Package evaluation of SnpArrays on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T12:05:27.132 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.16s ################################################################################ # Installation # Installing SnpArrays... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [4e780e97] + SnpArrays v0.3.22 Updating `~/.julia/environments/v1.10/Manifest.toml` [79e6a3ab] + Adapt v4.2.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.18.0 ⌅ [67c07d97] + Automa v0.8.4 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.6 [336ed68f] + CSV v0.10.15 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.3 [48062228] + FilePathsBase v0.9.23 [c27321d9] + Glob v1.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.171 [d125e4d3] + ManualMemory v0.1.8 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.15.0 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.0 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [91c51154] + SentinelArrays v1.4.8 [4e780e97] + SnpArrays v0.3.22 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [aedffcd0] + Static v1.1.1 [0d7ed370] + StaticArrayInterface v1.8.0 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [8290d209] + ThreadingUtilities v0.5.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [28eba6e3] + VariantCallFormat v0.5.6 [3d5dd08c] + VectorizationBase v0.21.71 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [ffd25f8a] + XZ_jll v5.6.4+1 [3161d3a3] + Zstd_jll v1.5.7+1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.1+4 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+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 6.16s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 147.77s ################################################################################ # Testing # Testing SnpArrays Status `/tmp/jl_WMmAyu/Project.toml` [79e6a3ab] Adapt v4.2.0 [336ed68f] CSV v0.10.15 [052768ef] CUDA v5.6.1 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.6 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [c27321d9] Glob v1.3.1 [bdcacae8] LoopVectorization v0.12.171 [e1d29d7a] Missings v1.2.0 [ae029012] Requires v1.3.0 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.5.0 [2913bbd2] StatsBase v0.34.4 [bd369af6] Tables v1.12.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [28eba6e3] VariantCallFormat v0.5.6 [3d5dd08c] VectorizationBase v0.21.71 [37e2e46d] LinearAlgebra [a63ad114] Mmap [de0858da] Printf [9a3f8284] Random [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [8dfed614] Test Status `/tmp/jl_WMmAyu/Manifest.toml` [621f4979] AbstractFFTs 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ExprTools v0.1.10 [48062228] FilePathsBase v0.9.23 [53c48c17] FixedPointNumbers v0.8.5 [0c68f7d7] GPUArrays v11.2.2 [46192b85] GPUArraysCore v0.2.0 [61eb1bfa] GPUCompiler v1.2.0 [c27321d9] Glob v1.3.1 [076d061b] HashArrayMappedTries v0.2.0 [3e5b6fbb] HostCPUFeatures v0.1.17 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [63c18a36] KernelAbstractions v0.9.34 [929cbde3] LLVM v9.2.0 [8b046642] LLVMLoopInfo v1.0.0 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.171 [1914dd2f] MacroTools v0.5.15 [d125e4d3] ManualMemory v0.1.8 [e1d29d7a] Missings v1.2.0 ⌅ [5da4648a] NVTX v0.3.5 [6fe1bfb0] OffsetArrays v1.15.0 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.1 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [74087812] Random123 v1.7.0 [e6cf234a] RandomNumbers v1.6.0 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.0 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [7e506255] ScopedValues v1.3.0 [6c6a2e73] Scratch v1.2.1 [91c51154] SentinelArrays v1.4.8 [4e780e97] SnpArrays v0.3.22 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [aedffcd0] Static v1.1.1 [0d7ed370] StaticArrayInterface v1.8.0 [90137ffa] StaticArrays v1.9.12 [1e83bf80] StaticArraysCore v1.4.3 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [8290d209] ThreadingUtilities v0.5.2 [a759f4b9] TimerOutputs v0.5.27 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [013be700] UnsafeAtomics v0.3.0 [28eba6e3] VariantCallFormat v0.5.6 [3d5dd08c] VectorizationBase v0.21.71 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 ⌅ [4ee394cb] CUDA_Driver_jll v0.10.4+0 ⌅ [76a88914] CUDA_Runtime_jll v0.15.5+0 [9c1d0b0a] JuliaNVTXCallbacks_jll v0.2.1+0 [dad2f222] LLVMExtra_jll v0.0.35+0 [e98f9f5b] NVTX_jll v3.1.1+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [ffd25f8a] XZ_jll v5.6.4+1 [3161d3a3] Zstd_jll v1.5.7+1 [1e29f10c] demumble_jll v1.3.0+0 [0dad84c5] ArgTools v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.1+4 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [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... Test Summary: | Pass Total Time size | 8 8 1.6s Test Summary: | Pass Total Time counts | 10 10 2.0s Test Summary: | Pass Total Time means | 33 33 1.4s Test Summary: | Pass Total Time var/std | 10 10 2.3s Test