Package evaluation to test HMMER on Julia 1.11.8 (29b3528cce*) started at 2026-01-20T01:55:44.792


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

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.11`

Set-up completed after 8.82s


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

Installing HMMER...
   Resolving package versions...
    Updating `~/.julia/environments/v1.11/Project.toml`
  [59c5aa83] + HMMER v1.5.1
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [59c5aa83] + HMMER v1.5.1
  [692b3bcd] + JLLWrappers v1.7.1
  [21216c6a] + Preferences v1.5.1
⌅ [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 v1.6.0
  [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
        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 To see why use `status --outdated -m`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 1.54s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...
Precompiling project...
   1635.3 ms  ✓ GSL_jll
   1720.5 ms  ✓ Pfam
  24961.3 ms  ✓ FASTX
   1709.7 ms  ✓ HMMER_jll
   3777.9 ms  ✓ HMMER
  5 dependencies successfully precompiled in 35 seconds. 76 already precompiled.

Precompilation completed after 52.68s


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

     Testing HMMER
      Status `/tmp/jl_Wf0lZi/Project.toml`
⌅ [4c88cf16] Aqua v0.7.4
  [336ed68f] CSV v0.10.15
  [a93c6f00] DataFrames v1.8.1
  [c2308a5c] FASTX v2.1.7
  [59c5aa83] HMMER v1.5.1
  [275cd14a] Pfam v2.2.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_Wf0lZi/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 v4.18.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.8.1
  [864edb3b] DataStructures v0.19.3
  [e2d170a0] DataValueInterfaces v1.0.0
  [c2308a5c] FASTX v2.1.7
  [48062228] FilePathsBase v0.9.24
  [59c5aa83] HMMER v1.5.1
  [842dd82b] InlineStrings v1.4.5
  [41ab1584] InvertedIndices v1.3.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
  [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 v1.2.1
  [21216c6a] Preferences v1.5.1
  [08abe8d2] PrettyTables v3.1.2
  [92933f4c] ProgressMeter v1.11.0
  [189a3867] Reexport v1.2.2
  [fdea26ae] SIMD v3.7.2
  [91c51154] SentinelArrays v1.4.9
  [a2af1166] SortingAlgorithms v1.2.2
  [10745b16] Statistics v1.11.1
  [892a3eda] StringManipulation v0.4.2
  [354b36f9] StringViews v1.3.6
  [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 v1.6.0
  [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
  [3fa0cd96] REPL 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 v1.1.1+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_bH02sJ set.
[ Info: Pfam version 35.0 set.
[ Info: Downloading pdbmap to /tmp/jl_bH02sJ/35.0/Pfam-A.hmm ...

