failed to Activate package environment (Rmath)

[XiaoyuZeng]

Hi,
Thanks for your time and effort to develop this package.

Problem

I'm new to this package, and faced with an environment setting problem.
After running jlmerclusterperm_setup(), I encountered an error:

Starting Julia with 7 threads [3.2s]
┌ Warning: could not download https://pkg.julialang.org/registries
│ exception = Downloads.RequestError("https://pkg.julialang.org/registries", 28, "Failed to connect to cn-northeast.pkg.juliacn.com port 443 after 21047 ms: Timed out", Downloads.Response("https", "https://cn-northeast.pkg.juliacn.com/registries", 301, "HTTP/1.1 301 CN northeast internal redirect trigger", ["connection" => "close", "content-length" => "0", "server" => "Varnish", "retry-after" => "0", "location" => "https://cn-northeast.pkg.juliacn.com/registries", "x-geo-continent" => "AS", "x-geo-country" => "CN", "x-geo-region" => "BJ", "accept-ranges" => "bytes", "date" => "Fri, 14 Jul 2023 04:20:32 GMT", "via" => "1.1 varnish", "x-served-by" => "cache-tyo11976-TYO", "x-cache" => "HIT", "x-cache-hits" => "0", "x-timer" => "S1689308433.892732,VS0,VE1"]))
└ @ Pkg.Registry C:\Users\xiaoy\AppData\Local\Programs\JULIA-~1.2\share\julia\stdlib\v1.9\Pkg\src\Registry\Registry.jl:69
Updating registry at C:\Users\xiaoy\.julia\registries\General
Updating git-repo https://github.com/JuliaRegistries/General.git
┌ Error: Some registries failed to update:
│ — C:\Users\xiaoy.julia\registries\General — failed to fetch from repo: failed to fetch from https://github.com/JuliaRegistries/General.git, error: GitError(Code:ERROR, Class:OS, failed to send request: 操作超时
│ )
└ @ Pkg.Registry C:\Users\xiaoy\AppData\Local\Programs\JULIA-~1.2\share\julia\stdlib\v1.9\Pkg\src\Registry\Registry.jl:510
┌ Warning: could not download https://pkg.julialang.org/registries
│ exception = Downloads.RequestError("https://pkg.julialang.org/registries", 28, "Failed to connect to cn-northeast.pkg.juliacn.com port 443 after 21039 ms: Timed out", Downloads.Response("https", "https://cn-northeast.pkg.juliacn.com/registries", 301, "HTTP/1.1 301 CN northeast internal redirect trigger", ["connection" => "close", "content-length" => "0", "server" => "Varnish", "retry-after" => "0", "location" => "https://cn-northeast.pkg.juliacn.com/registries", "x-geo-continent" => "AS", "x-geo-country" => "CN", "x-geo-region" => "BJ", "accept-ranges" => "bytes", "date" => "Fri, 14 Jul 2023 04:22:35 GMT", "via" => "1.1 varnish", "x-served-by" => "cache-tyo11971-TYO", "x-cache" => "HIT", "x-cache-hits" => "0", "x-timer" => "S1689308556.662519,VS0,VE0"]))