Summary: | Pass Total Time missingpos | 3 3 1.7s Test Summary: | Pass Total Time create bed | 4 4 1.3s Test Summary: | Pass Total Time convert | 12 12 2.5s Test Summary: | Pass Total Time convert (ADMIXTURE) | 3 3 0.0s Test Summary: | Pass Total Time maf | 4 4 1.8s convert genotype: 0.56 seconds Φ = GG': 0.39 seconds convert G to {0,1} matrix: 0.02 seconds S = GG': 0.39 seconds Test Summary: | Pass Total Time grm | 11 11 17.4s Test Summary: | Pass Total Time filter | 8 8 9.3s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time SnpBitMatrix-vector multiplication | 48 48 55.7s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time copyto bitmatrix | 36 36 21.4s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time convert (SnpBitMatrix) | 24 24 15.4s Test Summary: | Pass Total Time copyto SnpLinAlg | 36 36 10.0s Test Summary: | Pass Total Time convert (SnpLinAlg) | 24 24 9.2s Test Summary: | Pass Total Time SnpLinAlg-vector multiplication (zeroimpute) | 48 48 1m38.3s Test Summary: | Pass Total Time SnpLinAlg-matrix multiplication zeroimpute | 48 48 1m00.5s Test Summary: | Pass Total Time SnpLinAlg-vector multiplication (Miter > 0) | 1 1 10.2s Test Summary: | Pass Total Time SnpLinAlg-vector multiplication meanimpute | 48 48 1m15.0s Test Summary: | Pass Total Time SnpLinAlg-matrix multiplication meanimpute | 48 48 43.0s ┌ Warning: `SnpBitMatrix{T}` is deprecated and will be removed soon. Please use `SnpLinAlg{T}` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time subarrays | 4 4 7.5s 0.316077 seconds (230.08 k allocations: 13.887 MiB, 93.19% compilation time) 1.774020 seconds (73.43 k allocations: 5.403 MiB, 99.85% compilation time) 0.066674 seconds (22.78 k allocations: 1.600 MiB, 99.45% compilation time) 0.060419 seconds (13.84 k allocations: 1.515 MiB, 99.31% compilation time) 5.987368 seconds (3.41 M allocations: 233.803 MiB, 6.05% gc time, 98.68% compilation time) Test Summary: | Pass Total Time split-merge-readwrite | 20 20 45.0s 0.069029 seconds 0.068543 seconds 0.067950 seconds 0.068237 seconds 0.068213 seconds 0.068480 seconds 0.067769 seconds 0.067956 seconds 0.069182 seconds 0.068483 seconds 0.077688 seconds 0.079442 seconds Test Summary: | Pass Total Time (de)compress | 61 61 8.8s Test Summary: | Pass Total Time indexin | 3 3 0.4s Test Summary: | Pass Total Time concat | 9 9 5.0s reorder: Error During Test at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/test/runtests.jl:707 Got exception outside of a @test SystemError: opening file "mouse_testreorder.bed": Permission denied Stacktrace: [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) @ Base ./error.jl:176 [2] systemerror @ ./error.jl:175 [inlined] [3] open(fname::String; lock::Bool, read::Bool, write::Bool, create::Nothing, truncate::Nothing, append::Nothing) @ Base ./iostream.jl:293 [4] open @ ./iostream.jl:275 [inlined] [5] open(fname::String, mode::String; lock::Bool) @ Base ./iostream.jl:356 [6] open @ ./iostream.jl:355 [inlined] [7] makestream(filepath::String, args::String; kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/CSYLc/src/codec.jl:9 [8] makestream(filepath::String, args::String) @ SnpArrays ~/.julia/packages/SnpArrays/CSYLc/src/codec.jl:8 [9] makestream(::SnpArrays.var"#11#12"{String}, ::String, ::Vararg{String}) @ SnpArrays ~/.julia/packages/SnpArrays/CSYLc/src/codec.jl:29 [10] SnpArray(bednm::String, m::Int64, args::String; kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/CSYLc/src/snparray.jl:35 [11] SnpArray @ ~/.julia/packages/SnpArrays/CSYLc/src/snparray.jl:33 [inlined] [12] SnpArray(bednm::String, args::String; famnm::String, kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/CSYLc/src/snparray.jl:67 [13] SnpArray @ ~/.julia/packages/SnpArrays/CSYLc/src/snparray.jl:50 [inlined] [14] SnpData(plink_file::String, args::String; famnm::String, bimnm::String, kwargs::@Kwargs{}) @ SnpArrays ~/.julia/packages/SnpArrays/CSYLc/src/snpdata.jl:39 [15] SnpData(plink_file::String, args::String) @ SnpArrays ~/.julia/packages/SnpArrays/CSYLc/src/snpdata.jl:21 [16] macro expansion @ ~/.julia/packages/SnpArrays/CSYLc/test/runtests.jl:714 [inlined] [17] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [18] top-level scope @ ~/.julia/packages/SnpArrays/CSYLc/test/runtests.jl:708 [19] include(fname::String) @ Base.MainInclude ./client.jl:494 [20] top-level scope @ none:6 [21] eval @ ./boot.jl:385 [inlined] [22] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [23] _start() @ Base ./client.jl:557 Test Summary: | Error Total Time reorder | 1 1 1.5s ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/test/runtests.jl:707 Testing failed after 543.34s ERROR: LoadError: Package SnpArrays errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [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/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/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 712.46s: package tests unexpectedly errored