ERROR: MethodError: no method matching run when running latest release Julia 1.11

[kmunozforti]

I cannot initiate FlowAtlas. Below is the error.

julia> using FlowAtlas; FlowAtlas.run("08-Aug-2024.wsp"; files="/.fcs")
ERROR: MethodError: no method matching run(::String; files::String)
The function run exists, but no method is defined for this combination of argument types.

Closest candidates are:
run(::String, ::Any; port, url, cols, channelMap, drop, nlevels, channelRange, channelScheme, labelScheme, perplexity, maxIter) got unsupported keyword argument "files"
@ FlowAtlas ~/.julia/packages/FlowAtlas/HaV3Q/src/FlowAtlas.jl:55

Stacktrace:
[1] top-level scope
@ REPL[19]:1

[gszep]

Hi there! Thank you for using FlowAtlas! Happy to help with your issue. I am currently travelling and will attempt to get back to you on this later this week 😄

[gszep]

can you provide me a few more details to help to track down the bug? Can you run the following in the Julia env where the error is being produced?

versioninfo()
using Pkg; Pkg.status()

[kmunozforti]

julia> versioninfo()
Julia Version 1.11.1
Commit 8f5b7ca12ad (2024-10-16 10:53 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: macOS (arm64-apple-darwin22.4.0)
CPU: 12 × Apple M2 Max
WORD_SIZE: 64
LLVM: libLLVM-16.0.6 (ORCJIT, apple-m2)
Threads: 1 default, 0 interactive, 1 GC (on 8 virtual cores)

julia> using Pkg; Pkg.status()
Status ~/.julia/environments/v1.11/Project.toml
⌃ [ef7debb3] FlowAtlas v0.1.3
Info Packages marked with ⌃ have new versions available and may be upgradable.

[gszep]

the version of FlowAtlas shown (v0.1.3) is quite old. Would it be possible for you to upgrade to the latest version (v0.1.14) using

using Pkg; Pkg.update()

[kmunozforti]

julia> using Pkg; Pkg.update()
Updating registry at ~/.julia/registries/General.toml
No Changes to ~/.julia/environments/v1.11/Project.toml
No Changes to ~/.julia/environments/v1.11/Manifest.toml

julia> using Pkg; Pkg.status()
Status ~/.julia/environments/v1.11/Project.toml
⌃ [ef7debb3] FlowAtlas v0.1.3
Info Packages marked with ⌃ have new versions available and may be upgradable.

[gszep]

Interesting! It appears the latest release of Julia (1.11.1) is preventing FlowAtlas from being upgraded to its latest version. An immediate fix would be to use the LTS version of Julia (1.10).

This can be done from the command line if you used juliaup to install Julia. At the same time I would recommend using 1.10 by default as a lot of things start breaking if you use the latest version of things :)

juliaup add 1.10
juliaup default 1.10

You can re-launch julia and install FlowAtlas in the new environment. It should show up as v0.1.14 now

pkg> add FlowAtlas

In the meantime I will look into why this is happening for Julia 1.11

[kmunozforti]

Thank you for being so supportive and help with this

[gszep]

Okay as I thought something is up with version constrains..

