package evaluation of SimpleBio on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T10:47:05.714 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.11s ################################################################################ # Installation # Installing SimpleBio... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [d9eea77d] + SimpleBio v0.3.0 Updating `~/.julia/environments/v1.10/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 v5.1.3 [34da2185] + Compat v4.16.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.3 ⌅ [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 v2.8.1 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [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 [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 v2.47.1+0 [528830af] + Gumbo_jll v0.10.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [9bd350c2] + OpenSSH_jll v9.9.2+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [47bcb7c8] + libsass_jll v3.6.6+0 [0dad84c5] + ArgTools v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [14a3606d] + MozillaCACerts_jll v2023.1.10 [4536629a] + OpenBLAS_jll v0.3.23+4 [efcefdf7] + PCRE2_jll v10.42.0+1 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+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 6.16s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 19.74s ################################################################################ # Testing # Testing SimpleBio Status `/tmp/jl_ph4BUp/Project.toml` [00701ae9] BioAlignments v3.1.0 [7e6ae17a] BioSequences v3.4.1 [a93c6f00] DataFrames v1.7.0 [d9eea77d] SimpleBio v0.3.0 [8dfed614] Test Status `/tmp/jl_ph4BUp/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 v5.1.3 [34da2185] Compat v4.16.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.3 ⌅ [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 v2.8.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [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 [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 v2.47.1+0 [528830af] Gumbo_jll v0.10.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v9.9.2+0 [458c3c95] OpenSSL_jll v3.0.16+0 [47bcb7c8] libsass_jll v3.6.6+0 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Generated one random RNA sequence: sequence: 5'-TTACGGCATA-3' Generated one random RNA sequence: sequence: 5'-ATAGCCTCCT-3' Generated one random RNA sequence: sequence: 5'-GCTGTCGACG-3' Generated one random RNA sequence: sequence: 5'-ACACCTCGGC-3' Generated one random RNA sequence: sequence: 5'-TAGAGGCGTC-3' Generated one random RNA sequence: sequence: 5'-TATTGTTGTA-3' Generated one random RNA sequence: sequence: 5'-GGTAGCAGGA-3' Generated one random RNA sequence: sequence: 5'-ACGTTGGGAA-3' Generated one random DNA sequence: sequence: 5'-UUACGGCAUA-3' Generated one random DNA sequence: sequence: 5'-AUAGCCUCCU-3' Generated one random DNA sequence: sequence: 5'-GCUGUCGACG-3' Generated one random DNA sequence: sequence: 5'-ACACCUCGGC-3' Generated one random DNA sequence: sequence: 5'-UAGAGGCGUC-3' Generated one random DNA sequence: sequence: 5'-UAUUGUUGUA-3' Generated one random DNA sequence: sequence: 5'-GGUAGCAGGA-3' Generated one random DNA sequence: sequence: 