└ @ Pkg.Registry C:\Users\xiaoy\AppData\Local\Programs\JULIA-~1.2\share\julia\stdlib\v1.9\Pkg\src\Registry\Registry.jl:69
Installed DiffRules ─────────────── v1.15.1
Installed Adapt ─────────────────── v3.6.2
Installed MatrixFactorizations ──── v2.0.0
Installed HypergeometricFunctions ─ v0.3.20
Installed BandedMatrices ────────── v0.17.30
Installed MutableArithmetics ────── v1.3.0
Installed Suppressor ────────────── v0.2.4
Installed Preferences ───────────── v1.4.0
Installed JSON3 ─────────────────── v1.13.1
Installed Arrow ─────────────────── v2.6.2
Installed Mocking ───────────────── v0.7.7
Installed FastGaussQuadrature ───── v0.5.1
Installed IfElse ────────────────── v0.1.1
Installed SentinelArrays ────────── v1.4.0
Installed Parsers ───────────────── v2.7.1
Installed SpecialFunctions ──────── v2.3.0
Installed ArrowTypes ────────────── v2.2.2
Installed TimeZones ─────────────── v1.10.0
Installed RecipesBase ───────────── v1.3.4
Installed BSplineKit ────────────── v0.16.2
Installed ConcurrentUtilities ───── v2.2.1
Installed StaticArraysCore ──────── v1.4.1
Installed StaticArrays ──────────── v1.6.1
Installed PrecompileTools ───────── v1.1.2
Installed EnumX ─────────────────── v1.0.4
Installed PrettyTables ──────────── v2.2.5
Installed Random123 ─────────────── v1.6.1
Installed TranscodingStreams ────── v0.9.13
Installed FillArrays ────────────── v1.4.0
Installed BitIntegers ───────────── v0.3.0
Installed StatsModels ───────────── v0.7.2
Installed MixedModels ───────────── v4.15.0
Installed LazyArrays ────────────── v1.2.2
Installed DataFrames ────────────── v1.6.0
Installed GLM ───────────────────── v1.8.3
Installed DataStructures ────────── v0.18.14
Installed Static ────────────────── v0.8.7
Installed LogExpFunctions ───────── v0.3.24
Installed CodecZlib ─────────────── v0.7.2
Installed Compat ────────────────── v4.7.0
Installed SortingAlgorithms ─────── v1.1.1
Installed ArrayLayouts ──────────── v1.0.11
Installed Distributions ─────────── v0.25.98
Installed MathOptInterface ──────── v1.18.0
Error: Evaluation in Julia failed.
Original Julia error message:
LoadError: Unable to automatically download/install artifact 'Rmath' from sources listed in 'C:\Users\xiaoy.julia\packages\Rmath_jll\JeAlY\Artifacts.toml'.
Sources attempted:

