Pkg on Julia 0.3.12

Laura_Maria_Eslava · August 8, 2024, 9:04pm

Hey, I need to use Julia package Phylonetworks, it says it’s supported for Julia versions 0.3.X and not tested on 0.4 or above, thus why I need to use the ANCIENT version (I know it’s not ideal but the package won’t install on the newer version either for some reason), this is the error I get:

Pkg.clone (“Phylonetworks”)
INFO: Initializing package repository C:\Users\lmari.julia\v0.3
INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl
fatal: unable to connect to github.com:
github.com[0: 20.201.28.151]: errno=No such file or directory

ERROR: failed process: Process(git clone -q -b metadata-v2 git://github.com/JuliaLang/METADATA.jl METADATA, ProcessExited(128)) [128]
** in error at error.jl:22 (repeats 2 times)**

I figured out the error is likely because it’s trying to clone METADATA from git with the git:// but that one no longer works (I believe it was taken down and now works with https:// or ssh:// only) is there any way to change that so it downloads METADATA from the correct source and can proceed to download the Phylonetworks package?

I saw there is also a way to download everything into my pc so it doesn’t have to connect with github but I’m new to Julia so I don’t know how to do that

Please please help

sefffal · August 8, 2024, 9:15pm

Could you possibly use a newer version of the package? ~~It appears to support up to Julia 1.7:~~

giordano · August 9, 2024, 9:41am

If you’re referring to

github.com

JuliaPhylo/PhyloNetworks.jl/blob/e27d4c86784aa356567d82036e2d42889d2a7138/Project.toml#L45


      
          DataStructures = "0.9, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18"
          Distributions = "0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
          FASTX = "1.1, 2"
          Functors = "0.2, 0.3, 0.4"
          GLM = "1.1, 1.2, 1.3, 1.4"
          NLopt = "0.5.1, 0.6, 1"
          StaticArrays = "0.8.3, 0.9, 0.10, 0.11, 0.12, 1.0"
          StatsBase = "0.26, 0.27, 0.28, 0.29, 0.30, 0.31, 0.32, 0.33, 0.34"
          StatsFuns = "0.7, 0.8, 0.9, 1"
          StatsModels = "0.6, 0.7"
          julia = "1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7"
          
          [extras]
          Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
          
          [targets]
          test = ["Test"]

that effectively means “any version in the 1.x series, from 1.1 on”, and is equivalent to just "1.1".

tim.holy · August 9, 2024, 10:04am

Welcome to Julia! Since you are new, just to make it clear, this should be all you need to do:

launch julia
hit ] to enter pkg> mode
type add PhyloNetworks

Done. I tested and this works on the current Julia release.

While this is simple, it’s often better to do this for a specific project environment. To learn about this and other good practices, a good resource is https://modernjuliaworkflows.org/