Package evaluation of HMMER on Julia 1.12.0-DEV.1805 (a080deafdd*) started at 2025-03-24T12:14:25.954


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.91s


################################################################################
# Installation
#

Installing HMMER...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [59c5aa83] + HMMER v1.5.0
    Updating `~/.julia/environments/v1.12/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
  [dc6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [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 v1.12.0
  [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
  [deac9b47] + LibCURL_jll v8.6.0+0
  [e37daf67] + LibGit2_jll v1.8.0+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+1
  [14a3606d] + MozillaCACerts_jll v2024.11.26
  [83775a58] + Zlib_jll v1.3.1+1
  [8e850ede] + nghttp2_jll v1.63.0+1
  [3f19e933] + p7zip_jll v17.5.0+1

Installation completed after 1.42s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 52.39s


################################################################################
# Testing
#

     Testing HMMER
      Status `/tmp/jl_1HhBtr/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_1HhBtr/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 v1.10.2
  [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
  [dc6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [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 v1.12.0
  [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
  [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 v1.2.0+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.8.0+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+1
  [14a3606d] MozillaCACerts_jll v2024.11.26
  [4536629a] OpenBLAS_jll v0.3.28+3
  [83775a58] Zlib_jll v1.3.1+1
  [8e850b90] libblastrampoline_jll v5.11.2+0
  [8e850ede] nghttp2_jll v1.63.0+1
  [3f19e933] p7zip_jll v17.5.0+1
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
[ Info: PFAM directory /tmp/jl_A3f3TZ set.
[ Info: Pfam version 35.0 set.
[ Info: Downloading pdbmap to /tmp/jl_A3f3TZ/35.0/Pfam-A.hmm ...

Downloaded (bytes): 0    Time: 0:00:03
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Downloaded (bytes): 282543746    Time: 0:00:12
Downloaded (bytes): 289007746    Time: 0:00:12Skipping Base.active_repl
Test Summary: | Pass  Total   Time
aqua          |    9      9  32.5s
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] top-level scope
   @ ~/.julia/packages/HMMER/RvnjP/test/hmmer_programs.jl:10
 [2] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined]
 [3] macro expansion
   @ ~/.julia/packages/HMMER/RvnjP/test/hmmer_programs.jl:11 [inlined]
 [4] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:679 [inlined]
Test Summary: | Fail  Total  Time
hmmfetch      |    1      1  8.3s
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 271.22s

ERROR: LoadError: Package HMMER errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2359
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2214 [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/v1.12/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/v1.12/Pkg/src/API.jl:159
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:146 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:300
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:329
 [12] _start()
    @ Base ./client.jl:558
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 352.56s: package has test failures