BioJulia/BioSequences.jl

LongDNA, LongRNA "not defined"

fpmenninger opened this issue · 5 comments

fpmenninger commented

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Expected Behavior

julia> LongDNA{2}("TTAGC")
5nt DNA Sequence:
TTAGC

julia> LongRNA{2}("UUAGC")
5nt RNA Sequence:
UUAGC

Current Behavior

julia> LongDNA{2}("TTAGC")
ERROR: UndefVarError: LongDNA not defined
Stacktrace:
[1] top-level scope
@ REPL[20]:1

julia> LongRNA{2}("UUAGC")
ERROR: UndefVarError: LongRNA not defined
Stacktrace:
[1] top-level scope
@ REPL[21]:1

Possible Solution / Implementation

Steps to Reproduce (for bugs)

Context

Your Environment

  • Package Version used:
  • Julia Version used: 1.7.1
  • Operating System and version (desktop or mobile): Windows 10
  • Link to your project:
TransGirlCodes commented

I'm not able to replicate this behaviour for julia 1.6 and BioSequences v3.

             _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.2 (2021-07-14)
 _/ |\__'_|_|_|\__'_|  |  
|__/                   |

(@v1.6) pkg> add BioSequences
    Updating registry at `~/.julia/registries/General`
   Resolving package versions...
    Updating `~/.julia/environments/v1.6/Project.toml`
  [7e6ae17a] + BioSequences v3.0.0
    Updating `~/.julia/environments/v1.6/Manifest.toml`
  [7e6ae17a] + BioSequences v3.0.0
  [3c28c6f8] + BioSymbols v5.1.0
  [7200193e] + Twiddle v1.1.2

julia> using BioSequences

julia> LongDNA{2}("ATCG")
4nt DNA Sequence:
ATCG

julia> LongRNA{2}("AUCG")
4nt RNA Sequence:
AUCG
TransGirlCodes commented

Can you do a Pkg.status() to see which version of BioSequences you are on?

fpmenninger commented

after a package update...

(@v1.7) pkg> status
[7e6ae17a] BioSequences v2.0.5

TransGirlCodes commented

Ok so LongDNA and LongRNA are the type aliases used in v3 of BioSequences onwards, so you'll need to do

(@v1.7) pkg> up to make sure it's set to v3.

fpmenninger commented

Thank you for the help.
I see the issue isn't with BioSequences.
Instead, I have to figure out why the package won't upgrade...
Ah. Found (and deleted) a folder in .julia/registries: BioJuliaRegistry
which had a readme stating
The BioJulia Registry has been depreceated and merged into the JuliaRegistries/General registry.
... later edit ...
a more likely cause
had PhyloPlots and PhyloNetworks installed - both required BioSequences 2.0.5 as of 09Jan2022