biosequences - julia 1.0

New to Julia
1

Hi,
I am new to Julia and using v1.0.0. I am trying to install BioSequences and Pkg.add went fine. But while using it it throws an error. Is there something I am missing here?

> using BioSequences
julia> using BioSequences
[ Info: Precompiling BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59]
ERROR: LoadError: syntax: extra token "BioCore" after end of expression
Stacktrace:
 [1] include at ./boot.jl:317 [inlined]
 [2] include_relative(::Module, ::String) at ./loading.jl:1038
 [3] include(::Module, ::String) at ./sysimg.jl:29
 [4] top-level scope at none:2
 [5] eval at ./boot.jl:319 [inlined]
 [6] eval(::Expr) at ./client.jl:389
 [7] top-level scope at ./none:3
in expression starting at /nfs/users/nfs_v/vm11/.julia/packages/BioSequences/rJ5AR/src/BioSequences.jl:188
ERROR: Failed to precompile BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] to /nfs/users/nfs_v/vm11/.julia/compiled/v1.0/BioSequences/i7zyu.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] macro expansion at ./logging.jl:313 [inlined]
 [3] compilecache(::Base.PkgId, ::String) at ./loading.jl:1184
 [4] _require(::Base.PkgId) at ./logging.jl:311
 [5] require(::Base.PkgId) at ./loading.jl:852
 [6] macro expansion at ./logging.jl:311 [inlined]
 [7] require(::Module, ::Symbol) at ./loading.jl:834
2

It should work soonish. But if you want to do some work you should probably use v0.6.4 (or at least v0.7.0) since the package ecosystem hasn’t transitioned yet.

1 Like
3

Great news indeed! Looking forward to the major update. I am using it with Julia v0.6 now.

4

I’m sorry for inconvenience. We have a deep stack of package dependencies, and we need to support Julia 0.7/1.0 one by one from the bottom. Several packages including BioSequences.jl are placed on the top of the stack and hence it takes a little bit more time to fully resolve problems. But, yes, we are working on it now :smile:.

6 Likes
5

It should work now!
https://github.com/BioJulia/BioSequences.jl/releases/tag/v1.0.0

2 Likes
6

Hmmm… I did an update, and I still see this problem, with BioSequences and BioStructures. Is there something else I should be doing?

I’m on Mac with Julia 1.0, my error is:
[ Info: Precompiling BioStructures [de9282ab-8554-53be-b2d6-f6c222edabfc]
ERROR: LoadError: syntax: extra token “BioCore” after end of expression
Stacktrace:
[1] include at ./boot.jl:317 [inlined]
[2] include_relative(::Module, ::String) at ./loading.jl:1038
[3] include(::Module, ::String) at ./sysimg.jl:29
[4] top-level scope at none:2
[5] eval at ./boot.jl:319 [inlined]
[6] eval(::Expr) at ./client.jl:389
[7] top-level scope at ./none:3
in expression starting at /Users/alan/.julia/packages/BioSequences/rJ5AR/src/BioSequences.jl:188

and ]status yields:

(v1.0) pkg> status
Status ~/.julia/environments/v1.0/Project.toml
[7e6ae17a] BioSequences v0.8.3
[de9282ab] BioStructures v0.2.0

7

Okay, my bad, the release was out at that time but not merged into the Julia registry. However, BioSequences.jl v1.0.0 is all registered now so it should work. Apologies for the confusion.

BioStructures.jl will follow (hopefully within a few days), I was waiting on BioSequences.jl. But if you check out the julia-v0.7 branch locally it should work on Julia v0.7, and v1.0 if you checkout Formatting.jl to master.

1 Like
8

Thanks for all your work! Looking forward to it. :slightly_smiling_face:

1 Like
9

BioStructures.jl v0.3.0 is now in the Julia registry so it is just an add away in Julia v0.7/v1.0.

Let me know if you run into any problems or have any suggestions.

1 Like