Unsatisfiable requirements detected for package StatsFuns [4c63d2b9]:
 StatsFuns [4c63d2b9] log:
 ├─possible versions are: 0.7.0 - 1.3.2 or uninstalled
 ├─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.8.0 - 1.3.2
 │ └─Distributions [31c24e10] log:
 │   ├─possible versions are: 0.16.0 - 0.25.112 or uninstalled
 │   ├─restricted by compatibility requirements with StaticArrays [90137ffa] to versions: [0.16.0 - 0.23.11, 0.24.5 - 0.25.112] or uninstalled
 │   │ └─StaticArrays [90137ffa] log:
 │   │   ├─possible versions are: 0.8.0 - 1.9.8 or uninstalled
 │   │   ├─restricted to versions 1 by FlowAtlas [ef7debb3], leaving only versions: 1.0.0 - 1.9.8
 │   │   │ └─FlowAtlas [ef7debb3] log:
 │   │   │   ├─possible versions are: 0.1.14 or uninstalled
 │   │   │   └─FlowAtlas [ef7debb3] is fixed to version 0.1.14
 │   │   └─restricted by julia compatibility requirements to versions: [0.12.0 - 0.12.6, 1.5.0 - 1.9.8] or uninstalled, leaving only versions: 1.5.0 - 1.9.8
 │   ├─restricted by compatibility requirements with StatsBase [2913bbd2] to versions: 0.23.2 - 0.25.112 or uninstalled, leaving only versions: [0.23.2 - 0.23.11, 0.24.5 - 0.25.112] or uninstalled
 │   │ └─StatsBase [2913bbd2] log:
 │   │   ├─possible versions are: 0.24.0 - 0.34.3 or uninstalled
 │   │   ├─restricted to versions 0.33 by FlowAtlas [ef7debb3], leaving only versions: 0.33.0 - 0.33.21
 │   │   │ └─FlowAtlas [ef7debb3] log: see above
 │   │   └─restricted by compatibility requirements with SortingAlgorithms [a2af1166] to versions: 0.33.7 - 0.34.3 or uninstalled, leaving only versions: 0.33.7 - 0.33.21
 │   │     └─SortingAlgorithms [a2af1166] log:
 │   │       ├─possible versions are: 0.3.0 - 1.2.1 or uninstalled
 │   │       ├─restricted by julia compatibility requirements to versions: 1.1.0 - 1.2.1 or uninstalled
 │   ├─restricted by compatibility requirements with GigaSOM [a03a9c34] to versions: 0.21.1 - 0.25.112, leaving only versions: [0.23.2 - 0.23.11, 0.24.5 - 0.25.112]
 │   │ └─GigaSOM [a03a9c34] log:
 │   │   ├─possible versions are: 0.0.4 - 0.7.0 or uninstalled
 │   │   └─restricted to versions 0.7 by FlowAtlas [ef7debb3], leaving only versions: 0.7.0
 │   │     └─FlowAtlas [ef7debb3] log: see above
 │   └─restricted by compatibility requirements with FillArrays [1a297f60] to versions: [0.16.0 - 0.21.9, 0.25.49 - 0.25.112] or uninstalled, leaving only versions: 0.25.49 - 0.25.112
 │     └─FillArrays [1a297f60] log:
 │       ├─possible versions are: 0.2.0 - 1.13.0 or uninstalled
 │       ├─restricted by julia compatibility requirements to versions: 0.13.8 - 1.13.0 or uninstalled
 │       └─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.8.0 - 1.13.0, leaving only versions: 0.13.8 - 1.13.0
 │         └─Distributions [31c24e10] log: see above
 ├─restricted by compatibility requirements with Rmath [79098fc4] to versions: 0.9.2 - 1.3.2 or uninstalled, leaving only versions: 0.9.2 - 1.3.2
 │ └─Rmath [79098fc4] log:
 │   ├─possible versions are: 0.5.0 - 0.8.0 or uninstalled
 │   ├─restricted by compatibility requirements with BinaryProvider [b99e7846] to versions: 0.6.1 - 0.8.0 or uninstalled
 │   │ └─BinaryProvider [b99e7846] log:
 │   │   ├─possible versions are: 0.4.0 - 0.5.10 or uninstalled
 │   │   └─restricted by julia compatibility requirements to versions: uninstalled
 ├─restricted by compatibility requirements with Reexport [189a3867] to versions: 0.7.0 - 0.9.8 or uninstalled, leaving only versions: 0.9.2 - 0.9.8
 │ └─Reexport [189a3867] log:
 │   ├─possible versions are: 0.2.0 - 1.2.2 or uninstalled
 │   └─restricted by compatibility requirements with DataDeps [124859b0] to versions: 0.2.0
 │     └─DataDeps [124859b0] log:
 │       ├─possible versions are: 0.4.3 - 0.7.13 or uninstalled
