Package evaluation of SimpleBio on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T18:21:01.440 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.57s ################################################################################ # 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 v5.2.0 [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 v1.4.0 [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 v1.8.1 [69de0a69] + Parsers v2.8.3 [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 v1.12.1 [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 [458c3c95] + OpenSSL_jll v3.5.0+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 8.27s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 20.37s ################################################################################ # Testing # Testing SimpleBio Status `/tmp/jl_yiFf8n/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_yiFf8n/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 v1.4.0 [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 v1.8.1 [69de0a69] Parsers v2.8.3 [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 v1.12.1 [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 [458c3c95] OpenSSL_jll v3.5.0+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'-ATGAAGATTG-3' Generated one random RNA sequence: sequence: 5'-ATGAGCTATA-3' Generated one random RNA sequence: sequence: 5'-CGCACTCCTT-3' Generated one random RNA sequence: sequence: 5'-CGGCAATGGT-3' Generated one random RNA sequence: sequence: 5'-GTCCTCTGGT-3' Generated one random RNA sequence: sequence: 5'-ATCTATCGGA-3' Generated one random RNA sequence: sequence: 5'-GGCGCCCATT-3' Generated one random RNA sequence: sequence: 5'-ATAAATTCTT-3' Generated one random DNA sequence: sequence: 5'-AUGAAGAUUG-3' Generated one random DNA sequence: sequence: 5'-AUGAGCUAUA-3' Generated one random DNA sequence: sequence: 5'-CGCACUCCUU-3' Generated one random DNA sequence: sequence: 5'-CGGCAAUGGU-3' Generated one random DNA sequence: sequence: 5'-GUCCUCUGGU-3' Generated one random DNA sequence: sequence: 5'-AUCUAUCGGA-3' Generated one random DNA sequence: sequence: 5'-GGCGCCCAUU-3' Generated one random DNA sequence: sequence: 5'-AUAAAUUCUU-3' Generated one random amino acid peptide chain sequence: sequence: 5'-RIYNCTDQGT-3' Generated one random amino acid peptide chain sequence: sequence: 5'-NHVAVPECHR-3' Generated one random amino acid peptide chain sequence: sequence: 5'-KVPCMHLFGI-3' Generated one random amino acid peptide chain sequence: sequence: 5'-MVSFNDITWE-3' Generated one random amino acid peptide chain sequence: sequence: 5'-WIFPQMHWVE-3' Generated one random amino acid peptide chain sequence: sequence: 5'-CQLIDQFSWD-3' Generated one random RNA sequence: sequence: 5'-ATGAAGATTG-3' Generated one random RNA sequence: sequence: 5'-ATGAGCTATA-3' Generated one random RNA sequence: sequence: 5'-CGCACTCCTT-3' Generated one random RNA sequence: sequence: 5'-CGGCAATGGT-3' Generated one random RNA sequence: sequence: 5'-GTCCTCTGGT-3' Generated one random RNA sequence: sequence: 5'-ATCTATCGGA-3' Generated one random RNA sequence: sequence: 5'-GGCGCCCATT-3' Generated one random RNA sequence: sequence: 5'-ATAAATTCTT-3' Generated one random DNA sequence: sequence: 5'-CGCUGUUCCG-3' Generated one random DNA sequence: sequence: 5'-UUGGCUGUUC-3' Generated one random DNA sequence: sequence: 5'-CGGGCCAAUG-3' Generated one random DNA sequence: sequence: 5'-UCCCAACCGC-3' Generated one random DNA sequence: sequence: 5'-CAGGAUAGUC-3' Generated one random DNA sequence: sequence: 5'-UGGAGCUGCA-3' Generated one random DNA sequence: sequence: 5'-UCCACACGAC-3' Generated one random DNA sequence: sequence: 5'-UCAGGCUACG-3' Generated one random amino acid peptide chain sequence: sequence: 5'-DATRDAIKIE-3' Generated one random amino acid peptide chain sequence: sequence: 5'-TDIGNVKKLD-3' Generated one random amino acid peptide chain sequence: sequence: 5'-WVERVNVGWK-3' Generated one random amino acid peptide chain sequence: sequence: 5'-WHILPYVADR-3' Generated