• https://pkg.julialang.org/artifact/abc0091a4956da8c501a50e1b1eba2735299c04e
  Error: RequestError: HTTP/1.1 301 CN northeast internal redirect trigger (Failed to connect to cn-northeast.pkg.juliacn.com port 443 after 21057 ms: Timed out) while requesting https://pkg.julialang.org/artifact/abc0091a4956da8c501a50e1b1eba2735299c04e
• https://github.com/JuliaBinaryWrappers/Rmath_jll.jl/releases/download/Rmath-v0.4.0+0/Rmath.v0.4.0.x86_64-w64-mingw32.tar.gz
  Error: RequestError: Failed to connect to github.com port 443 after 21026 ms: Timed out while requesting https://github.com/JuliaBinaryWrappers/Rmath_jll.jl/releases/download/Rmath-v0.4.0+0/Rmath.v0.4.0.x86_64-w64-mingw32.tar.gz

Stacktrace:
[1] error(s::String)
@ Base .\error.jl:35
[2
✖ Activating package environment [8m 7s]

Attempts

I've tried:

• reboot
• re-installed Julia
• re-installed jlmerclusterperm
  but none of these attempts worked to install Rmath
  is it just a network problem?
  Any ideas to solve this problem?

[XiaoyuZeng]

I reset my network connection, it seems the problem has been solved~

Show in New Window
Warning: : ... may be used in an incorrect context: ‘.fun(piece, ...)’
Warning: : ... may be used in an incorrect context: ‘.fun(piece, ...)’
Saving 9.55 x 7.2 in image
Show in New Window
✔ Starting Julia with 7 threads [3.3s]
┌ Warning: could not download https://pkg.julialang.org/registries
│ exception = Downloads.RequestError("https://pkg.julialang.org/registries", 28, "Failed to connect to cn-northeast.pkg.juliacn.com port 443 after 21049 ms: Timed out", Downloads.Response("https", "https://cn-northeast.pkg.juliacn.com/registries", 301, "HTTP/1.1 301 CN northeast internal redirect trigger", ["connection" => "close", "content-length" => "0", "server" => "Varnish", "retry-after" => "0", "location" => "https://cn-northeast.pkg.juliacn.com/registries", "x-geo-continent" => "AS", "x-geo-country" => "CN", "x-geo-region" => "BJ", "accept-ranges" => "bytes", "date" => "Fri, 14 Jul 2023 04:45:36 GMT", "via" => "1.1 varnish", "x-served-by" => "cache-nrt-rjtf7700028-NRT", "x-cache" => "HIT", "x-cache-hits" => "0", "x-timer" => "S1689309936.076401,VS0,VE0"]))
└ @ Pkg.Registry C:\Users\xiaoy.julia\juliaup\julia-1.9.2+0.x64.w64.mingw32\share\julia\stdlib\v1.9\Pkg\src\Registry\Registry.jl:69
Updating registry at C:\Users\xiaoy\.julia\registries\General
Updating git-repo https://github.com/JuliaRegistries/General.git
Updating D:\Program Files\R\R-4.3.1\library\jlmerclusterperm\julia\Project.toml
[a93c6f00] + DataFrames v1.6.0
[38e38edf] + GLM v1.8.3
[ff71e718] + MixedModels v4.15.0
[92933f4c] + ProgressMeter v1.7.2
[74087812] + Random123 v1.6.1
⌃ [2913bbd2] + StatsBase v0.33.21
[3eaba693] + StatsModels v0.7.2
[fd094767] + Suppressor v0.2.4
Updating D:\Program Files\R\R-4.3.1\library\jlmerclusterperm\julia\Manifest.toml
[79e6a3ab] + Adapt v3.6.2
[4c555306] + ArrayLayouts v1.0.11
[69666777] + Arrow v2.6.2
[31f734f8] + ArrowTypes v2.2.2
[093aae92] + BSplineKit v0.16.2
[aae01518] + BandedMatrices v0.17.30
[6e4b80f9] + BenchmarkTools v1.3.2
