running svfilter.jl fails

[alexandrupaler]

ERROR: LoadError: LoadError: LoadError: syntax: invalid function name "SSignedDecorrelator <: SOperator"
Stacktrace:
 [1] include at ./boot.jl:317 [inlined]
 [2] include_relative(::Module, ::String) at ./loading.jl:1044
 [3] include at ./sysimg.jl:29 [inlined]
 [4] include(::String) at /home/alexandru/.julia/packages/BitSAD/Fqsov/src/BitSAD.jl:1
 [5] top-level scope at none:0
 [6] include at ./boot.jl:317 [inlined]
 [7] include_relative(::Module, ::String) at ./loading.jl:1044
 [8] include at ./sysimg.jl:29 [inlined]
 [9] include(::String) at /home/alexandru/.julia/packages/BitSAD/Fqsov/src/BitSAD.jl:1
 [10] top-level scope at none:0
 [11] include at ./boot.jl:317 [inlined]
 [12] include_relative(::Module, ::String) at ./loading.jl:1044
 [13] include(::Module, ::String) at ./sysimg.jl:29
 [14] top-level scope at none:2
 [15] eval at ./boot.jl:319 [inlined]
 [16] eval(::Expr) at ./client.jl:393
 [17] top-level scope at ./none:3
in expression starting at /home/alexandru/.julia/packages/BitSAD/Fqsov/src/types/soperators.jl:38
in expression starting at /home/alexandru/.julia/packages/BitSAD/Fqsov/src/types/sbitstream.jl:100
in expression starting at /home/alexandru/.julia/packages/BitSAD/Fqsov/src/BitSAD.jl:20
ERROR: LoadError: Failed to precompile BitSAD [7f90e340-ca22-4a3e-a259-118ed254aff3] to /home/alexandru/.julia/compiled/v1.0/BitSAD/v3ETk.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1203
 [3] _require(::Base.PkgId) at ./loading.jl:960
 [4] require(::Base.PkgId) at ./loading.jl:858
 [5] require(::Module, ::Symbol) at ./loading.jl:853
 [6] include at ./boot.jl:317 [inlined]
 [7] include_relative(::Module, ::String) at ./loading.jl:1044
 [8] include(::Module, ::String) at ./sysimg.jl:29
 [9] exec_options(::Base.JLOptions) at ./client.jl:266
 [10] _start() at ./client.jl:425
in expression starting at /home/alexandru/github/BitSAD.jl/examples/svfilter.jl:1

[darsnack]

Yeah, the package is currently in flux as I refactor the original implementation. I'm hoping to iron this out in the next few weeks.

[alexandrupaler]

Thank you for the very fast response. No problem. Do you have a fast workaround for this? Or is it safer to wait for the refactor?

[darsnack]

I would recommend waiting for the refactor. Out of curiosity, which version of Julia are you using?

[alexandrupaler]

Version 1.0.5 (2019-09-09)

[darsnack]

That's the source of the error. Base.@kwdef only supports super-types in >= Julia 1.1. So the line

Base.@kwdef struct SSignedDecorrelator <: SOperator

is not parsed correctly.

The package only supports Julia 1.3, so I am guessing the package manager is installing one of the initial versions for you (before I added the compatibility bound). Could you try the latest Julia? I think it should work without the refactor.

[alexandrupaler]

I installed Julia 1.6.0 and before succeeding to run the example I had the error below

ERROR: LoadError: ArgumentError: Package Makie not found in current path:
- Run `import Pkg; Pkg.add("Makie")` to install the Makie package.

I have also another question: Is there a way to run BitSAD directly from the cloned repo instead of adding it as a package?

[darsnack]

Some of the examples use some additional packages like Makie.jl or DataStructures.jl, so you will need to install those separately. You can comment out the plotting code at the bottom as well as using Makie if you want to skip that part.

I would recommend installing with ]add https://github.com/UW-PHARM/BitSAD.jl. You can also close the repo, then run Julia in the repo root as julia --project=. as well.