Cannot install a BioJulia package, GenomeGraphs.jl

New to Julia
,
1

cannot install the package. my Julia version is Version 1.6.3 (2021-09-23).
Errors as below:

(@v1.6) pkg> add GenomeGraphs
   Resolving package versions...
ERROR: Unsatisfiable requirements detected for package BioSequences [7e6ae17a]:
 BioSequences [7e6ae17a] log:
 ├─possible versions are: 1.0.0-2.0.5 or uninstalled
 ├─restricted to versions * by an explicit requirement, leaving only versions 1.0.0-2.0.5
 ├─restricted by compatibility requirements with FASTX [c2308a5c] to versions: 1.1.0-2.0.5
 │ └─FASTX [c2308a5c] log:
 │   ├─possible versions are: 1.0.0-1.2.0 or uninstalled
 │   ├─restricted to versions * by an explicit requirement, leaving only versions 1.0.0-1.2.0
 │   └─restricted by compatibility requirements with GenomeGraphs [3aa97884] to versions: 1.1.0-1.2.0
 │     └─GenomeGraphs [3aa97884] log:
 │       ├─possible versions are: 0.1.0-0.2.0 or uninstalled
 │       └─restricted to versions * by an explicit requirement, leaving only versions 0.1.0-0.2.0
 ├─restricted by compatibility requirements with GenomeGraphs [3aa97884] to versions: 2.0.0-2.0.5
 │ └─GenomeGraphs [3aa97884] log: see above
 └─restricted by compatibility requirements with GeneticVariation [9bc6ac9d] to versions: 1.0.0-1.1.0 — no versions left
   └─GeneticVariation [9bc6ac9d] log:
     ├─possible versions are: 0.4.0 or uninstalled
     └─restricted to versions * by VariantVisualization [7f8bf45c], leaving only versions 0.4.0
       └─VariantVisualization [7f8bf45c] log:
         ├─possible versions are: 0.4.1 or uninstalled
         └─VariantVisualization [7f8bf45c] is fixed to version 0.4.1

(@v1.6) pkg>

Thank you!

2

It works now after activated a localised environment, as below:

 ] activate /path/to/your/project

Dose it mean I must activate the env every time before using GenomeGraphs?

BYW, there is no problem at all when install the package in Jupyter Notebook.

3

This is due to having packages in your default environment which has incompatible requirements with the package you are trying to add (GenomeGraphs). You can look at the section in the Pkg docs which explain why this occurs and possible resolutions.

Also it is always better to install packages into different environments instead of the default one, based on the project. You should be able to find discussions in different posts about this.

2 Likes
4

The reply below is from Ben J.Ward, the developer of GenomeGraphs (BioSequences) and it’s very helpful. Thanks Ben!

“Hi GenomeGraphs is very much in a development state, and I would not recommend using it for production or projects yet. You are correct some of the functionality is different to that documented. It really needs an update once v3 of BioSequences is released, along with the kmer tools.”