5'-ACGUUGGGAA-3' Generated one random amino acid peptide chain sequence: sequence: 5'-QICLYSLNGN-3' Generated one random amino acid peptide chain sequence: sequence: 5'-NIRSMPGFPH-3' Generated one random amino acid peptide chain sequence: sequence: 5'-SLHYEMWCFW-3' Generated one random amino acid peptide chain sequence: sequence: 5'-NMAPPHMWSP-3' Generated one random amino acid peptide chain sequence: sequence: 5'-INWRVYFSHM-3' Generated one random amino acid peptide chain sequence: sequence: 5'-QDHHWIITEC-3' Generated one random RNA sequence: sequence: 5'-TTACGGCATA-3' Generated one random RNA sequence: sequence: 5'-ATAGCCTCCT-3' Generated one random RNA sequence: sequence: 5'-GCTGTCGACG-3' Generated one random RNA sequence: sequence: 5'-ACACCTCGGC-3' Generated one random RNA sequence: sequence: 5'-TAGAGGCGTC-3' Generated one random RNA sequence: sequence: 5'-TATTGTTGTA-3' Generated one random RNA sequence: sequence: 5'-GGTAGCAGGA-3' Generated one random RNA sequence: sequence: 5'-ACGTTGGGAA-3' Generated one random DNA sequence: sequence: 5'-AUCCCGGAGA-3' Generated one random DNA sequence: sequence: 5'-CCUACUAUGG-3' Generated one random DNA sequence: sequence: 5'-GCCACAGUUA-3' Generated one random DNA sequence: sequence: 5'-AAUAUGAUUG-3' Generated one random DNA sequence: sequence: 5'-CAAUCCCCCG-3' Generated one random DNA sequence: sequence: 5'-GGUGGUGCGG-3' Generated one random DNA sequence: sequence: 5'-CGUCCUAUCA-3' Generated one random DNA sequence: sequence: 5'-AUACUAUACG-3' Generated one random amino acid peptide chain sequence: sequence: 5'-RIHQMVHSSE-3' Generated one random amino acid peptide chain sequence: sequence: 5'-KHHHTNAEPF-3' Generated one random amino acid peptide chain sequence: sequence: 5'-WPGAYDGTVA-3' Generated one random amino acid peptide chain sequence: sequence: 5'-NPKWSGLCAP-3' Generated one random amino acid peptide chain sequence: sequence: 5'-WTSITLLGPK-3' Generated one random amino acid peptide chain sequence: sequence: 5'-FNVMLVKFAT-3' Generated 10 random DNA sequences: sequences (5'-3"): TTACGGCATA ATAGCCTCCT GCTGTCGACG ACACCTCGGC TAGAGGCGTC TATTGTTGTA GGTAGCAGGA ACGTTGGGAA ATCCCGGAGA CCTACTATGG Generated 10 random DNAs sequences: sequences (5'-3"): GCCACAGTTA AATATGATTG CAATCCCCCG GGTGGTGCGG CGTCCTATCA ATACTATACG ATTTCGTGGT CTTTGAATCC GCTAGATGGA ACCGGTCAAC Generated 10 random DNA nucleotides sequences: sequences (5'-3"): GGGTGCCTCC CAGCCGCCAG GAGCGCTTCC CGCCCATTGG TTACGCCTCC ATAGTTCTCA TCGTCGATAC CGGCGGTCTG ATCGCGCCAG CTCTAACTAT Generated 10 random DNA chain sequences: sequences (5'-3"): TGCGTAGCTT TTGTCGTCAT GCGTGGCCCC GGGATCTAAT TGAGCTCTTA GCAGCTATTC CACCTGACAC CATTGTTTTC GACTTGCAGT CTGTTGGTCA Generated 10 random dna sequences: sequences (5'-3"): AGACGATAAA AATGGGTGTG TCCACCTTAC TATTCTAACG AGTGCTGATG CCCCGGGGAT GCTCGACTAG GGTTGTGAGG CCAGCGCGGC TAGCCCGAGA Generated 10 random dnas sequences: sequences (5'-3"): CTAGCGTCTA AAGAAGGGCA ACTAAAGTGT TACTAGTTGT TCAGCCTATA ACCTCCTGGT TCCGATGGCG ATTCGGGATT TCATTTTCTG TAGTAATACC Generated 10 random dna nucleotides sequences: sequences (5'-3"): CTAGCCAATC GACGTGAGCA GATAGCATCG CTGTTCAACA AGGCAAGCCA TAGGCGACTA CTGCCGGAAC TACCTTTTGG CGGATGGTCC GATCTGAATC Generated 10 random dna chain sequences: sequences (5'-3"): AAGGGCTTAT CGTTGCGACC CCCCTAGCGG ATCACTGCTT AGCATCTTAT ATTGCCGGGT GGCAGAATAA TTTACGTATC TATGGCTGTA ACGAATAACT Generated 10 random RNA sequences: sequences (5'-3"): UUACGGCAUA AUAGCCUCCU GCUGUCGACG ACACCUCGGC UAGAGGCGUC UAUUGUUGUA GGUAGCAGGA ACGUUGGGAA AUCCCGGAGA CCUACUAUGG Generated 10 random RNAs sequences: sequences (5'-3"): GCCACAGUUA AAUAUGAUUG CAAUCCCCCG GGUGGUGCGG CGUCCUAUCA AUACUAUACG AUUUCGUGGU CUUUGAAUCC GCUAGAUGGA ACCGGUCAAC Generated 10 random RNA nucleotides sequences: sequences (5'-3"): GGGUGCCUCC CAGCCGCCAG GAGCGCUUCC CGCCCAUUGG UUACGCCUCC AUAGUUCUCA UCGUCGAUAC CGGCGGUCUG AUCGCGCCAG CUCUAACUAU Generated 10 random RNA chain sequences: sequences (5'-3"): UGCGUAGCUU UUGUCGUCAU GCGUGGCCCC GGGAUCUAAU UGAGCUCUUA GCAGCUAUUC CACCUGACAC CAUUGUUUUC GACUUGCAGU CUGUUGGUCA Generated 10 random rna sequences: sequences (5'-3"): AGACGAUAAA AAUGGGUGUG UCCACCUUAC UAUUCUAACG AGUGCUGAUG CCCCGGGGAU GCUCGACUAG GGUUGUGAGG CCAGCGCGGC UAGCCCGAGA Generated 10 random rnas sequences: sequences (5'-3"): CUAGCGUCUA AAGAAGGGCA ACUAAAGUGU UACUAGUUGU UCAGCCUAUA ACCUCCUGGU UCCGAUGGCG AUUCGGGAUU UCAUUUUCUG UAGUAAUACC Generated 10 random rna nucleotides sequences: sequences (5'-3"): CUAGCCAAUC GACGUGAGCA GAUAGCAUCG CUGUUCAACA AGGCAAGCCA UAGGCGACUA CUGCCGGAAC UACCUUUUGG CGGAUGGUCC GAUCUGAAUC Generated 10 random rna chain sequences: sequences (5'-3"): AAGGGCUUAU CGUUGCGACC CCCCUAGCGG AUCACUGCUU AGCAUCUUAU AUUGCCGGGU GGCAGAAUAA UUUACGUAUC UAUGGCUGUA ACGAAUAACU Generated 10 random AminoAcid sequences: sequences (5'-3"): QICLYSLNGN NIRSMPGFPH SLHYEMWCFW NMAPPHMWSP INWRVYFSHM QDHHWIITEC WTGAYPASSC RKYHETSSND AHFLKTTAVC LKICFICQVS Generated 10 random aminoacid sequences: sequences (5'-3"): WPFNLDSGER RAICGYAEET PRAGLLPPKT VVGWWQSMTW LWGMFGDHFA RGAMHAIRLV RIHQMVHSSE KHHHTNAEPF WPGAYDGTVA NPKWSGLCAP Generated 10 random amino acid sequences: sequences (5'-3"): WTSITLLGPK FNVMLVKFAT SCWFWFEHKM PSPKPCHGTV QECLSLMQMK NICSIQFQFR QMWGKTRHCP MVWLVTQLQW RIPSKWLLCT PHMGANFEDQ Generated 10 random peptide sequences: sequences (5'-3"): IWPVENSKEI HIWQMYQFDE SPWQYVKLPP VWYDGFINNG EWDYMEPQIC YKNSMIRHGK KRMPGSCKAL FNIQWHIEEL VDFHETLNSI MHTHEYTEPD Generated 10 random aa sequences: sequences (5'-3"): CVAKWAGCCC NAEWVSGYEV IMKDMLQHCK EDEQFQAALS CWHVLEVCHW KLLFWVWSDG SMQFVCPQCV TYQIVIWRWT FLDVMVFTTM GDSPLPYNSA Generated 10 random AA sequences: sequences (5'-3"): FHNSLYEKID ACYNNSYSKD NMEAANWHVH HNLHDSHHWG QMNWKKIDIN APMHLFQWSE QFPWNHTYMT CHHKTVTRHE HMCQQGIMGS IAVERDERMK Test Summary: | Pass Total Time SimpleBio | 161 161 2.4s identify | 6 6 0.7s nucleotidetools | 5 5 0.0s RandSeq-DNA | 22 22 0.0s RandSeq-DNA-1 | 8 8 0.0s 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 0.0s 10 rand dna | 8 8 0.0s 10 rand rna | 8 8 0.0s 10 rand aa | 6 6 0.0s 10 rand seqs arr out | 22 22 0.0s 10 rand dna | 8 8 0.0s 10 rand rna | 8 8 0.0s 10 rand aa | 6 6 0.0s 10 rand dna-rna dataframe | 1 1 0.1s alignment | 6 6 0.0s translation to aa | 5 5 0.3s primer design tools | 50 50 0.2s dnatm | 3 3 0.1s step_gen | 5 5 0.0s step_from_end | 4 4 0.0s multidnatm | 2 2 0.1s fwd primers | 18 18 0.0s rev primers | 18 18 0.0s Testing SimpleBio tests passed Testing completed after 27.71s PkgEval succeeded after 65.45s