Downloaded (bytes): 0    Time: 0:00:08
Downloaded (bytes): 103746    Time: 0:00:09
Downloaded (bytes): 375746    Time: 0:00:09
Downloaded (bytes): 1031746    Time: 0:00:09
Downloaded (bytes): 3623746    Time: 0:00:09
Downloaded (bytes): 7087746    Time: 0:00:09
Downloaded (bytes): 12943746    Time: 0:00:10
Downloaded (bytes): 16359746    Time: 0:00:10
Downloaded (bytes): 21815746    Time: 0:00:10
Downloaded (bytes): 26383746    Time: 0:00:10
Downloaded (bytes): 28495746    Time: 0:00:10
Downloaded (bytes): 34015746    Time: 0:00:10
Downloaded (bytes): 39047746    Time: 0:00:10
Downloaded (bytes): 44415746    Time: 0:00:11
Downloaded (bytes): 49679746    Time: 0:00:11
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Downloaded (bytes): 79479746    Time: 0:00:12
Downloaded (bytes): 84807746    Time: 0:00:12
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Downloaded (bytes): 109127746    Time: 0:00:12
Downloaded (bytes): 114671746    Time: 0:00:12
Downloaded (bytes): 118943746    Time: 0:00:13
Downloaded (bytes): 124319746    Time: 0:00:13
Downloaded (bytes): 129407746    Time: 0:00:13
Downloaded (bytes): 134911746    Time: 0:00:13
Downloaded (bytes): 138935746    Time: 0:00:13
Downloaded (bytes): 144375746    Time: 0:00:13
Downloaded (bytes): 149095746    Time: 0:00:13
Downloaded (bytes): 154311746    Time: 0:00:14
Downloaded (bytes): 155631746    Time: 0:00:14
Downloaded (bytes): 161463746    Time: 0:00:14
Downloaded (bytes): 167063746    Time: 0:00:14
Downloaded (bytes): 170775746    Time: 0:00:14
Downloaded (bytes): 174511746    Time: 0:00:14
Downloaded (bytes): 179807746    Time: 0:00:14
Downloaded (bytes): 184839746    Time: 0:00:15
Downloaded (bytes): 190879746    Time: 0:00:15
Downloaded (bytes): 196575746    Time: 0:00:15
Downloaded (bytes): 200919746    Time: 0:00:15
Downloaded (bytes): 206103746    Time: 0:00:15
Downloaded (bytes): 211183746    Time: 0:00:15
Downloaded (bytes): 216975746    Time: 0:00:15
Downloaded (bytes): 222719746    Time: 0:00:16
Downloaded (bytes): 227039746    Time: 0:00:16
Downloaded (bytes): 232511746    Time: 0:00:16
Downloaded (bytes): 237191746    Time: 0:00:16
Downloaded (bytes): 242479746    Time: 0:00:16
Downloaded (bytes): 248135746    Time: 0:00:16
Downloaded (bytes): 253255746    Time: 0:00:17
Downloaded (bytes): 258535746    Time: 0:00:17
Downloaded (bytes): 262951746    Time: 0:00:17
Downloaded (bytes): 269207746    Time: 0:00:17
Downloaded (bytes): 274599746    Time: 0:00:17
Downloaded (bytes): 278791746    Time: 0:00:17
Downloaded (bytes): 284247746    Time: 0:00:17
Downloaded (bytes): 288335746    Time: 0:00:18Precompiling HMMER...
   1351.4 ms  ✓ GSL_jll
   1703.1 ms  ✓ HMMER_jll
   3527.2 ms  ✓ HMMER
  3 dependencies successfully precompiled in 7 seconds. 26 already precompiled.
Skipping Base.active_repl
Skipping Base.active_repl_backend
Skipping Base.cwstring
Test Summary: | Pass  Total   Time
aqua          |    9      9  31.4s
Precompiling FASTX...
  21109.3 ms  ✓ Automa
  21123.1 ms  ✓ FASTX
  2 dependencies successfully precompiled in 42 seconds. 10 already precompiled.
Test Summary: | Pass  Total   Time
hmmfetch      |    1      1  41.5s
Test Summary: | Pass  Total     Time
hmmalign      |    1      1  1m30.6s
[ Info: Downloading to /tmp/jl_bH02sJ/alignment_files/PF00013.alignment.full.stk ...

Downloaded (bytes): 0    Time: 0:00:00
Downloaded (bytes): 0    Time: 0:00:00
Downloaded (bytes): 0    Time: 0:00:00
Downloaded (bytes): 0    Time: 0:00:00
Downloaded (bytes): 16384    Time: 0:00:01
Downloaded (bytes): 70456    Time: 0:00:01
Downloaded (bytes): 138932    Time: 0:00:01
Downloaded (bytes): 319277    Time: 0:00:01
Downloaded (bytes): 679967    Time: 0:00:01
Downloaded (bytes): 1466927    Time: 0:00:01
Downloaded (bytes): 3139217    Time: 0:00:01
Downloaded (bytes): 5482128    Time: 0:00:01
Downloaded (bytes): 11091059    Time: 0:00:02
Downloaded (bytes): 13779839    Time: 0:00:02Test Summary: | Pass  Total  Time
esl_reformat  |    1      1  6.9s
     Testing HMMER tests passed 

Testing completed after 270.99s

PkgEval succeeded after 346.25s