[c3b6d118] + BitIntegers v0.3.0
[fa961155] + CEnum v0.4.2
[49dc2e85] + Calculus v0.5.1
[523fee87] + CodecBzip2 v0.7.2
[5ba52731] + CodecLz4 v0.4.0
[944b1d66] + CodecZlib v0.7.2
[6b39b394] + CodecZstd v0.7.2
[bbf7d656] + CommonSubexpressions v0.3.0
[34da2185] + Compat v4.7.0
[f0e56b4a] + ConcurrentUtilities v2.2.1
[a8cc5b0e] + Crayons v4.1.1
[9a962f9c] + DataAPI v1.15.0
[a93c6f00] + DataFrames v1.6.0
[864edb3b] + DataStructures v0.18.14
[e2d170a0] + DataValueInterfaces v1.0.0
[85a47980] + Dictionaries v0.3.25
[163ba53b] + DiffResults v1.1.0
[b552c78f] + DiffRules v1.15.1
[31c24e10] + Distributions v0.25.98
[ffbed154] + DocStringExtensions v0.9.3
[fa6b7ba4] + DualNumbers v0.6.8
[4e289a0a] + EnumX v1.0.4
[e2ba6199] + ExprTools v0.1.9
[442a2c76] + FastGaussQuadrature v0.5.1
[1a297f60] + FillArrays v1.4.0
[59287772] + Formatting v0.4.2
[f6369f11] + ForwardDiff v0.10.35
[38e38edf] + GLM v1.8.3
[34004b35] + HypergeometricFunctions v0.3.20
[615f187c] + IfElse v0.1.1
[313cdc1a] + Indexing v1.1.1
[842dd82b] + InlineStrings v1.4.0
[41ab1584] + InvertedIndices v1.3.0
[92d709cd] + IrrationalConstants v0.2.2
[82899510] + IteratorInterfaceExtensions v1.0.0
[692b3bcd] + JLLWrappers v1.4.1
[682c06a0] + JSON v0.21.4
[0f8b85d8] + JSON3 v1.13.1
[b964fa9f] + LaTeXStrings v1.3.0
[5078a376] + LazyArrays v1.2.2
[2ab3a3ac] + LogExpFunctions v0.3.24
[e6f89c97] + LoggingExtras v1.0.0
[1914dd2f] + MacroTools v0.5.10
[b8f27783] + MathOptInterface v1.18.0
[fdba3010] + MathProgBase v0.7.8
[a3b82374] + MatrixFactorizations v2.0.0
[e1d29d7a] + Missings v1.1.0
[ff71e718] + MixedModels v4.15.0
[78c3b35d] + Mocking v0.7.7
[d8a4904e] + MutableArithmetics v1.3.0
[76087f3c] + NLopt v0.6.5
[77ba4419] + NaNMath v1.0.2
[bac558e1] + OrderedCollections v1.6.0
[90014a1f] + PDMats v0.11.17
[69de0a69] + Parsers v2.7.1
[2dfb63ee] + PooledArrays v1.4.2
[aea7be01] + PrecompileTools v1.1.2
[21216c6a] + Preferences v1.4.0
[08abe8d2] + PrettyTables v2.2.5
[92933f4c] + ProgressMeter v1.7.2
[1fd47b50] + QuadGK v2.8.2
[74087812] + Random123 v1.6.1
[e6cf234a] + RandomNumbers v1.5.3
[3cdcf5f2] + RecipesBase v1.3.4
[189a3867] + Reexport v1.2.2
[ae029012] + Requires v1.3.0
[79098fc4] + Rmath v0.7.1
[6c6a2e73] + Scratch v1.2.0
[91c51154] + SentinelArrays v1.4.0
[1277b4bf] + ShiftedArrays v2.0.0
[a2af1166] + SortingAlgorithms v1.1.1
[276daf66] + SpecialFunctions v2.3.0
[03a91e81] + SplitApplyCombine v1.2.2
[aedffcd0] + Static v0.8.7
[90137ffa] + StaticArrays v1.6.1
[1e83bf80] + StaticArraysCore v1.4.1
[82ae8749] + StatsAPI v1.6.0
⌃ [2913bbd2] + StatsBase v0.33.21
[4c63d2b9] + StatsFuns v1.3.0
[3eaba693] + StatsModels v0.7.2
[892a3eda] + StringManipulation v0.3.0
[856f2bd8] + StructTypes v1.10.0
[fd094767] + Suppressor v0.2.4
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.10.1
[f269a46b] + TimeZones v1.10.0
[3bb67fe8] + TranscodingStreams v0.9.13
[9d95f2ec] + TypedTables v1.4.3
[6e34b625] + Bzip2_jll v1.0.8+0
[5ced341a] + Lz4_jll v1.9.3+0
[079eb43e] + NLopt_jll v2.7.1+0
[efe28fd5] + OpenSpecFun_jll v0.5.5+0
[f50d1b31] + Rmath_jll v0.4.0+0
[3161d3a3] + Zstd_jll v1.5.5+0
