Package evaluation of HMMER on Julia 1.13.0-DEV.868 (f2a8e18a98*) started at 2025-07-15T12:24:48.239


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.98s


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

Installing HMMER...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [59c5aa83] + HMMER v1.5.1
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [59c5aa83] + HMMER v1.5.1
  [692b3bcd] + JLLWrappers v1.7.0
  [21216c6a] + Preferences v1.4.3
⌅ [1b77fbbe] + GSL_jll v2.7.2+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 v1.7.0
  [7b1f6079] + FileWatching v1.11.0
  [ac6e5ff7] + 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 v1.3.0
  [44cfe95a] + Pkg v1.13.0
  [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 v8.14.1+1
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [efcefdf7] + PCRE2_jll v10.45.0+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850ede] + nghttp2_jll v1.65.0+0
  [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 To see why use `status --outdated -m`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 1.77s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 55.66s


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

     Testing HMMER
      Status `/tmp/jl_o2s9Mz/Project.toml`
⌅ [4c88cf16] Aqua v0.7.4
  [336ed68f] CSV v0.10.15
  [a93c6f00] DataFrames v1.7.0
  [c2308a5c] FASTX v2.1.7
  [59c5aa83] HMMER v1.5.1
  [275cd14a] Pfam v2.2.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_o2s9Mz/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 v4.17.0
  [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 v1.5.1
  [842dd82b] InlineStrings v1.4.4
  [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 v1.8.1
  [69de0a69] Parsers v2.8.3
  [275cd14a] Pfam v2.2.0
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.3.2
  [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 v1.12.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
⌅ [1b77fbbe] GSL_jll v2.7.2+0
  [be1be57a] Gzip_jll v1.14.0+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 v1.7.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] 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 v1.12.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.13.0
  [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 v1.3.0+1
  [deac9b47] LibCURL_jll v8.14.1+1
  [e37daf67] LibGit2_jll v1.9.1+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.5.20
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.5.1+0
  [efcefdf7] PCRE2_jll v10.45.0+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.13.1+0
  [8e850ede] nghttp2_jll v1.65.0+0
  [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: PFAM directory /tmp/jl_ayHwzB set.
[ Info: Pfam version 35.0 set.
[ Info: Downloading pdbmap to /tmp/jl_ayHwzB/35.0/Pfam-A.hmm ...

Downloaded (bytes): 0    Time: 0:00:03Error During Test at /home/pkgeval/.julia/packages/HMMER/3OXmS/test/runtests.jl:8
  Test threw exception
  Expression: isfile(Pfam.Pfam_A_hmm())
  RequestError: Failed to connect to ftp.ebi.ac.uk port 443 after 243 ms: Could not connect to server while requesting https://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam35.0/Pfam-A.hmm.gz
  Stacktrace:
    [1] (::Downloads.var"#26#27"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Downloads.var"#p_func##0#p_func##1"{Pfam.var"#42#43"{ProgressMeter.ProgressUnknown}}, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy)
      @ Downloads /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:479
    [2] with_handle(f::Downloads.var"#26#27"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Downloads.var"#p_func##0#p_func##1"{Pfam.var"#42#43"{ProgressMeter.ProgressUnknown}}, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy)
      @ Downloads.Curl /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Curl/Curl.jl:105
    [3] #24
      @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:390 [inlined]
    [4] arg_write(f::Downloads.var"#24#25"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Downloads.var"#p_func##0#p_func##1"{Pfam.var"#42#43"{ProgressMeter.ProgressUnknown}}, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream)
      @ ArgTools /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:134
    [5] #22
      @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:389 [inlined]
    [6] arg_read
      @ /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:76 [inlined]
    [7] #request#9
      @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:388 [inlined]
    [8] request
      @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:355 [inlined]
    [9] (::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Pfam.var"#42#43"{ProgressMeter.ProgressUnknown}, Bool, Nothing, Nothing, String})(output::IOStream)
      @ Downloads /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:273
   [10] open(f::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Pfam.var"#42#43"{ProgressMeter.ProgressUnknown}, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool})
      @ Base ./io.jl:420
   [11] open_nolock
      @ /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:35 [inlined]
   [12] arg_write(f::Function, arg::String)
      @ ArgTools /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:103
   [13] #download#5
      @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:272 [inlined]
   [14] download
      @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:252 [inlined]
   [15] #download_progress#40
      @ ~/.julia/packages/Pfam/RIF25/src/Pfam.jl:146 [inlined]
   [16] download_progress
      @ ~/.julia/packages/Pfam/RIF25/src/Pfam.jl:144 [inlined]
   [17] (::Pfam.var"#14#15"{String, String})()
      @ Pfam ~/.julia/packages/Pfam/RIF25/src/Pfam.jl:56
   [18] lock(f::Pfam.var"#14#15"{String, String}, l::ReentrantLock)
      @ Base ./lock.jl:335
   [19] Pfam_A_hmm(; pfam_dir::String, pfam_version::String)
      @ Pfam ~/.julia/packages/Pfam/RIF25/src/Pfam.jl:53
   [20] Pfam_A_hmm()
      @ Pfam ~/.julia/packages/Pfam/RIF25/src/Pfam.jl:51
   [21] top-level scope
      @ ~/.julia/packages/HMMER/3OXmS/test/runtests.jl:529
   [22] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:738 [inlined]
ERROR: LoadError: There was an error during testing
in expression starting at /home/pkgeval/.julia/packages/HMMER/3OXmS/test/runtests.jl:8

Testing failed after 21.09s

ERROR: LoadError: Package HMMER errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68
  [2] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.13/Pkg/src/Operations.jl:2661
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2510 [inlined]
  [4] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.13/Pkg/src/API.jl:537
  [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:168
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:320
 [12] _start()
    @ Base ./client.jl:553
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 105.04s: package tests unexpectedly errored