No plots been plotted

[omaryangtw]

I started to play with this package by following the main Readme
Initially, my Pluto notebook reported that WebIO not detected, so I just imported it.
Rest of the steps remained the same with the example.
When I called plotbarcode_pjs(C, dim=1), it seems to be executed successfully, but it didn't plot anything.

---

versioninfo()
Julia Version 1.6.1
Commit 6aaedecc44 (2021-04-23 05:59 UTC)
Platform Info:
OS: Windows (x86_64-w64-mingw32)
CPU: AMD Ryzen 7 5800X 8-Core Processor
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-11.0.1 (ORCJIT, generic)
Environment: JULIA_REVISE_WORKER_ONLY = 1

[henselman-petrusek]

This seems related to a known issue with PlotlyJS.

I also had an issue, not on Jupyter but on mac OS.

It sounds like the folks at PlotlyJS are working on a patch, but for now I had success reverting back to a prior version of plotly:

Step 1

using Pkg
Pkg.add(Pkg.PackageSpec(;name="PlotlyJS", version ="0.13.0"))

Step 2

Shut everything down and open a new Julia session.

How does that work for you?

[omaryangtw]

When I downgrade to 0.13.0, my Julia automatically deleted Kaledio.

Even if I install Kaledio back manually, it still showed that Kaledio is not available.

[henselman-petrusek]

Hmm. I wonder if this has to do with the compat changes in the most recent release. What version or Eirene do you have installed?
] status Eirene

[DavidLapous]

Same issue here on linux (julia v1.6.1).

(@v1.6) pkg> update
    Updating registry at `~/.julia/registries/General`
    Updating git-repo `https://github.com/JuliaRegistries/General.git`
  No Changes to `~/.julia/environments/v1.6/Project.toml`
  No Changes to `~/.julia/environments/v1.6/Manifest.toml`

(@v1.6) pkg> status Eirene
      Status `~/.julia/environments/v1.6/Project.toml`
  [9c0f25c4] Eirene v1.3.5

Stock latest fails to plot anything.

Julia fails to build Eirene if I try to downgrade PlotlyJS to v13.0. Here is the error dump.

[ Info: Precompiling Eirene [9c0f25c4-2ca1-5870-89f6-52640788da1d]
WARNING: Method definition savehtml(PlotlyBase.Plot{TT, TL, TF} where TF<:(AbstractArray{var"#s64", 1} where var"#s64"<:(PlotlyBase.PlotlyFrame{T} where T<:Base.AbstractDict{Symbol, Any})) where TL<:PlotlyBase.AbstractLayout where TT<:(AbstractArray{var"#s65", 1} where var"#s65"<:PlotlyBase.AbstractTrace), AbstractString) in module PlotlyBase at /home/---/.julia/packages/PlotlyBase/NxSlF/src/output.jl:50 overwritten in module PlotlyJS at /home/---/.julia/packages/PlotlyJS/b9Efu/src/display.jl:361.
  ** incremental compilation may be fatally broken for this module **

WARNING: Method definition savehtml(IO, PlotlyBase.Plot{TT, TL, TF} where TF<:(AbstractArray{var"#s64", 1} where var"#s64"<:(PlotlyBase.PlotlyFrame{T} where T<:Base.AbstractDict{Symbol, Any})) where TL<:PlotlyBase.AbstractLayout where TT<:(AbstractArray{var"#s65", 1} where var"#s65"<:PlotlyBase.AbstractTrace)) in module PlotlyBase at /home/---/.julia/packages/PlotlyBase/NxSlF/src/output.jl:37 overwritten in module PlotlyJS at /home/---/.julia/packages/PlotlyJS/b9Efu/src/display.jl:332.
  ** incremental compilation may be fatally broken for this module **

ERROR: LoadError: InitError: SystemError: opening file "/home/---/.julia/packages/PlotlyJS/b9Efu/deps/build.log": Aucun fichier ou dossier de ce type
Stacktrace:
 [1] open
   @ ./io.jl:328 [inlined]
 [2] read
   @ ./io.jl:434 [inlined]
 [3] __init__()
   @ PlotlyJS ~/.julia/packages/PlotlyJS/b9Efu/src/PlotlyJS.jl:84
 [4] top-level scope (repeats 2 times)
   @ none:1
during initialization of module PlotlyJS
in expression starting at /home/---/.julia/packages/Eirene/ecj8G/src/Eirene.jl:29
ERROR: Failed to precompile Eirene [9c0f25c4-2ca1-5870-89f6-52640788da1d] to /home/---/.julia/compiled/v1.6/Eirene/jl_M2Wpni.
Stacktrace:
 [1] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY)
   @ Base ./loading.jl:1360

[henselman-petrusek]

There seems to be a relevant issue (Pluto and PlotlyJS) open here:

fonsp/Pluto.jl#299

Others have had similar-sounding issues as recently as May 1. It sounds as though this a Pluto-specific issue. If anyone is still having problems getting the two to talk to each other, perhaps consider contributing to the issue report on Pluto.jl!

[henselman-petrusek]

If anyone has found that this issue persists outside Pluto please let me know. Otherwise I'll close the issue in the near future.

[DavidLapous]

I have this issue outside of Pluto, just using the terminal, the output of plotbarcode_pjs makes a small loading animation, and then stays blank. That's on linux, julia 1.6.2, and Eirene v1.3.5.

[esorinas]

I am facing the same problem, plots show a loading animation and then stay blank. When I downgrade PlotlyJS to v13.0, Eirene fails to precompile (I get an error output from the command "using Eirene").

Is this solved somehow? Any workaround that worked for you?

[henselman-petrusek]

Hi all,
Thanks for these reports and apologies for the slow turn around; things have been busy this season. The ultimate work-around to all of this is use the barcode function to get the complete list of birth/death pairs; you can then use pretty much any plotting function you'd like to visualize the data. This is admittedly a hassle so we'll try to address the issue eventually. In the meantime if anyone has time to play around with the package the developers would be grateful for any patch suggestions!
Thanks!