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compbiocore / VariantVisualization.jl

Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
https://compbiocore.github.io/VariantVisualization.jl/stable/
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Unable to automatically install 'MbedTLS' toml' #93

Open Caro-Ca opened 3 years ago

Caro-Ca commented 3 years ago

Dear, after instaling Julia, adding Julia and jdk1.8.0/bin to the PATH, and typing ]add VariantVisualization in Julia, I got this error message: 

 Installing known registries into `~/.julia`
┌ Warning: could not download https://pkg.julialang.org/registries
└ @ Pkg.Types ~/julia/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:951
┌ Warning: could not download https://pkg.julialang.org/registries
└ @ Pkg.Types ~/julia/usr/share/julia/stdlib/v1.5/Pkg/src/Types.jl:951
    Cloning registry from "https://github.com/JuliaRegistries/General.git"
      Added registry `General` to `~/.julia/registries/General`
  Resolving package versions...
    Cloning [7f8bf45c-0ad5-53b5-97e6-33c1305e0aa4] VariantVisualization from https://github.com/compbiocore/VariantVisualization.jl.git
  Installed VariantVisualization ──────── v0.4.0
    Cloning [e2d170a0-9d28-54be-80f0-106bbe20a464] DataValueInterfaces from https://github.com/queryverse/DataValueInterfaces.jl.git
  Installed DataValueInterfaces ───────── v1.0.0
    Cloning [3c28c6f8-a34d-59c4-9654-267d177fcfa9] BioSymbols from https://github.com/BioJulia/BioSymbols.jl.git
  Installed BioSymbols ────────────────── v3.1.0
    Cloning [c8ffd9c3-330d-5841-b78e-0817d7145fa1] MbedTLS_jll from https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl.git
  Installed MbedTLS_jll ───────────────── v2.16.6+1
    Cloning [944b1d66-785c-5afd-91f1-9de20f533193] CodecZlib from https://github.com/JuliaIO/CodecZlib.jl.git
  Installed CodecZlib ─────────────────── v0.7.0
    Cloning [3cdcf5f2-1ef4-517c-9805-6587b60abb01] RecipesBase from https://github.com/JuliaPlots/RecipesBase.jl.git
  Installed RecipesBase ───────────────── v1.0.2
    Cloning [e2ba6199-217a-4e67-a87a-7c52f15ade04] ExprTools from https://github.com/invenia/ExprTools.jl.git
  Installed ExprTools ─────────────────── v0.1.1
    Cloning [28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6] BGZFStreams from https://github.com/BioJulia/BGZFStreams.jl.git
  Installed BGZFStreams ───────────────── v0.3.0
    Cloning [bf4720bc-e11a-5d0c-854e-bdca1663c893] AssetRegistry from https://github.com/JuliaGizmos/AssetRegistry.jl.git
  Installed AssetRegistry ─────────────── v0.1.0
    Cloning [41ab1584-1d38-5bbf-9106-f11c6c58b48f] InvertedIndices from https://github.com/mbauman/InvertedIndices.jl.git
  Installed InvertedIndices ───────────── v1.0.0
    Cloning [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8] DataStructures from https://github.com/JuliaCollections/DataStructures.jl.git
  Installed DataStructures ────────────── v0.17.20
    Cloning [ffbed154-4ef7-542d-bbb7-c09d3a79fcae] DocStringExtensions from https://github.com/JuliaDocs/DocStringExtensions.jl.git
  Installed DocStringExtensions ───────── v0.8.2
    Cloning [524e6230-43b7-53ae-be76-1e9e4d08d11b] IntervalTrees from https://github.com/BioJulia/IntervalTrees.jl.git
  Installed IntervalTrees ─────────────── v1.0.0
    Cloning [682c06a0-de6a-54ab-a142-c8b1cf79cde6] JSON from https://github.com/JuliaIO/JSON.jl.git
