Package evaluation of GeneNetworkAPI on Julia 1.12.0-DEV.1805 (a080deafdd*) started at 2025-03-24T18:06:53.771


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.84s


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

Installing GeneNetworkAPI...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [5ef98721] + GeneNetworkAPI v0.3.1
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [d1d4a3ce] + BitFlags v0.1.9
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [34da2185] + Compat v4.16.0
  [f0e56b4a] + ConcurrentUtilities v2.5.0
  [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
  [460bff9d] + ExceptionUnwrapping v0.1.11
  [48062228] + FilePathsBase v0.9.24
  [5ef98721] + GeneNetworkAPI v0.3.1
  [cd3eb016] + HTTP v1.10.15
  [842dd82b] + InlineStrings v1.4.3
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.0
  [682c06a0] + JSON v0.21.4
  [b964fa9f] + LaTeXStrings v1.4.0
  [e6f89c97] + LoggingExtras v1.1.0
  [739be429] + MbedTLS v1.1.9
  [e1d29d7a] + Missings v1.2.0
  [4d8831e6] + OpenSSL v1.4.3
  [bac558e1] + OrderedCollections v1.8.0
  [69de0a69] + Parsers v2.8.1
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [189a3867] + Reexport v1.2.2
  [91c51154] + SentinelArrays v1.4.8
  [777ac1f9] + SimpleBufferStream v1.2.0
  [a2af1166] + SortingAlgorithms v1.2.1
  [10745b16] + Statistics v1.11.1
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [3bb67fe8] + TranscodingStreams v0.11.3
  [5c2747f8] + URIs v1.5.1
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [458c3c95] + OpenSSL_jll v3.0.16+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
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [dc6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [b27032c2] + LibCURL v0.6.4
  [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
  [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
  [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
  [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

Installation completed after 1.87s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 62.27s


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

     Testing GeneNetworkAPI
      Status `/tmp/jl_Ku7V1X/Project.toml`
  [5ef98721] GeneNetworkAPI v0.3.1
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_Ku7V1X/Manifest.toml`
  [d1d4a3ce] BitFlags v0.1.9
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.16.0
  [f0e56b4a] ConcurrentUtilities v2.5.0
  [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
  [460bff9d] ExceptionUnwrapping v0.1.11
  [48062228] FilePathsBase v0.9.24
  [5ef98721] GeneNetworkAPI v0.3.1
  [cd3eb016] HTTP v1.10.15
  [842dd82b] InlineStrings v1.4.3
  [41ab1584] InvertedIndices v1.3.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.0
  [682c06a0] JSON v0.21.4
  [b964fa9f] LaTeXStrings v1.4.0
  [e6f89c97] LoggingExtras v1.1.0
  [739be429] MbedTLS v1.1.9
  [e1d29d7a] Missings v1.2.0
  [4d8831e6] OpenSSL v1.4.3
  [bac558e1] OrderedCollections v1.8.0
  [69de0a69] Parsers v2.8.1
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.4.0
  [189a3867] Reexport v1.2.2
  [91c51154] SentinelArrays v1.4.8
  [777ac1f9] SimpleBufferStream v1.2.0
  [a2af1166] SortingAlgorithms v1.2.1
  [10745b16] Statistics v1.11.1
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [5c2747f8] URIs v1.5.1
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
  [458c3c95] OpenSSL_jll v3.0.16+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
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [dc6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [b27032c2] LibCURL v0.6.4
  [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
  [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
  [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
  [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
     Testing Running tests...
Get species list test 1: Test Passed
Get list group for a species test 2: Test Passed
GeneNetworkAPI.jl: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:30
  Expression: dfRslt1 == dfMetaGeno1 && length(dfRslt2.location) == 1

Stacktrace:
 [1] top-level scope
   @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:0
 [2] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:679 [inlined]
 [3] include(mapexpr::Function, mod::Module, _path::String)
   @ Base ./Base.jl:301
 [4] top-level scope
   @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7
 [5] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined]
 [6] macro expansion
   @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [inlined]
Get meta geno for a group test 3: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:30
  Expression: dfRslt1 == dfMetaGeno1 && length(dfRslt2.location) == 1

Get genotypes for a group test 4: Test Passed
Get sample data for a group test 5: Test Passed
GeneNetworkAPI.jl: Error During Test at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:6
  Got exception outside of a @test
  LoadError: RequestError: Operation too slow. Less than 1 bytes/sec transferred the last 300 seconds while requesting https://genenetwork.org/api/v_pre1/sample_data/INIA_AmgCoh_0311
  Stacktrace:
    [1] (::Downloads.var"#23#24"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool})(easy::Downloads.Curl.Easy)
      @ Downloads /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:452
    [2] with_handle(f::Downloads.var"#23#24"{IOStream, Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, handle::Downloads.Curl.Easy)
      @ Downloads.Curl /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Curl/Curl.jl:105
    [3] #21
      @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:363 [inlined]
    [4] arg_write(f::Downloads.var"#21#22"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream)
      @ ArgTools /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:134
    [5] #19
      @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:362 [inlined]
    [6] arg_read
      @ /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:76 [inlined]
    [7] #request#6
      @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:361 [inlined]
    [8] request
      @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:328 [inlined]
    [9] #4
      @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:259 [inlined]
   [10] open(f::Downloads.var"#4#5"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Downloads.Downloader, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool})
      @ Base ./io.jl:410
   [11] open_nolock
      @ /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:35 [inlined]
   [12] arg_write(f::Function, arg::String)
      @ ArgTools /opt/julia/share/julia/stdlib/v1.12/ArgTools/src/ArgTools.jl:103
   [13] #download#2
      @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:258 [inlined]
   [14] download
      @ /opt/julia/share/julia/stdlib/v1.12/Downloads/src/Downloads.jl:247 [inlined]
   [15] #download_omics#14
      @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/src/download_data.jl:89 [inlined]
   [16] get_omics(dataset::String; gn_url::String)
      @ GeneNetworkAPI ~/.julia/packages/GeneNetworkAPI/Lrt9h/src/get_data.jl:63
   [17] get_omics(dataset::String)
      @ GeneNetworkAPI ~/.julia/packages/GeneNetworkAPI/Lrt9h/src/get_data.jl:62
   [18] top-level scope
      @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:66
   [19] include(mapexpr::Function, mod::Module, _path::String)
      @ Base ./Base.jl:301
   [20] top-level scope
      @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7
   [21] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined]
   [22] macro expansion
      @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [inlined]
   [23] include(mapexpr::Function, mod::Module, _path::String)
      @ Base ./Base.jl:301
   [24] top-level scope
      @ none:6
   [25] eval(m::Module, e::Any)
      @ Core ./boot.jl:485
   [26] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:295
   [27] _start()
      @ Base ./client.jl:558
  in expression starting at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:66
Test Summary:     | Pass  Fail  Error  Total     Time
GeneNetworkAPI.jl |    4     1      1      6  6m59.6s
ERROR: LoadError: Some tests did not pass: 4 passed, 1 failed, 1 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:6

Testing failed after 129.49s

ERROR: LoadError: Package GeneNetworkAPI 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 536.89s: package tests unexpectedly errored