Package evaluation of BioServices on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T11:41:13.504 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.25s ################################################################################ # Installation # Installing BioServices... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [a0d4ced5] + BioServices v0.4.1 Updating `~/.julia/environments/v1.11/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [a0d4ced5] + BioServices v0.4.1 [d1d4a3ce] + BitFlags v0.1.9 [944b1d66] + CodecZlib v0.7.8 [f0e56b4a] + ConcurrentUtilities v2.5.0 [460bff9d] + ExceptionUnwrapping v0.1.11 [8f5d6c58] + EzXML v1.2.1 [708ec375] + Gumbo v0.8.3 [cd3eb016] + HTTP v1.10.15 [c8e1da08] + IterTools v1.10.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [e6f89c97] + LoggingExtras v1.1.0 [739be429] + MbedTLS v1.1.9 [4d8831e6] + OpenSSL v1.4.3 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [777ac1f9] + SimpleBufferStream v1.2.0 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.5.2 [228000da] + XMLDict v0.4.1 [528830af] + Gumbo_jll v0.10.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [02c8fc9c] + XML2_jll v2.13.6+1 [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 [b77e0a4c] + InteractiveUtils 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 [a63ad114] + Mmap 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 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets 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 [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 2.12s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 17.55s ################################################################################ # Testing # Testing BioServices Status `/tmp/jl_VgS4ao/Project.toml` [a0d4ced5] BioServices v0.4.1 [708ec375] Gumbo v0.8.3 [cd3eb016] HTTP v1.10.15 [682c06a0] JSON v0.21.4 [228000da] XMLDict v0.4.1 [ade2ca70] Dates v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_VgS4ao/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [a0d4ced5] BioServices v0.4.1 [d1d4a3ce] BitFlags v0.1.9 [944b1d66] CodecZlib v0.7.8 [f0e56b4a] ConcurrentUtilities v2.5.0 [460bff9d] ExceptionUnwrapping v0.1.11 [8f5d6c58] EzXML v1.2.1 [708ec375] Gumbo v0.8.3 [cd3eb016] HTTP v1.10.15 [c8e1da08] IterTools v1.10.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [e6f89c97] LoggingExtras v1.1.0 [739be429] MbedTLS v1.1.9 [4d8831e6] OpenSSL v1.4.3 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.1 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [777ac1f9] SimpleBufferStream v1.2.0 [3bb67fe8] TranscodingStreams v0.11.3 [5c2747f8] URIs v1.5.2 [228000da] XMLDict v0.4.1 [528830af] Gumbo_jll v0.10.2+0 [94ce4f54] Libiconv_jll v1.18.0+0 [458c3c95] OpenSSL_jll v3.0.16+0 [02c8fc9c] XML2_jll v2.13.6+1 [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 [b77e0a4c] InteractiveUtils 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 [a63ad114] Mmap 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 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets 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 [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. Testing Running tests... Running tests: ----------------------------------------- ----------------------------------------- Testing: EUtils ----------------------------------------- ----------------------------------------- egquery: Error During Test at /home/pkgeval/.julia/packages/BioServices/EkekK/test/eutils.jl:112 Got exception outside of a @test HTTP.ConnectError for url = `https://ext-http-eutils.linkerd.ncbi.nlm.nih.gov/gquery?term=%28Asthma%5BMeSH%20Major%20Topic%5D%29%20AND%0A%28%28%222018%2F01%2F01%22%5BDate%20-%20Publication%5D%20%3A%20%0A%223000%22%5BDate%20-%20Publication%5D%29%29&retmode=xml`: DNSError: ext-http-eutils.linkerd.ncbi.nlm.nih.gov, unknown node or service (EAI_NONAME) Stacktrace: [1] getalladdrinfo(host::String) @ Sockets /opt/julia/share/julia/stdlib/v1.11/Sockets/src/addrinfo.jl:113 [2] getalladdrinfo @ /opt/julia/share/julia/stdlib/v1.11/Sockets/src/addrinfo.jl:122 [inlined] [3] getconnection(::Type{Sockets.TCPSocket}, host::SubString{String}, port::String; keepalive::Bool, readtimeout::Int64, kw::@Kwargs{require_ssl_verification::Bool, iofunction::Nothing, decompress::Nothing, verbose::Int64, status_exception::Bool}) @ HTTP.Connections ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:520 [4] getconnection @ ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:508 [inlined] [5] getconnection(::Type{OpenSSL.SSLStream}, host::SubString{String}, port::SubString{String}; kw::@Kwargs{require_ssl_verification::Bool, keepalive::Bool, readtimeout::Int64, iofunction::Nothing, decompress::Nothing, verbose::Int64, status_exception::Bool}) @ HTTP.Connections ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:585 [6] getconnection @ ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:578 [inlined] [7] #10 @ ~/.julia/packages/HTTP/4AUPl/src/Connections.jl:467 [inlined] [8] macro expansion @ ~/.julia/packages/ConcurrentUtilities/ofY4K/src/try_with_timeout.jl:92 [inlined] [9] (::ConcurrentUtilities.var"#2#4"{Any, Channel{Any}, HTTP.Connections.var"#10#13"{OpenSSL.SSLStream, Bool, Bool, @Kwargs{readtimeout::Int64, iofunction::Nothing, decompress::Nothing, verbose::Int64, status_exception::Bool}, SubString{String}, SubString{String}}, Timer})() @ ConcurrentUtilities ~/.julia/packages/ConcurrentUtilities/ofY4K/src/ConcurrentUtilities.jl:10 Stacktrace: [1] request(method::String, URL::String, headers::Vector{Pair{String, String}}; params::@Kwargs{query::Dict{Symbol, Any}}) @ BioServices ~/.julia/packages/BioServices/EkekK/src/common.jl:36 [2] request (repeats 2 times) @ ~/.julia/packages/BioServices/EkekK/src/common.jl:4 [inlined] [3] #egquery#7 @ ~/.julia/packages/BioServices/EkekK/src/eutils.jl:153 [inlined] [4] egquery @ ~/.julia/packages/BioServices/EkekK/src/eutils.jl:151 [inlined] [5] macro expansion @ ~/.julia/packages/BioServices/EkekK/test/eutils.jl:113 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [7] macro expansion @ ~/.julia/packages/BioServices/EkekK/test/eutils.jl:113 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [9] top-level scope @ ~/.julia/packages/BioServices/EkekK/test/eutils.jl:4 [10] include(mod::Module, _path::String) @ Base ./Base.jl:557 [11] include(x::String) @ Main.TestBioServices ~/.julia/packages/BioServices/EkekK/test/runtests.jl:1 [12] top-level scope @ ~/.julia/packages/BioServices/EkekK/test/runtests.jl:25 [13] include(fname::String) @ Main ./sysimg.jl:38 [14] top-level scope @ none:6 [15] eval @ ./boot.jl:430 [inlined] [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [17] _start() @ Base ./client.jl:531 Test Summary: | Pass Error Total Time EUtils | 42 1 43 1m01.5s einfo | 4 4 34.6s esearch | 4 4 3.3s epost | 5 5 1.9s esummary | 12 12 6.7s efetch | 9 9 8.9s elink | 3 3 0.3s egquery | 1 1 5.1s espell | 4 4 0.1s ecitmatch | 1 1 0.4s ERROR: LoadError: Some tests did not pass: 42 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BioServices/EkekK/test/eutils.jl:2 in expression starting at /home/pkgeval/.julia/packages/BioServices/EkekK/test/runtests.jl:1 Testing failed after 65.26s ERROR: LoadError: Package BioServices errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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/v1.11/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/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 120.86s: package tests unexpectedly errored