Package evaluation to test HMMER on Julia 1.11.7 (58327cce5e*) started at 2025-10-28T16:19:23.479


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# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.75s


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# 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 v1.5.0
⌅ [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 To see why use `status --outdated -m`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 1.55s


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# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 52.0s


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# Testing
#

     Testing HMMER
      Status `/tmp/jl_LAklpd/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_LAklpd/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 v0.19.1
  [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 v1.5.0
  [08abe8d2] PrettyTables v3.1.0
  [92933f4c] ProgressMeter v1.11.0
  [189a3867] Reexport v1.2.2
  [fdea26ae] SIMD v3.7.2
  [91c51154] SentinelArrays v1.4.8
  [a2af1166] SortingAlgorithms v1.2.2
  [10745b16] Statistics v1.11.1
  [892a3eda] StringManipulation v0.4.1
  [354b36f9] StringViews v1.3.5
  [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_NeQnR1 set.
[ Info: Pfam version 35.0 set.
[ Info: Downloading pdbmap to /tmp/jl_NeQnR1/35.0/Pfam-A.hmm ...

Downloaded (bytes): 0    Time: 0:00:08
Downloaded (bytes): 15746    Time: 0:00:09
Downloaded (bytes): 223746    Time: 0:00:09
Downloaded (bytes): 639746    Time: 0:00:09
Downloaded (bytes): 1935746    Time: 0:00:10
Downloaded (bytes): 4063746    Time: 0:00:10
Downloaded (bytes): 9031746    Time: 0:00:10
Downloaded (bytes): 13847746    Time: 0:00:10
Downloaded (bytes): 19711746    Time: 0:00:10
Downloaded (bytes): 23863746    Time: 0:00:10
Downloaded (bytes): 28647746    Time: 0:00:10
Downloaded (bytes): 32735746    Time: 0:00:11
Downloaded (bytes): 37303746    Time: 0:00:11
Downloaded (bytes): 42663746    Time: 0:00:11
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Downloaded (bytes): 52831746    Time: 0:00:11
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Downloaded (bytes): 68735746    Time: 0:00:12
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Downloaded (bytes): 113471746    Time: 0:00:13
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Downloaded (bytes): 130551746    Time: 0:00:13
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Downloaded (bytes): 149031746    Time: 0:00:14
Downloaded (bytes): 154407746    Time: 0:00:14
Downloaded (bytes): 159055746    Time: 0:00:14
Downloaded (bytes): 165519746    Time: 0:00:14
Downloaded (bytes): 171503746    Time: 0:00:14
Downloaded (bytes): 177927746    Time: 0:00:14
Downloaded (bytes): 184383746    Time: 0:00:14
Downloaded (bytes): 189607746    Time: 0:00:14
Downloaded (bytes): 195727746    Time: 0:00:15
Downloaded (bytes): 200295746    Time: 0:00:15
Downloaded (bytes): 205711746    Time: 0:00:15
Downloaded (bytes): 210791746    Time: 0:00:15
Downloaded (bytes): 215807746    Time: 0:00:15
Downloaded (bytes): 220799746    Time: 0:00:15
Downloaded (bytes): 225663746    Time: 0:00:15
Downloaded (bytes): 232255746    Time: 0:00:15
Downloaded (bytes): 238695746    Time: 0:00:16
Downloaded (bytes): 244847746    Time: 0:00:16
Downloaded (bytes): 251343746    Time: 0:00:16
Downloaded (bytes): 255751746    Time: 0:00:16
Downloaded (bytes): 262343746    Time: 0:00:16
Downloaded (bytes): 267023746    Time: 0:00:16
Downloaded (bytes): 273511746    Time: 0:00:16
Downloaded (bytes): 278191746    Time: 0:00:16
Downloaded (bytes): 284655746    Time: 0:00:17
Downloaded (bytes): 289119746    Time: 0:00:17Precompiling HMMER...
   1348.6 ms  ✓ GSL_jll
   1650.2 ms  ✓ HMMER_jll
   3633.4 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  31.3s
Precompiling FASTX...
   1151.5 ms  ✓ BioGenerics
  13402.0 ms  ✓ SIMD
  21077.5 ms  ✓ Automa
  23112.3 ms  ✓ FASTX
  4 dependencies successfully precompiled in 59 seconds. 8 already precompiled.
Precompiling DataFrames...
   3601.1 ms  ✓ StringManipulation
  48561.0 ms  ✓ PrettyTables
  91136.1 ms  ✓ DataFrames
  3 dependencies successfully precompiled in 144 seconds. 32 already precompiled.
Test Summary: | Pass  Total   Time
hmmfetch      |    1      1  41.7s
Test Summary: | Pass  Total     Time
hmmalign      |    1      1  1m27.2s
[ Info: Downloading to /tmp/jl_NeQnR1/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: 0:00:01
Downloaded (bytes): 28464    Time: 0:00:01
Downloaded (bytes): 74800    Time: 0:00:01
Downloaded (bytes): 173170    Time: 0:00:01
Downloaded (bytes): 402700    Time: 0:00:01
Downloaded (bytes): 812453    Time: 0:00:01
Downloaded (bytes): 2452075    Time: 0:00:02
Downloaded (bytes): 5124460    Time: 0:00:02
Downloaded (bytes): 8649385    Time: 0:00:02
Downloaded (bytes): 11484388    Time: 0:00:02Test Summary: | Pass  Total  Time
esl_reformat  |    1      1  6.5s
     Testing HMMER tests passed 

Testing completed after 425.74s

PkgEval succeeded after 500.48s