From 804a70016b1ffa945d43fc593824d81bbccc03d0 Mon Sep 17 00:00:00 2001 From: Seyoon Ko Date: Tue, 27 Jul 2021 09:03:44 -0700 Subject: [PATCH] compat update --- Manifest.toml | 75 +++++++++++++++++++++++++++------------------------ Project.toml | 3 +++ 2 files changed, 43 insertions(+), 35 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index af388e7..757e089 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -17,9 +17,9 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "045ff5e1bc8c6fb1ecb28694abba0a0d55b5f4f5" +git-tree-sha1 = "a71d224f61475b93c9e196e83c17c6ac4dedacfa" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.17" +version = "3.1.18" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -32,7 +32,7 @@ version = "0.8.0" [[BGEN]] deps = ["CodecZlib", "CodecZstd", "Printf", "SIMD", "SQLite", "SpecialFunctions", "Statistics", "Tables", "TranscodingStreams"] -git-tree-sha1 = "3809273134723bcb0474be661b4dd49752bc8e5e" +git-tree-sha1 = "ee6cf98c88e14936b613b23afa7c90e171ece024" repo-rev = "main" repo-url = "https://github.com/OpenMendel/BGEN.jl" uuid = "6db4b851-9beb-4b83-9d64-eb1cfb37721d" @@ -91,9 +91,9 @@ version = "0.10.0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "f53ca8d41e4753c41cdafa6ec5f7ce914b34be54" +git-tree-sha1 = "ad613c934ec3a3aa0ff19b91f15a16d56ed404b5" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "0.10.13" +version = "1.0.2" [[CodecBzip2]] deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"] @@ -211,10 +211,10 @@ uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" version = "1.10.1" [[FillArrays]] -deps = ["LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "25b9cc23ba3303de0ad2eac03f840de9104c9253" +deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] +git-tree-sha1 = "8c8eac2af06ce35973c3eadb4ab3243076a408e7" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.0" +version = "0.12.1" [[Formatting]] deps = ["Printf"] @@ -238,10 +238,10 @@ uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" version = "1.3.0" [[HTTP]] -deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"] -git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508" +deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] +git-tree-sha1 = "c6a1fff2fd4b1da29d3dccaffb1e1001244d844e" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.8.19" +version = "0.9.12" [[Hwloc]] deps = ["Hwloc_jll"] @@ -284,15 +284,15 @@ version = "1.0.0" [[Ipopt]] deps = ["BinaryProvider", "Ipopt_jll", "Libdl", "LinearAlgebra", "MathOptInterface", "MathProgBase"] -git-tree-sha1 = "d0f3cc6fa341859910a8ee0fdd397862042af290" +git-tree-sha1 = "380786b4929b8d18d76e909c6b2eca355b7c3bd6" uuid = "b6b21f68-93f8-5de0-b562-5493be1d77c9" -version = "0.6.3" +version = "0.7.0" [[Ipopt_jll]] -deps = ["ASL_jll", "CompilerSupportLibraries_jll", "Libdl", "MUMPS_seq_jll", "OpenBLAS32_jll", "Pkg"] -git-tree-sha1 = "4247bc93c3f0cb3d23a9d221e6d23d5449b4d90d" +deps = ["ASL_jll", "Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "MUMPS_seq_jll", "OpenBLAS32_jll", "Pkg"] +git-tree-sha1 = "82124f27743f2802c23fcb05febc517d0b15d86e" uuid = "9cc047cb-c261-5740-88fc-0cf96f7bdcc7" -version = "3.13.1+1" +version = "3.13.4+2" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -361,9 +361,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[LoopVectorization]] deps = ["ArrayInterface", "DocStringExtensions", "IfElse", "LinearAlgebra", "OffsetArrays", "Polyester", "Requires", "SLEEFPirates", "Static", "StrideArraysCore", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "06c91d5495c32bca6b843551a1331c3cd2fb23d0" +git-tree-sha1 = "b844cb320457812f739fe75f216a481095daf5c2" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.53" +version = "0.12.55" [[METIS_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -373,9 +373,9 @@ version = "5.1.0+5" [[MUMPS_seq_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "METIS_jll", "OpenBLAS32_jll", "Pkg"] -git-tree-sha1 = "a1d469a2a0acbfe219ef9bdfedae97daacac5a0e" +git-tree-sha1 = "1a11a84b2af5feb5a62a820574804056cdc59c39" uuid = "d7ed1dd3-d0ae-5e8e-bfb4-87a502085b8d" -version = "5.4.0+0" +version = "5.2.1+4" [[ManualMemory]] git-tree-sha1 = "71c64ebe61a12bad0911f8fc4f91df8a448c604c" @@ -472,7 +472,7 @@ version = "1.4.1" [[OrdinalMultinomialModels]] deps = ["Distributions", "GLM", "Ipopt", "LinearAlgebra", "MathProgBase", "NLopt", "RDatasets", "Random", "Reexport", "StatsBase", "StatsModels"] -git-tree-sha1 = "636b99b00955b248dcc5f66c885263c87b2d311b" +git-tree-sha1 = "28f2d6345d21afe4c55873dc993ebafea2793f9d" repo-rev = "master" repo-url = "https://github.com/OpenMendel/OrdinalMultinomialModels.jl" uuid = "b51826c6-2bc1-4eb0-a3af-c080fd29f1d0" @@ -496,9 +496,9 @@ uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" [[Polyester]] deps = ["ArrayInterface", "IfElse", "ManualMemory", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities", "VectorizationBase"] -git-tree-sha1 = "2a5e179a459867e0046d4e74e1a8cfc88a06ee4a" +git-tree-sha1 = "4b692c8ce1912bae5cd3b90ba22d1b54eb581195" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.3.6" +version = "0.3.7" [[PooledArrays]] deps = ["DataAPI", "Future"] @@ -598,9 +598,9 @@ version = "3.3.1" [[SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "da6d214ffc85b1292f300649ef86d3c4f9aaf25d" +git-tree-sha1 = "bfdf9532c33db35d2ce9df4828330f0e92344a52" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.22" +version = "0.6.25" [[SQLite]] deps = ["BinaryProvider", "DBInterface", "Dates", "Libdl", "Random", "SQLite_jll", "Serialization", "Tables", "Test", "WeakRefStrings"] @@ -634,7 +634,7 @@ version = "1.0.0" [[SnpArrays]] deps = ["Adapt", "CSV", "CodecBzip2", "CodecXz", "CodecZlib", "CodecZstd", "DataFrames", "DelimitedFiles", "Glob", "LinearAlgebra", "LoopVectorization", "Missings", "Mmap", "Printf", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Tables", "TranscodingStreams", "VariantCallFormat", "VectorizationBase"] -git-tree-sha1 = "9feadd65d7bf786ed7bb46ebf0c4e61ae6d897ed" +git-tree-sha1 = "4d2211b0ff821d896ddad58f54e6eba3486462fc" repo-rev = "master" repo-url = "https://github.com/OpenMendel/SNPArrays.jl" uuid = "4e780e97-f5bf-4111-9dc4-b70aaf691b06" @@ -655,15 +655,15 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SpecialFunctions]] deps = ["ChainRulesCore", "LogExpFunctions", "OpenSpecFun_jll"] -git-tree-sha1 = "a50550fa3164a8c46747e62063b4d774ac1bcf49" +git-tree-sha1 = "508822dca004bf62e210609148511ad03ce8f1d8" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.5.1" +version = "1.6.0" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "2740ea27b66a41f9d213561a04573da5d3823d4b" +git-tree-sha1 = "62701892d172a2fa41a1f829f66d2b0db94a9a63" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.2.5" +version = "0.3.0" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -694,9 +694,9 @@ version = "0.6.23" [[StrideArraysCore]] deps = ["ArrayInterface", "ManualMemory", "Requires", "ThreadingUtilities", "VectorizationBase"] -git-tree-sha1 = "2525850b6887e217c3cc149ab29eb2a7a6360d37" +git-tree-sha1 = "e1c37dd3022ba6aaf536541dd607e8d5fb534377" uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.1.16" +version = "0.1.17" [[StringEncodings]] deps = ["Libiconv_jll"] @@ -740,9 +740,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[ThreadingUtilities]] deps = ["ManualMemory"] -git-tree-sha1 = "593009385e6536dc50baedc2c8bc1a3717ef358f" +git-tree-sha1 = "03013c6ae7f1824131b2ae2fc1d49793b51e8394" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" -version = "0.4.5" +version = "0.4.6" [[TimeZones]] deps = ["Dates", "Future", "LazyArtifacts", "Mocking", "Pkg", "Printf", "RecipesBase", "Serialization", "Unicode"] @@ -756,6 +756,11 @@ git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.5" +[[URIs]] +git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" +uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" +version = "1.3.0" + [[UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" @@ -770,7 +775,7 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" [[VCFTools]] deps = ["CodecZlib", "Dates", "DelimitedFiles", "Distributions", "HypothesisTests", "ProgressMeter", "SpecialFunctions", "VariantCallFormat"] -git-tree-sha1 = "8e42021ff8c380ce554212f58e7f87bff0a64168" +git-tree-sha1 = "0d99c5d4b672598d5a28f9944ab69de0ace04ac6" repo-rev = "master" repo-url = "https://github.com/OpenMendel/VCFTools.jl" uuid = "a620830f-fdd7-5ebc-8d26-3621ab35fbfe" diff --git a/Project.toml b/Project.toml index 4ca3f52..bf68a31 100644 --- a/Project.toml +++ b/Project.toml @@ -19,8 +19,11 @@ VariantCallFormat = "28eba6e3-a997-4ad9-87c6-d933b8bca6c1" [compat] BGEN = "0.1.2" +CSV = "0.8" DataFrames = "0.21.0 - 1" +Distributions = "0.22 - 0.25" OrdinalMultinomialModels = "0.3" +Reexport = "1" SnpArrays = "0.3.3" StatsModels = "0.6" VCFTools = "0.2.1"