Package evaluation of GeneNetworkAPI on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T14:35:11.635 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.67s ################################################################################ # Installation # Installing GeneNetworkAPI... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [5ef98721] + GeneNetworkAPI v0.3.1 Updating `~/.julia/environments/v1.11/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 v1.5.2 [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 [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 [fa267f1f] + TOML v1.0.3 [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 [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 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 2.21s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 22.95s ################################################################################ # Testing # Testing GeneNetworkAPI Status `/tmp/jl_cMrpQO/Project.toml` [5ef98721] GeneNetworkAPI v0.3.1 [8dfed614] Test v1.11.0 Status `/tmp/jl_cMrpQO/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 v1.5.2 [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 [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 [fa267f1f] TOML v1.0.3 [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 [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 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. 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 @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [2] include(fname::String) @ Main ./sysimg.jl:38 [3] macro expansion @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [6] include(fname::String) @ Main ./sysimg.jl:38 [7] top-level scope @ none:6 [8] eval @ ./boot.jl:430 [inlined] [9] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [10] _start() @ Base ./client.jl:531 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 Get value about omic data 6: Test Passed Get information about traits test 7: Test Passed GeneNetworkAPI.jl: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:98 Expression: dfRslt1 == dfInfoPheno1 && (dfRslt2 == dfInfoPheno2 && dfRslt3 == dfInfoPheno3) Stacktrace: [1] top-level scope @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [2] include(fname::String) @ Main ./sysimg.jl:38 [3] macro expansion @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [6] include(fname::String) @ Main ./sysimg.jl:38 [7] top-level scope @ none:6 [8] eval @ ./boot.jl:430 [inlined] [9] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [10] _start() @ Base ./client.jl:531 Get summary information on traits test 8: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:98 Expression: dfRslt1 == dfInfoPheno1 && (dfRslt2 == dfInfoPheno2 && dfRslt3 == dfInfoPheno3) GeneNetworkAPI.jl: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:107 Expression: dfRslt1 == dfGemma Evaluated: 1×6 DataFrame Row │ Mb additive chr lod_score name p_value │ Float64 Float64 Any Float64 String Float64 ─────┼─────────────────────────────────────────────────────────── 1 │ 24.9169 -2.2929 2 15.186 rs32869517 6.5161e-16 == 1×6 DataFrame Row │ Mb additive chr lod_score name p_value │ Float64 Float64 Any Float64 String Float64 ─────┼──────────────────────────────────────────────────────────── 1 │ 24.9169 -2.2929 2 15.186 rs32869517 6.51628e-16 Stacktrace: [1] top-level scope @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [2] include(fname::String) @ Main ./sysimg.jl:38 [3] macro expansion @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [6] include(fname::String) @ Main ./sysimg.jl:38 [7] top-level scope @ none:6 [8] eval @ ./boot.jl:430 [inlined] [9] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [10] _start() @ Base ./client.jl:531 Get Gemma results test 9: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:107 Expression: dfRslt1 == dfGemma Evaluated: 1×6 DataFrame Row │ Mb additive chr lod_score name p_value │ Float64 Float64 Any Float64 String Float64 ─────┼─────────────────────────────────────────────────────────── 1 │ 24.9169 -2.2929 2 15.186 rs32869517 6.5161e-16 == 1×6 DataFrame Row │ Mb additive chr lod_score name p_value │ Float64 Float64 Any Float64 String Float64 ─────┼──────────────────────────────────────────────────────────── 1 │ 24.9169 -2.2929 2 15.186 rs32869517 6.51628e-16 GeneNetworkAPI.jl: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:116 Expression: dfRslt1 == dfCorrelation Evaluated: 0×3 DataFrame Row │ p_value sample_r trait │ Float64 Float64 String ─────┴─────────────────────────── == 1×3 DataFrame Row │ p_value sample_r trait │ Float64 Float64 Int64 ─────┼─────────────────────────────── 1 │ 0.000189298 -0.875658 12762 Stacktrace: [1] top-level scope @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [2] include(fname::String) @ Main ./sysimg.jl:38 [3] macro expansion @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [6] include(fname::String) @ Main ./sysimg.jl:38 [7] top-level scope @ none:6 [8] eval @ ./boot.jl:430 [inlined] [9] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [10] _start() @ Base ./client.jl:531 Get correlation test 10: Test Failed at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:116 Expression: dfRslt1 == dfCorrelation Evaluated: 0×3 DataFrame Row │ p_value sample_r trait │ Float64 Float64 String ─────┴─────────────────────────── == 1×3 DataFrame Row │ p_value sample_r trait │ Float64 Float64 Int64 ─────┼─────────────────────────────── 1 │ 0.000189298 -0.875658 12762 Download geno file test 11: Test Passed Download pheno file test 12: 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"#9#19"{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/v1.11/Downloads/src/Downloads.jl:452 [2] with_handle(f::Downloads.var"#9#19"{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/v1.11/Downloads/src/Curl/Curl.jl:105 [3] #8 @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:363 [inlined] [4] arg_write(f::Downloads.var"#8#18"{Base.DevNull, Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Bool, Nothing, String, Bool, Bool}, arg::IOStream) @ ArgTools /opt/julia/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:134 [5] #7 @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:362 [inlined] [6] arg_read @ /opt/julia/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:76 [inlined] [7] request(url::String; input::Nothing, output::IOStream, method::Nothing, headers::Vector{Pair{String, String}}, timeout::Float64, progress::Nothing, verbose::Bool, debug::Nothing, throw::Bool, downloader::Downloads.Downloader, interrupt::Nothing) @ Downloads /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:361 [8] request @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:328 [inlined] [9] #3 @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:259 [inlined] [10] open(f::Downloads.var"#3#4"{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/v1.11/ArgTools/src/ArgTools.jl:35 [inlined] [12] arg_write(f::Function, arg::String) @ ArgTools /opt/julia/share/julia/stdlib/v1.11/ArgTools/src/ArgTools.jl:103 [13] #download#2 @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:258 [inlined] [14] download @ /opt/julia/share/julia/stdlib/v1.11/Downloads/src/Downloads.jl:247 [inlined] [15] download_omics(dataset::String; gn_url::String, path::String) @ GeneNetworkAPI ~/.julia/packages/GeneNetworkAPI/Lrt9h/src/download_data.jl:89 [16] download_omics(dataset::String) @ GeneNetworkAPI ~/.julia/packages/GeneNetworkAPI/Lrt9h/src/download_data.jl:80 [17] top-level scope @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:137 [18] include(fname::String) @ Main ./sysimg.jl:38 [19] macro expansion @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [inlined] [20] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [21] top-level scope @ ~/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:7 [22] include(fname::String) @ Main ./sysimg.jl:38 [23] top-level scope @ none:6 [24] eval @ ./boot.jl:430 [inlined] [25] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [26] _start() @ Base ./client.jl:531 in expression starting at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/gnAPI_tests.jl:137 Test Summary: | Pass Fail Error Total Time GeneNetworkAPI.jl | 8 4 1 13 11m50.2s ERROR: LoadError: Some tests did not pass: 8 passed, 4 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/GeneNetworkAPI/Lrt9h/test/runtests.jl:6 Testing failed after 153.36s ERROR: LoadError: Package GeneNetworkAPI 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 774.42s: package tests unexpectedly errored