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BioJulia / Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
http://biojulia.dev
MIT License
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Error loading Bio #495

Closed JokingHero closed 6 years ago

JokingHero commented 6 years ago

Expected Behavior

I expect that using "using Bio" will load the package

Current Behavior

julia> using Bio
[ Info: Precompiling Bio [3637df68-df41-5d16-b00c-95ac8c2142c5]
ERROR: LoadError: LoadError: syntax: extra token "FileFormat" after end of expression
Stacktrace:
 [1] include at ./boot.jl:317 [inlined]
 [2] include_relative(::Module, ::String) at ./loading.jl:1038
 [3] include at ./sysimg.jl:29 [inlined]
 [4] include(::String) at /home/ai/.julia/packages/Bio/te4TB/src/Bio.jl:3
 [5] top-level scope at none:0
 [6] include at ./boot.jl:317 [inlined]
 [7] include_relative(::Module, ::String) at ./loading.jl:1038
 [8] include(::Module, ::String) at ./sysimg.jl:29
 [9] top-level scope at none:2
 [10] eval at ./boot.jl:319 [inlined]
 [11] eval(::Expr) at ./client.jl:389
 [12] top-level scope at ./none:3
in expression starting at /home/ai/.julia/packages/Bio/te4TB/src/IO.jl:16
in expression starting at /home/ai/.julia/packages/Bio/te4TB/src/Bio.jl:5
ERROR: Failed to precompile Bio [3637df68-df41-5d16-b00c-95ac8c2142c5] to /home/ai/.julia/compiled/v1.0/Bio/FLUQr.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] macro expansion at ./logging.jl:311 [inlined]
 [5] _require(::Base.PkgId) at ./loading.jl:941
 [6] require(::Base.PkgId) at ./loading.jl:852
 [7] macro expansion at ./logging.jl:311 [inlined]
 [8] require(::Module, ::Symbol) at ./loading.jl:834
 [9] eval at ./boot.jl:319 [inlined]
 [10] #9 at /home/ai/.julia/packages/Atom/jJn7Y/src/repl.jl:125 [inlined]
julia> using Bio
[ Info: Precompiling Bio [3637df68-df41-5d16-b00c-95ac8c2142c5]
ERROR: LoadError: LoadError: syntax: extra token "FileFormat" after end of expression
Stacktrace:
 [1] include at ./boot.jl:317 [inlined]
 [2] include_relative(::Module, ::String) at ./loading.jl:1038
 [3] include at ./sysimg.jl:29 [inlined]
 [4] include(::String) at /home/ai/.julia/packages/Bio/te4TB/src/Bio.jl:3
 [5] top-level scope at none:0
 [6] include at ./boot.jl:317 [inlined]
 [7] include_relative(::Module, ::String) at ./loading.jl:1038
 [8] include(::Module, ::String) at ./sysimg.jl:29
 [9] top-level scope at none:2
 [10] eval at ./boot.jl:319 [inlined]
 [11] eval(::Expr) at ./client.jl:389
 [12] top-level scope at ./none:3
in expression starting at /home/ai/.julia/packages/Bio/te4TB/src/IO.jl:16
in expression starting at /home/ai/.julia/packages/Bio/te4TB/src/Bio.jl:5
ERROR: Failed to precompile Bio [3637df68-df41-5d16-b00c-95ac8c2142c5] to /home/ai/.julia/compiled/v1.0/Bio/FLUQr.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] macro expansion at ./logging.jl:311 [inlined]
 [5] _require(::Base.PkgId) at ./loading.jl:941
 [6] require(::Base.PkgId) at ./loading.jl:852
 [7] macro expansion at ./logging.jl:311 [inlined]
 [8] require(::Module, ::Symbol) at ./loading.jl:834
 [9] eval at ./boot.jl:319 [inlined]
 [10] #17 at /home/ai/.julia/packages/Atom/jJn7Y/src/repl.jl:125 [inlined]
 [11] with_logstate(::getfield(Main, Symbol("##17#19")), ::Base.CoreLogging.LogState) at ./logging.jl:397
 [12] with_logger(::Function, ::Atom.Progress.JunoProgressLogger) at ./logging.jl:493
 [13] top-level scope at /home/ai/.julia/packages/Atom/jJn7Y/src/repl.jl:124

Context

I just installed julia 1.0.0:

~/Soft/julia-1.0.0/bin/julia --version
julia version 1.0.0

I also installed some packages:

julia> Pkg.status()
    Status `~/.julia/environments/v1.0/Project.toml`
  [c52e3926] Atom v0.7.3
  [67c07d97] Automa v0.7.0
  [28d598bf] BGZFStreams v0.2.0
  [3637df68] Bio v0.4.7
  [54a738f6] BioBridgeR v0.1.1
  [37cfa864] BioCore v2.0.0
  [7e6ae17a] BioSequences v0.8.3
  [a0d4ced5] BioServices v0.2.0
  [de9282ab] BioStructures v0.2.0
  [3c28c6f8] BioSymbols v2.0.1
  [e1450e63] BufferedStreams v1.0.0
  [f92d4219] FMIndexes v0.1.0
  [c91e804a] Gadfly v0.7.0
  [9bc6ac9d] GeneticVariation v0.3.2
  [1cb3b9ac] IndexableBitVectors v0.1.2
  [524e6230] IntervalTrees v0.1.0
  [e5e0dc1b] Juno v0.5.2
  [509eaf56] NaturalSelection v0.2.0
  [875022e3] Phylogenies v0.1.0
  [8365b1bb] SubstitutionModels v0.1.0

Environment

Please let me know what I did wrong, just wanted to try out BioJulia.

kescobo commented 6 years ago

Hi @JokingHero, you didn't do anything wrong, Bio.jl isn't yet ready for julia 1.0. That said, it's an omnibus package that's sort of covers a bunch of other packages many of which are ready or are nearly so (largely thanks to the monumental effort of @BenJWard). Do you have something in particular you'd like to do?

I'm not sure exactly what the time frame on complete 1.0 compatibility is, but if you're really rearing to go, you might try to download julia 0.7 - It's pretty much the same as 1.0, except that there are deprecation warnings for the stuff that's changed, rather than warnings. A lot of packages that aren't quite ready for 1.0 are working there.

JokingHero commented 6 years ago

Ok, I will try 0.7 then, thanks!

TransGirlCodes commented 6 years ago

Hi @JokingHero

The timeline for Julia 1.0 support should be by next weekend at the most. But most stuff will work on 0.7, it will throw warnings about deprecations, which are annoying and slow things down a bit, but are still functional.

On 13 Aug 2018, at 02:39, Kevin Bonham notifications@github.com wrote:

Hi @JokingHero https://github.com/JokingHero, you didn't do anything wrong, Bio.jl isn't yet ready for julia 1.0. That said, it's an omnibus package that's sort of covers a bunch of other packages many of which are ready or are nearly so (largely thanks to the monumental effort of @BenJWard https://github.com/BenJWard). Do you have something in particular you'd like to do?

I'm not sure exactly what the time frame on complete 1.0 compatibility is, but if you're really rearing to go, you might try to download julia 0.7 - It's pretty much the same as 1.0, except that there are deprecation warnings for the stuff that's changed, rather than warnings. A lot of packages that aren't quite ready for 1.0 are working there.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BioJulia/Bio.jl/issues/495#issuecomment-412388181, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPejU9x5-1ROS3bwmoGM3VBSAmFurqIks5uQNjcgaJpZM4V5jDs.

y9c commented 6 years ago

Not work in 0.7 either