[0dad84c5] + ArgTools v1.1.1
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8ba89e20] + Distributed
[f43a241f] + Downloads v1.6.0
[7b1f6079] + FileWatching
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL v0.6.3
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions v1.2.0
[44cfe95a] + Pkg v1.9.2
[de0858da] + Printf
[9abbd945] + Profile
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics v1.9.0
[4607b0f0] + SuiteSparse
[fa267f1f] + TOML v1.0.3
[a4e569a6] + Tar v1.10.0
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll v1.0.5+0
[deac9b47] + LibCURL_jll v7.84.0+0
[29816b5a] + LibSSH2_jll v1.10.2+0
[c8ffd9c3] + MbedTLS_jll v2.28.2+0
[14a3606d] + MozillaCACerts_jll v2022.10.11
[4536629a] + OpenBLAS_jll v0.3.21+4
[05823500] + OpenLibm_jll v0.8.1+0
[bea87d4a] + SuiteSparse_jll v5.10.1+6
[83775a58] + Zlib_jll v1.2.13+0
[8e850b90] + libblastrampoline_jll v5.8.0+0
[8e850ede] + nghttp2_jll v1.48.0+0
[3f19e933] + p7zip_jll v17.4.0+0
Info Packages marked with ⌃ have new versions available and may be upgradable.
Precompiling project...
✓ Suppressor
✓ Compat
✓ Calculus
✓ MathProgBase
✓ EnumX
✓ LaTeXStrings
✓ StructTypes
✓ Requires
✓ InvertedIndices
✓ ArrowTypes
✓ Reexport
✓ SentinelArrays
✓ DocStringExtensions
✓ ExprTools
✓ IfElse
✓ StatsAPI
✓ CompilerSupportLibraries_jll
✓ BitIntegers
✓ IrrationalConstants
✓ ProgressMeter
✓ Scratch
✓ LoggingExtras
✓ Indexing
✓ Crayons
✓ Formatting
✓ CEnum
✓ StaticArraysCore
✓ ConcurrentUtilities
✓ TranscodingStreams
✓ MacroTools
✓ Preferences
✓ ShiftedArrays
✓ StringManipulation
✓ NaNMath
✓ PDMats
✓ Missings
✓ PooledArrays
✓ FillArrays
✓ Compat → CompatLinearAlgebraExt
✓ Adapt
✓ Static
✓ RandomNumbers
✓ LogExpFunctions
✓ DiffResults
✓ Dictionaries
✓ CodecZlib
✓ CommonSubexpressions
✓ PrecompileTools
✓ JLLWrappers
✓ MutableArithmetics
✓ Mocking
✓ DataStructures
✓ Random123
✓ SplitApplyCombine
✓ ArrayLayouts
✓ RecipesBase
✓ Rmath_jll
✓ StaticArrays
✓ NLopt_jll
✓ Zstd_jll
✓ Bzip2_jll
✓ Lz4_jll
✓ SortingAlgorithms
✓ OpenSpecFun_jll
✓ QuadGK
✓ TypedTables
✓ MatrixFactorizations
✓ Rmath
✓ StaticArrays → StaticArraysStatisticsExt
✓ Adapt → AdaptStaticArraysExt
✓ CodecBzip2
✓ CodecZstd
✓ PrettyTables
✓ CodecLz4
✓ StatsBase
✓ SpecialFunctions
✓ LazyArrays
✓ DualNumbers
✓ DiffRules
✓ FastGaussQuadrature
✓ HypergeometricFunctions
✓ StatsFuns
✓ ForwardDiff
✓ StatsModels
✓ ForwardDiff → ForwardDiffStaticArraysExt
✓ Distributions
✓ Parsers
✓ InlineStrings
✓ GLM
✓ JSON
✓ BenchmarkTools
✓ TimeZones
✓ Arrow
✓ JSON3
✓ BandedMatrices
✓ BSplineKit
✓ DataFrames
✓ MathOptInterface
✓ NLopt
✓ MixedModels
100 dependencies successfully precompiled in 283 seconds. 13 already precompiled.
1 dependency had warnings during precompilation:
┌ MixedModels [ff71e718-51f3-5ec2-a782-8ffcbfa3c316]
│ Downloading artifact: TestData
│ Downloading artifact: TestData
└
✔ Activating package environment [11m 16.6s]
✔ Running package setup scripts (15/15) [11.4s]

[yjunechoe]

Thanks for the report! Glad to hear that it was just a network issue (that's also what I suspected from the error messages).