  Installed JSON ──────────────────────── v0.21.0
    Cloning [30578b45-9adc-5946-b283-645ec420af67] URIParser from https://github.com/JuliaWeb/URIParser.jl.git
  Installed URIParser ─────────────────── v0.4.1
    Cloning [189a3867-3050-52da-a836-e630ba90ab69] Reexport from https://github.com/simonster/Reexport.jl.git
  Installed Reexport ──────────────────── v0.2.0
    Cloning [f0f68f2c-4968-5e81-91da-67840de0976a] PlotlyJS from https://github.com/sglyon/PlotlyJS.jl.git
  Installed PlotlyJS ──────────────────── v0.13.1
    Cloning [94ce4f54-9a6c-5748-9c1c-f9c7231a4531] Libiconv_jll from https://github.com/JuliaBinaryWrappers/Libiconv_jll.jl.git
  Installed Libiconv_jll ──────────────── v1.16.0+5
    Cloning [83775a58-1f1d-513f-b197-d71354ab007a] Zlib_jll from https://github.com/JuliaBinaryWrappers/Zlib_jll.jl.git
  Installed Zlib_jll ──────────────────── v1.2.11+15
    Cloning [2bd173c7-0d6d-553b-b6af-13a54713934c] NodeJS from https://github.com/davidanthoff/NodeJS.jl.git
  Installed NodeJS ────────────────────── v1.1.1
    Cloning [9e28174c-4ba2-5203-b857-d8d62c4213ee] BinDeps from https://github.com/JuliaPackaging/BinDeps.jl.git
  Installed BinDeps ───────────────────── v1.0.1
    Cloning [a2af1166-a08f-5f64-846c-94a0d3cef48c] SortingAlgorithms from https://github.com/JuliaCollections/SortingAlgorithms.jl.git
  Installed SortingAlgorithms ─────────── v0.3.1
    Cloning [861a8166-3701-5b0c-9a16-15d98fcdc6aa] Combinatorics from https://github.com/JuliaMath/Combinatorics.jl.git
  Installed Combinatorics ─────────────── v0.7.0
    Cloning [c7e460c6-2fb9-53a9-8c5b-16f535851c63] ArgParse from https://github.com/carlobaldassi/ArgParse.jl.git
  Installed ArgParse ──────────────────── v1.1.0
    Cloning [67c07d97-cdcb-5c2c-af73-a7f9c32a568b] Automa from https://github.com/BioJulia/Automa.jl.git
  Installed Automa ────────────────────── v0.8.0
    Cloning [8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615] EzXML from https://github.com/bicycle1885/EzXML.jl.git
  Installed EzXML ─────────────────────── v1.1.0
    Cloning [bd369af6-aec1-5ad0-b16a-f7cc5008161c] Tables from https://github.com/JuliaData/Tables.jl.git
  Installed Tables ────────────────────── v1.0.5
    Cloning [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] BioSequences from https://github.com/BioJulia/BioSequences.jl.git
  Installed BioSequences ──────────────── v1.1.0
    Cloning [53c48c17-4a7d-5ca2-90c5-79b7896eea93] FixedPointNumbers from https://github.com/JuliaMath/FixedPointNumbers.jl.git
  Installed FixedPointNumbers ─────────── v0.8.4
    Cloning [97c1335a-c9c5-57fe-bc5d-ec35cebe8660] JSExpr from https://github.com/JuliaGizmos/JSExpr.jl.git
  Installed JSExpr ────────────────────── v0.5.2
    Cloning [f27b6e38-b328-58d1-80ce-0feddd5e7a45] Polynomials from https://github.com/JuliaMath/Polynomials.jl.git
  Installed Polynomials ───────────────── v0.8.0
    Cloning [5ae59095-9a9b-59fe-a467-6f913c188581] Colors from https://github.com/JuliaGraphics/Colors.jl.git
  Installed Colors ────────────────────── v0.12.3
    Cloning [7200193e-83a8-5a55-b20d-5d36d44a0795] Twiddle from https://github.com/BenJWard/Twiddle.jl.git
  Installed Twiddle ───────────────────── v1.1.2
    Cloning [1cb3b9ac-1ffd-5777-9e6b-a3d42300664d] IndexableBitVectors from https://github.com/BioJulia/IndexableBitVectors.jl.git
  Installed IndexableBitVectors ───────── v1.0.0
    Cloning [ad839575-38b3-5650-b840-f874b8c74a25] Blink from https://github.com/JuliaGizmos/Blink.jl.git