 │       ├─restricted by compatibility requirements with HTTP [cd3eb016] to versions: 0.7.4 - 0.7.8 or uninstalled
 │       │ └─HTTP [cd3eb016] log:
 │       │   ├─possible versions are: 0.6.10 - 1.10.9 or uninstalled
 │       │   └─restricted to versions 0.9 by FlowAtlas [ef7debb3], leaving only versions: 0.9.0 - 0.9.17
 │       │     └─FlowAtlas [ef7debb3] log: see above
 │       ├─restricted by compatibility requirements with Impute [f7bf1975] to versions: 0.7.0 - 0.7.13, leaving only versions: 0.7.4 - 0.7.8
 │       │ └─Impute [f7bf1975] log:
 │       │   ├─possible versions are: 0.1.0 - 0.6.12 or uninstalled
 │       │   ├─restricted to versions 0.6 by FlowAtlas [ef7debb3], leaving only versions: 0.6.0 - 0.6.12
 │       │   │ └─FlowAtlas [ef7debb3] log: see above
 │       │   ├─restricted by compatibility requirements with StatsBase [2913bbd2] to versions: [0.1.0 - 0.2.0, 0.6.1 - 0.6.12] or uninstalled, leaving only versions: 0.6.1 - 0.6.12
 │       │   │ └─StatsBase [2913bbd2] log: see above
 │       │   └─restricted by compatibility requirements with CSV [336ed68f] to versions: [0.1.0 - 0.5.1, 0.6.2 - 0.6.12] or uninstalled, leaving only versions: 0.6.2 - 0.6.12
 │       │     └─CSV [336ed68f] log:
 │       │       ├─possible versions are: 0.3.0 - 0.10.15 or uninstalled
 │       │       ├─restricted by compatibility requirements with GigaSOM [a03a9c34] to versions: [0.5.12 - 0.8.5, 0.10.0 - 0.10.15]
 │       │       │ └─GigaSOM [a03a9c34] log: see above
 │       │       ├─restricted by compatibility requirements with Impute [f7bf1975] to versions: 0.6.0 - 0.10.15, leaving only versions: [0.6.0 - 0.8.5, 0.10.0 - 0.10.15]
 │       │       │ └─Impute [f7bf1975] log: see above
 │       │       ├─restricted by compatibility requirements with DataFrames [a93c6f00] to versions: 0.8.0 - 0.10.15 or uninstalled, leaving only versions: [0.8.0 - 0.8.5, 0.10.0 - 0.10.15]
 │       │       │ └─DataFrames [a93c6f00] log:
 │       │       │   ├─possible versions are: 0.11.7 - 1.7.0 or uninstalled
 │       │       │   ├─restricted to versions 1 by FlowAtlas [ef7debb3], leaving only versions: 1.0.0 - 1.7.0
 │       │       │   │ └─FlowAtlas [ef7debb3] log: see above
 │       │       │   └─restricted by compatibility requirements with Reexport [189a3867] to versions: 0.11.7 - 1.5.0 or uninstalled, leaving only versions: 1.0.0 - 1.5.0
 │       │       │     └─Reexport [189a3867] log: see above
 │       │       └─restricted by compatibility requirements with PooledArrays [2dfb63ee] to versions: [0.3.0 - 0.4.3, 0.8.3 - 0.10.15] or uninstalled, leaving only versions: [0.8.3 - 0.8.5, 0.10.0 - 0.10.15]
 │       │         └─PooledArrays [2dfb63ee] log:
 │       │           ├─possible versions are: 0.3.0 - 1.4.3 or uninstalled
 │       │           └─restricted by compatibility requirements with DataFrames [a93c6f00] to versions: 1.2.1 - 1.4.3
 │       │             └─DataFrames [a93c6f00] log: see above
 │       └─restricted by compatibility requirements with BinaryProvider [b99e7846] to versions: [0.4.3 - 0.7.4, 0.7.10 - 0.7.13] or uninstalled, leaving only versions: 0.7.4
 │         └─BinaryProvider [b99e7846] log: see above
 └─restricted by compatibility requirements with Distributions [31c24e10] to versions: 0.9.15 - 1.3.2 — no versions left
   └─Distributions [31c24e10] log: see above

... this looks like a mess to solve... did you manage to get it working with 1.10?

[gszep]

It looks like I'm finally going to have to upgrade JSServe.jl to Bonito.jl to fix this
#34

[kmunozforti]

You suggesting of using 1.10 fixed the original issue. Now I am battling it not "finding the metadata". I do not know if this is related to the switch for 1.10.

[gszep]

Please do open a separate issue including a tiny bit of sample data which demonstrates the the new issue.

I will gladly try to help