one random amino acid peptide chain sequence: sequence: 5'-DEYNWMGFQW-3' Generated one random amino acid peptide chain sequence: sequence: 5'-AEWGYKAMFM-3' Generated 10 random DNA sequences: sequences (5'-3"): ATGAAGATTG ATGAGCTATA CGCACTCCTT CGGCAATGGT GTCCTCTGGT ATCTATCGGA GGCGCCCATT ATAAATTCTT CGCTGTTCCG TTGGCTGTTC Generated 10 random DNAs sequences: sequences (5'-3"): CGGGCCAATG TCCCAACCGC CAGGATAGTC TGGAGCTGCA TCCACACGAC TCAGGCTACG AAGAAATCTT GATTAGCCCA GGTAGAGTGC GTTCCGGAAA Generated 10 random DNA nucleotides sequences: sequences (5'-3"): ATGAGCTCTG ATGTGCACCC ACCATGGTAG TTAGTGGTTC GGGCTGCCGT GGGCCACTTC GACCCTATAA ACACTGGCCG CAACAACCGT TAGTGAGCAG Generated 10 random DNA chain sequences: sequences (5'-3"): ATGTCTGACC AAGGCGCATG GAGGGATGGG AATCAATGTG TCTCAAATGT AAAGTTCACT CGGCGTTGGT ACGGGGGTAG CAGATACAAT GGAAGCGGTG Generated 10 random dna sequences: sequences (5'-3"): AGCGACGGAC CGAATCAACT GTTTATATTG ATGGGCGGCG GGGCTAAACA CGGCAGTACG TGATGATATA AACCGAATCG AGCCTTACCA GCTACGCGGG Generated 10 random dnas sequences: sequences (5'-3"): CAATCCACTG GATCCCTGGG GAGTGGTTGC CGCGCTGCGA CAAAATTGGG ATTTACCTGT TGCATTGAAT GTCCAGGCTT CGTCTAAGCC GCATCCATCT Generated 10 random dna nucleotides sequences: sequences (5'-3"): GTTAAGTGCA ATTTGGGGCC CTGGTATACA AATTATGACT GTAATATTTT AAGTACGGTG AGATGCTTAG GTTGCTGCAC AGCGGAGAAT TCCTTGGACA Generated 10 random dna chain sequences: sequences (5'-3"): AACATTGTAA CTATTCGCTC TAGAGAGAAA CTTCGTCAGA TGCCAATTTC TTAGTGGAGT TTATAATGTG CCAACACCTG AAGCCCCACG CAATTTCCAT Generated 10 random RNA sequences: sequences (5'-3"): AUGAAGAUUG AUGAGCUAUA CGCACUCCUU CGGCAAUGGU GUCCUCUGGU AUCUAUCGGA GGCGCCCAUU AUAAAUUCUU CGCUGUUCCG UUGGCUGUUC Generated 10 random RNAs sequences: sequences (5'-3"): CGGGCCAAUG UCCCAACCGC CAGGAUAGUC UGGAGCUGCA UCCACACGAC UCAGGCUACG AAGAAAUCUU GAUUAGCCCA GGUAGAGUGC GUUCCGGAAA Generated 10 random RNA nucleotides sequences: sequences (5'-3"): AUGAGCUCUG AUGUGCACCC ACCAUGGUAG UUAGUGGUUC GGGCUGCCGU GGGCCACUUC GACCCUAUAA ACACUGGCCG CAACAACCGU UAGUGAGCAG Generated 10 random RNA chain sequences: sequences (5'-3"): AUGUCUGACC AAGGCGCAUG GAGGGAUGGG AAUCAAUGUG UCUCAAAUGU AAAGUUCACU CGGCGUUGGU ACGGGGGUAG CAGAUACAAU GGAAGCGGUG Generated 10 random rna sequences: sequences (5'-3"): AGCGACGGAC CGAAUCAACU GUUUAUAUUG AUGGGCGGCG GGGCUAAACA CGGCAGUACG UGAUGAUAUA AACCGAAUCG AGCCUUACCA GCUACGCGGG Generated 10 random rnas sequences: sequences (5'-3"): CAAUCCACUG GAUCCCUGGG GAGUGGUUGC CGCGCUGCGA CAAAAUUGGG AUUUACCUGU UGCAUUGAAU GUCCAGGCUU CGUCUAAGCC GCAUCCAUCU Generated 10 random rna nucleotides sequences: sequences (5'-3"): GUUAAGUGCA AUUUGGGGCC CUGGUAUACA AAUUAUGACU GUAAUAUUUU AAGUACGGUG AGAUGCUUAG GUUGCUGCAC AGCGGAGAAU UCCUUGGACA Generated 10 random rna chain sequences: sequences (5'-3"): AACAUUGUAA CUAUUCGCUC UAGAGAGAAA CUUCGUCAGA UGCCAAUUUC UUAGUGGAGU UUAUAAUGUG CCAACACCUG AAGCCCCACG CAAUUUCCAU Generated 10 random AminoAcid sequences: sequences (5'-3"): RIYNCTDQGT NHVAVPECHR KVPCMHLFGI MVSFNDITWE WIFPQMHWVE CQLIDQFSWD VYMTFFFNHE NGAADQELHE LSLEVHGMPS IHWVLIWHHP Generated 10 random aminoacid sequences: sequences (5'-3"): MVYSLMAAGY QMFFACKMSP LCSWNHNWHK QWWNVLHSKA QMMRFNLWCL IPNWTPQRLY DATRDAIKIE TDIGNVKKLD WVERVNVGWK WHILPYVADR Generated 10 random amino acid sequences: sequences (5'-3"): DEYNWMGFQW AEWGYKAMFM NMMAHSVICV IIRVISTGIL VTVMQYPPWH TVSMFAKEHK SALKKEAQAR AKAPGTWFMY FADFADFPYH IRWHSNWPCW Generated 10 random peptide sequences: sequences (5'-3"): RGYQPIYNMF RAYWFVLCEW YRTTWNEYYS NAELCNISIS GKEMARNEYH RDDWIILNKG PTYKTQQTVE ALVWYSSGNV PCSAICPANI SSANSPVTGW Generated 10 random aa sequences: sequences (5'-3"): CYFWDFSWCP LTDAEMRDMH YGHHAQNQEY DQTTWLVSMY WWVLGACDPR LWVPRTHNLW QSAQSDEAIA ARFFWRAELS AYPMHGCPFR WFQRLYFSST Generated 10 random AA sequences: sequences (5'-3"): LNRQPKRPQS SNGLPLGWWT VAYEYVEQYK KTPWFEVKWR MCRCCGQTWS REQEDKLGWE HYLCIQTNDI VEFMCWWKIQ PTGFGCAWLF TLAQPFNQME Test Summary: | Pass Total Time SimpleBio | 161 161 2.8s identify | 6 6 0.9s 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 30.79s PkgEval succeeded after 87.5s