  Installed Blink ─────────────────────── v0.12.3
    Cloning [e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d] BufferedStreams from https://github.com/BioJulia/BufferedStreams.jl.git
  Installed BufferedStreams ───────────── v1.0.0
    Cloning [a03496cd-edff-5a9b-9e67-9cda94a718b5] PlotlyBase from https://github.com/sglyon/PlotlyBase.jl.git
  Installed PlotlyBase ────────────────── v0.3.1
    Cloning [1914dd2f-81c6-5fcd-8719-6d5c9610ff09] MacroTools from https://github.com/MikeInnes/MacroTools.jl.git
  Installed MacroTools ────────────────── v0.5.5
    Cloning [3783bdb8-4a98-5b6b-af9a-565f29a5fe9c] TableTraits from https://github.com/queryverse/TableTraits.jl.git
  Installed TableTraits ───────────────── v1.0.0
    Cloning [510215fc-4207-5dde-b226-833fc4488ee2] Observables from https://github.com/JuliaGizmos/Observables.jl.git
  Installed Observables ───────────────── v0.3.1
    Cloning [d8418881-c3e1-53bb-8760-2df7ec849ed5] Intervals from https://github.com/invenia/Intervals.jl.git
  Installed Intervals ─────────────────── v1.4.2
    Cloning [de31a74c-ac4f-5751-b3fd-e18cd04993ca] FunctionalCollections from https://github.com/JuliaCollections/FunctionalCollections.jl.git
  Installed FunctionalCollections ─────── v0.5.0
    Cloning [cd3eb016-35fb-5094-929b-558a96fad6f3] HTTP from https://github.com/JuliaWeb/HTTP.jl.git
  Installed HTTP ──────────────────────── v0.8.17
    Cloning [ffc61752-8dc7-55ee-8c37-f3e9cdd09e70] Mustache from https://github.com/jverzani/Mustache.jl.git
  Installed Mustache ──────────────────── v1.0.4
    Cloning [324d7699-5711-5eae-9e2f-1d82baa6b597] CategoricalArrays from https://github.com/JuliaData/CategoricalArrays.jl.git
  Installed CategoricalArrays ─────────── v0.8.1
    Cloning [69de0a69-1ddd-5017-9359-2bf0b02dc9f0] Parsers from https://github.com/JuliaData/Parsers.jl.git
  Installed Parsers ───────────────────── v1.0.10
    Cloning [a975b10e-0019-58db-a62f-e48ff68538c9] Mux from https://github.com/JuliaWeb/Mux.jl.git
  Installed Mux ───────────────────────── v0.7.0
    Cloning [37cfa864-2cd6-5c12-ad9e-b6597d696c81] BioCore from https://github.com/BioJulia/BioCore.jl.git
  Installed BioCore ───────────────────── v2.0.5
    Cloning [82899510-4779-5014-852e-03e436cf321d] IteratorInterfaceExtensions from https://github.com/queryverse/IteratorInterfaceExtensions.jl.git
  Installed IteratorInterfaceExtensions ─ v1.0.0
    Cloning [02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a] XML2_jll from https://github.com/JuliaBinaryWrappers/XML2_jll.jl.git
  Installed XML2_jll ──────────────────── v2.9.10+1
    Cloning [47be7bcc-f1a6-5447-8b36-7eeeff7534fd] ORCA from https://github.com/sglyon/ORCA.jl.git
  Installed ORCA ──────────────────────── v0.4.0
    Cloning [9bc6ac9d-e6b2-5f70-b0a8-242a01662520] GeneticVariation from https://github.com/BioJulia/GeneticVariation.jl.git
  Installed GeneticVariation ──────────── v0.4.0
    Cloning [739be429-bea8-5141-9913-cc70e7f3736d] MbedTLS from https://github.com/JuliaLang/MbedTLS.jl.git
  Installed MbedTLS ───────────────────── v1.0.2
    Cloning [50d2b5c4-7a5e-59d5-8109-a42b560f39c0] Lazy from https://github.com/MikeInnes/Lazy.jl.git
  Installed Lazy ──────────────────────── v0.15.1
    Cloning [e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28] Missings from https://github.com/JuliaData/Missings.jl.git
  Installed Missings ──────────────────── v0.4.3
