Package evaluation of Infernal on Julia 1.13.0-DEV.111 (ce76dbf07d*) started at 2025-02-28T00:07:52.151 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.78s ################################################################################ # Installation # Installing Infernal... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [4aa08641] + Infernal v1.4.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [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 [48062228] + FilePathsBase v0.9.23 [4aa08641] + Infernal v1.4.0 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [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 [91c51154] + SentinelArrays v1.4.8 [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 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [1b77fbbe] + GSL_jll v2.7.2+0 [5109d7c4] + Infernal_jll v1.1.5+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 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.11.1+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 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [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 1.37s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 31.1s ################################################################################ # Testing # Testing Infernal Status `/tmp/jl_RboEn6/Project.toml` [4c88cf16] Aqua v0.8.11 [7e6ae17a] BioSequences v3.4.1 [c2308a5c] FASTX v2.1.7 [4aa08641] Infernal v1.4.0 [38c5b72b] Rfam v3.2.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_RboEn6/Manifest.toml` [4c88cf16] Aqua v0.8.11 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [3c28c6f8] BioSymbols v5.1.3 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [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 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.23 [4aa08641] Infernal v1.4.0 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [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 [38c5b72b] Rfam v3.2.0 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [10745b16] Statistics v1.11.1 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 ⌅ [1b77fbbe] GSL_jll v2.7.2+0 [be1be57a] Gzip_jll v1.13.0+0 [5109d7c4] Infernal_jll v1.1.5+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 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization 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 v8.11.1+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 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: RFAM Directory /tmp set. [ Info: Rfam version 14.8 set. Test Summary: | Pass Total Time aqua | 10 10 1m20.4s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.4s Stale dependencies | 1 1 12.0s Compat bounds | 4 4 0.8s Piracy | 1 1 0.4s Persistent tasks | 1 1 36.3s [ Info: Downloading Rfam.seed to /tmp/14.8/Rfam.seed ... Test Summary: | Pass Total Time esl_afetch | 3 3 6.5s Test Summary: | Pass Total Time esl_reformat | 3 3 0.1s [ Info: Downloading Rfam.cm to /tmp/14.8/Rfam.cm ... Test Summary: | Pass Total Time cmfetch | 3 3 4.2s [ Info: Downloading RF00162 to /tmp/14.8/fasta_files/RF00162.fa ... Test Summary: | Pass Total Time cmalign | 5 5 5m24.9s Test Summary: | Pass Total Time cmbuild | 6 6 1.1s Precompiling packages... 29191.2 ms ✓ FASTX 1 dependency successfully precompiled in 30 seconds. 11 already precompiled. Precompiling packages... 4312.4 ms ✓ FASTX → BioSequencesExt 1 dependency successfully precompiled in 4 seconds. 15 already precompiled. Test Summary: | Pass Total Time cmemit | 6 6 7.0s Test Summary: | Pass Total Time cmsearch | 3 3 37.4s Testing Infernal tests passed Testing completed after 526.58s PkgEval succeeded after 588.61s