Package evaluation of HMMER on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T08:24:18.858 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.91s ################################################################################ # Installation # Installing HMMER... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [59c5aa83] + HMMER v1.5.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [59c5aa83] + HMMER v1.5.0 [692b3bcd] + JLLWrappers v1.7.0 [21216c6a] + Preferences v1.4.3 [1b77fbbe] + GSL_jll v2.8.0+0 [9a00dd6d] + HMMER_jll v3.4.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [83775a58] + Zlib_jll v1.2.13+1 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Installation completed after 1.73s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 48.57s ################################################################################ # Testing # Testing HMMER Status `/tmp/jl_Vydz8D/Project.toml` ⌅ [4c88cf16] Aqua v0.7.4 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [c2308a5c] FASTX v2.1.7 [59c5aa83] HMMER v1.5.0 [275cd14a] Pfam v2.0.1 [8dfed614] Test v1.11.0 Status `/tmp/jl_Vydz8D/Manifest.toml` ⌅ [4c88cf16] Aqua v0.7.4 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [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 v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [59c5aa83] HMMER v1.5.0 [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 [275cd14a] Pfam v2.0.1 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [189a3867] Reexport v1.2.2 [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 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [1b77fbbe] GSL_jll v2.8.0+0 [be1be57a] Gzip_jll v1.13.0+0 [9a00dd6d] HMMER_jll v3.4.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets 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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [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... [ Info: PFAM directory /tmp/jl_RPWMTL set. [ Info: Pfam version 35.0 set. [ Info: Downloading pdbmap to /tmp/jl_RPWMTL/35.0/Pfam-A.hmm ... Downloaded (bytes): 0 Time: 0:00:08 Downloaded (bytes): 191746 Time: 0:00:09 Downloaded (bytes): 575746 Time: 0:00:09 Downloaded (bytes): 1815746 Time: 0:00:09 Downloaded (bytes): 5943746 Time: 0:00:09 Downloaded (bytes): 7055746 Time: 0:00:09 Downloaded (bytes): 13079746 Time: 0:00:09 Downloaded (bytes): 18439746 Time: 0:00:09 Downloaded (bytes): 24015746 Time: 0:00:10 Downloaded (bytes): 28519746 Time: 0:00:10 Downloaded (bytes): 34535746 Time: 0:00:10 Downloaded (bytes): 40647746 Time: 0:00:10 Downloaded (bytes): 46599746 Time: 0:00:10 Downloaded (bytes): 50895746 Time: 0:00:10 Downloaded (bytes): 56663746 Time: 0:00:10 Downloaded (bytes): 62719746 Time: 0:00:11 Downloaded (bytes): 68719746 Time: 0:00:11 Downloaded (bytes): 72615746 Time: 0:00:11 Downloaded (bytes): 78631746 Time: 0:00:11 Downloaded (bytes): 84559746 Time: 0:00:11 Downloaded (bytes): 88215746 Time: 0:00:11 Downloaded (bytes): 93559746 Time: 0:00:11 Downloaded (bytes): 99319746 Time: 0:00:12 Downloaded (bytes): 105327746 Time: 0:00:12 Downloaded (bytes): 110567746 Time: 0:00:12 Downloaded (bytes): 116447746 Time: 0:00:12 Downloaded (bytes): 122111746 Time: 0:00:12 Downloaded (bytes): 128295746 Time: 0:00:12 Downloaded (bytes): 133399746 Time: 0:00:12 Downloaded (bytes): 139639746 Time: 0:00:13 Downloaded (bytes): 144807746 Time: 0:00:13 Downloaded (bytes): 150895746 Time: 0:00:13 Downloaded (bytes): 156695746 Time: 0:00:13 Downloaded (bytes): 163095746 Time: 0:00:13 Downloaded (bytes): 168999746 Time: 0:00:13 Downloaded (bytes): 173887746 Time: 0:00:13 Downloaded (bytes): 180095746 Time: 0:00:14 Downloaded (bytes): 186343746 Time: 0:00:14 Downloaded (bytes): 192503746 Time: 0:00:14 Downloaded (bytes): 198831746 Time: 0:00:14 Downloaded (bytes): 202823746 Time: 0:00:14 Downloaded (bytes): 209415746 Time: 0:00:14 Downloaded (bytes): 215975746 Time: 0:00:14 Downloaded (bytes): 221831746 Time: 0:00:15 Downloaded (bytes): 226687746 Time: 0:00:15 Downloaded (bytes): 232711746 Time: 0:00:15 Downloaded (bytes): 237175746 Time: 0:00:15 Downloaded (bytes): 243895746 Time: 0:00:15 Downloaded (bytes): 248575746 Time: 0:00:15 Downloaded (bytes): 255263746 Time: 0:00:15 Downloaded (bytes): 261847746 Time: 0:00:15 Downloaded (bytes): 268167746 Time: 0:00:16 Downloaded (bytes): 273903746 Time: 0:00:16 Downloaded (bytes): 280335746 Time: 0:00:16 Downloaded (bytes): 286847746 Time: 0:00:16Precompiling HMMER... 1854.7 ms ✓ HMMER_jll 3548.7 ms ✓ HMMER 2 dependencies successfully precompiled in 6 seconds. 27 already precompiled. Skipping Base.active_repl Skipping Base.active_repl_backend Skipping Base.cwstring Test Summary: | Pass Total Time aqua | 9 9 31.8s Precompiling FASTX... 1161.9 ms ✓ BioGenerics 21869.4 ms ✓ Automa 23706.9 ms ✓ FASTX 3 dependencies successfully precompiled in 47 seconds. 9 already precompiled. hmmfetch: Test Failed at /home/pkgeval/.julia/packages/HMMER/RvnjP/test/hmmer_programs.jl:11 Expression: isfile((hmmfetch(pfam_hmm, "PF00397.29")).o) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [inlined] [2] macro expansion @ ~/.julia/packages/HMMER/RvnjP/test/hmmer_programs.jl:11 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [4] top-level scope @ ~/.julia/packages/HMMER/RvnjP/test/hmmer_programs.jl:10 Test Summary: | Fail Total Time hmmfetch | 1 1 6.2s ERROR: LoadError: Some tests did not pass: 0 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/HMMER/RvnjP/test/hmmer_programs.jl:9 in expression starting at /home/pkgeval/.julia/packages/HMMER/RvnjP/test/runtests.jl:10 Testing failed after 143.11s ERROR: LoadError: Package HMMER errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 215.56s: package has test failures