    Cloning [f269a46b-ccf7-5d73-abea-4c690281aa53] TimeZones from https://github.com/JuliaTime/TimeZones.jl.git
  Installed TimeZones ─────────────────── v1.3.2
    Cloning [0f1e0344-ec1d-5b48-a673-e5cf874b6c29] WebIO from https://github.com/JuliaGizmos/WebIO.jl.git
  Installed WebIO ─────────────────────── v0.8.14
    Cloning [104b5d7c-a370-577a-8038-80a2059c5097] WebSockets from https://github.com/JuliaWeb/WebSockets.jl.git
  Installed WebSockets ────────────────── v1.5.2
    Cloning [b718987f-49a8-5099-9789-dcd902bef87d] TextWrap from https://github.com/carlobaldassi/TextWrap.jl.git
  Installed TextWrap ──────────────────── v1.0.1
    Cloning [cc8bc4a8-27d6-5769-a93b-9d913e69aa62] Widgets from https://github.com/piever/Widgets.jl.git
  Installed Widgets ───────────────────── v0.6.2
    Cloning [9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a] DataAPI from https://github.com/JuliaData/DataAPI.jl.git
  Installed DataAPI ───────────────────── v1.3.0
    Cloning [2dfb63ee-cc39-5dd5-95bd-886bf059d720] PooledArrays from https://github.com/JuliaData/PooledArrays.jl.git
  Installed PooledArrays ──────────────── v0.5.3
    Cloning [83e8ac13-25f8-5344-8a64-a9f2b223428f] IniFile from https://github.com/JuliaIO/IniFile.jl.git
  Installed IniFile ───────────────────── v0.5.0
    Cloning [9fb69e20-1954-56bb-a84f-559cc56a8ff7] Hiccup from https://github.com/JunoLab/Hiccup.jl.git
  Installed Hiccup ────────────────────── v0.2.2
    Cloning [ddb6d928-2868-570f-bddf-ab3f9cf99eb6] YAML from https://github.com/JuliaData/YAML.jl.git
  Installed YAML ──────────────────────── v0.4.0
    Cloning [3da002f7-5984-5a60-b8a6-cbb66c0b333f] ColorTypes from https://github.com/JuliaGraphics/ColorTypes.jl.git
  Installed ColorTypes ────────────────── v0.10.8
    Cloning [3bb67fe8-82b1-5028-8e26-92a6c54297fa] TranscodingStreams from https://github.com/bicycle1885/TranscodingStreams.jl.git
  Installed TranscodingStreams ────────── v0.9.5
    Cloning [a93c6f00-e57d-5684-b7b6-d8193f3e46c0] DataFrames from https://github.com/JuliaData/DataFrames.jl.git
  Installed DataFrames ────────────────── v0.21.6
    Cloning [bac558e1-5e72-5ebc-8fee-abe8a469f55d] OrderedCollections from https://github.com/JuliaCollections/OrderedCollections.jl.git
  Installed OrderedCollections ────────── v1.3.0
    Cloning [78c3b35d-d492-501b-9361-3d52fe80e533] Mocking from https://github.com/invenia/Mocking.jl.git
  Installed Mocking ───────────────────── v0.7.1
    Cloning [fa939f87-e72e-5be4-a000-7fc836dbe307] Pidfile from https://github.com/vtjnash/Pidfile.jl.git
  Installed Pidfile ───────────────────── v1.2.0
    Cloning [b964fa9f-0449-5b57-a5c2-d3ea65f4040f] LaTeXStrings from https://github.com/stevengj/LaTeXStrings.jl.git
  Installed LaTeXStrings ──────────────── v1.1.0
    Cloning [34da2185-b29b-5c13-b0c7-acf172513d20] Compat from https://github.com/JuliaLang/Compat.jl.git
  Installed Compat ────────────────────── v3.13.0
    Cloning [ae029012-a4dd-5104-9daa-d747884805df] Requires from https://github.com/MikeInnes/Requires.jl.git
  Installed Requires ──────────────────── v1.0.1
Downloading artifact: MbedTLS
curl: (60) Cert verify failed: BADCERT_NOT_TRUSTED
More details here: https://curl.haxx.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
Downloading artifact: MbedTLS
curl: (60) Cert verify failed: BADCERT_NOT_TRUSTED
More details here: https://curl.haxx.se/docs/sslcerts.html

curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
ERROR: Unable to automatically install 'MbedTLS' from '/home/silviav/.julia/packages/MbedTLS_jll/txOzO/Artifacts.toml'
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] ensure_artifact_installed(::String, ::Dict{String,Any}, ::String; platform::Pkg.BinaryPlatforms.Platform, verbose::Bool, quiet_download::Bool) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/Artifacts.jl:898
 [3] ensure_all_artifacts_installed(::String; platform::Pkg.BinaryPlatforms.Platform, pkg_uuid::Nothing, include_lazy::Bool, verbose::Bool, quiet_download::Bool) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/Artifacts.jl:962
 [4] download_artifacts(::Pkg.Types.Context, ::Array{String,1}; platform::Pkg.BinaryPlatforms.Linux, verbose::Bool) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:656
 [5] download_artifacts(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; platform::Pkg.BinaryPlatforms.Linux, verbose::Bool) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:635
 [6] add(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}, ::Array{Base.UUID,1}; preserve::Pkg.Types.PreserveLevel, platform::Pkg.BinaryPlatforms.Linux) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/Operations.jl:1134
 [7] add(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}; preserve::Pkg.Types.PreserveLevel, platform::Pkg.BinaryPlatforms.Linux, kwargs::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:189
 [8] add(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:140
 [9] #add#21 at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:67 [inlined]
 [10] add(::Array{Pkg.Types.PackageSpec,1}) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/API.jl:67
 [11] do_cmd!(::Pkg.REPLMode.Command, ::REPL.LineEditREPL) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/REPLMode/REPLMode.jl:404
 [12] do_cmd(::REPL.LineEditREPL, ::String; do_rethrow::Bool) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/REPLMode/REPLMode.jl:382
 [13] do_cmd at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/REPLMode/REPLMode.jl:377 [inlined]
 [14] (::Pkg.REPLMode.var"#24#27"{REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/Pkg/src/REPLMode/REPLMode.jl:546
 [15] #invokelatest#1 at ./essentials.jl:710 [inlined]
 [16] invokelatest at ./essentials.jl:709 [inlined]
 [17] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/REPL/src/LineEdit.jl:2355
 [18] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /home/silviav/julia/usr/share/julia/stdlib/v1.5/REPL/src/REPL.jl:1143
 [19] (::REPL.var"#38#42"{REPL.LineEditREPL,REPL.REPLBackendRef})() at ./task.jl:356

(@v1.5) pkg>

Hoping you could help me out. Thank you in advance

gtollefson commented 3 years ago

Hi @Caro-Ca , I apologize for my late response. Our research focus was not on software development over the summer and I missed this message. This error looks to be an issue with Julia Pkg.jl. I would open an issue here