Installation issue (dependency error).

[tsvvas]

Hello CellScopes team,

I have encountered a dependency error while installing the CellScope package – Unsatisfiable requirements for package ImageTransformations. Here is the traceback:

ERROR: Unsatisfiable requirements detected for package ImageTransformations [02fcd773]:
 ImageTransformations [02fcd773] log:
 ├─possible versions are: 0.2.0-0.10.0 or uninstalled
 ├─restricted by compatibility requirements with Colors [5ae59095] to versions: 0.8.1-0.10.0 or uninstalled
 │ └─Colors [5ae59095] log:
 │   ├─possible versions are: 0.9.0-0.12.10 or uninstalled
 │   └─restricted to versions 0.12 by Baysor [cc9f9468], leaving only versions: 0.12.0-0.12.10
 │     └─Baysor [cc9f9468] log:
 │       ├─possible versions are: 0.6.2 or uninstalled
 │       └─Baysor [cc9f9468] is fixed to version 0.6.2
 ├─restricted by compatibility requirements with Augmentor [02898b10] to versions: 0.5.0-0.8.13, leaving only versions: 0.8.1-0.8.13
 │ └─Augmentor [02898b10] log:
 │   ├─possible versions are: 0.6.0-0.6.6 or uninstalled
 │   └─restricted to versions * by CellScopes [708d50d9], leaving only versions: 0.6.0-0.6.6
 │     └─CellScopes [708d50d9] log:
 │       ├─possible versions are: 0.1.0 or uninstalled
 │       └─CellScopes [708d50d9] is fixed to version 0.1.0
 └─restricted by compatibility requirements with Images [916415d5] to versions: 0.9.0-0.9.5 — no versions left
   └─Images [916415d5] log:
     ├─possible versions are: 0.17.3-0.26.0 or uninstalled
     ├─restricted to versions * by CellScopes [708d50d9], leaving only versions: 0.17.3-0.26.0
     │ └─CellScopes [708d50d9] log: see above
     ├─restricted by compatibility requirements with Colors [5ae59095] to versions: 0.19.3-0.26.0 or uninstalled, leaving only versions: 0.19.3-0.26.0
     │ └─Colors [5ae59095] log: see above
     └─restricted by compatibility requirements with ImageMorphology [787d08f9] to versions: 0.25.0-0.25.3 or uninstalled, leaving only versions: 0.25.0-0.25.3
       └─ImageMorphology [787d08f9] log:
         ├─possible versions are: 0.1.0-0.4.5 or uninstalled
         └─restricted to versions 0.3 by Baysor [cc9f9468], leaving only versions: 0.3.0-0.3.2
           └─Baysor [cc9f9468] log: see above

I am only starting with Julia and I couldn't figure where these requirements are stated explicitly, nor how to fix the issue. I am running Julia v1.9.3. and installing the package using instructions from readme.

Best regards, Vasily

[HaojiaWu]

@tsvvas Thanks for your interest in our package. We have not tested on Julia v1.9.3. Maybe there are some dependency issues. I am using Julia V1.7.3 currently. I also tested CellScopes.jl on Julia V1.8.+ as well and it worked. You may give it a try on V1.7.3+ or V1.8 and let me know if there is any issue. We will test it on V1.9.+ on the next phase of the package development.

[MaximilianNuber]

I had the same problem. There was a compatibility issue with several packages which were installed as dependency for Gadfly in my case. In your case, try to remove "ImageTransformations", "Colors", "Augmentor", and/or "Images". Did it for me.

[HaojiaWu]

I will test it on a newer version of Julia later. The issues you came across are most likely the dependencies compatibility issue. That happened to me when I used other Julia packages. I will fix it later. Stay tuned.

[HaojiaWu]

Hi @tsvvas @MaximilianNuber , I made a new branch for Julia 1.9 to fix the dependency issue. Please re-install the package using the commands below:

using Pkg
Pkg.add(url="https://github.com/bicycle1885/Leiden.jl")
Pkg.add(url="https://github.com/HaojiaWu/CellScopes.jl#julia_v1_9")

Let me know if you find any issues.

[ddcham]

Running into the same problem here. Tried it with Julia 1.7.3/1.8.0/1.9.3 and with the fix you proposed. As soon as I try to install Baysor and CellScopes is already installed this error persists.

ERROR: Unsatisfiable requirements detected for package ImageTransformations [02fcd773]:
 ImageTransformations [02fcd773] log:
 ├─possible versions are: 0.2.0-0.10.0 or uninstalled
 ├─restricted by compatibility requirements with Colors [5ae59095] to versions: 0.8.1-0.10.0 or uninstalled
 │ └─Colors [5ae59095] log:
 │   ├─possible versions are: 0.9.0-0.12.10 or uninstalled
 │   └─restricted to versions 0.12 by Baysor [cc9f9468], leaving only versions 0.12.0-0.12.10
 │     └─Baysor [cc9f9468] log:
 │       ├─possible versions are: 0.6.2 or uninstalled
 │       └─Baysor [cc9f9468] is fixed to version 0.6.2
 ├─restricted by compatibility requirements with Images [916415d5] to versions: 0.9.0-0.9.5
 │ └─Images [916415d5] log:
 │   ├─possible versions are: 0.17.3-0.26.0 or uninstalled
 │   ├─restricted to versions * by CellScopes [708d50d9], leaving only versions 0.17.3-0.26.0
 │   │ └─CellScopes [708d50d9] log:
 │   │   ├─possible versions are: 0.1.0 or uninstalled
 │   │   └─CellScopes [708d50d9] is fixed to version 0.1.0
 │   └─restricted by compatibility requirements with ImageMorphology [787d08f9] to versions: 0.25.0-0.25.3 or uninstalled, leaving only versions: 0.25.0-0.25.3
 │     └─ImageMorphology [787d08f9] log:
 │       ├─possible versions are: 0.1.0-0.4.5 or uninstalled
 │       └─restricted to versions 0.3 by Baysor [cc9f9468], leaving only versions 0.3.0-0.3.2
 │         └─Baysor [cc9f9468] log: see above
 └─restricted by compatibility requirements with Augmentor [02898b10] to versions: 0.5.0-0.8.13 — no versions left
   └─Augmentor [02898b10] log:
     ├─possible versions are: 0.6.0-0.6.6 or uninstalled
     └─restricted to versions * by CellScopes [708d50d9], leaving only versions 0.6.0-0.6.6
       └─CellScopes [708d50d9] log: see above

As I am not that familiar with Julia I'm not sure how to get it to work

Hope you can help

[BuilderPie]

Running into the same problem here. Tried it with Julia 1.7.3/1.8.0/1.9.3 and with the fix you proposed. As soon as I try to install Baysor and CellScopes is already installed this error persists.

ERROR: Unsatisfiable requirements detected for package ImageTransformations [02fcd773]:
 ImageTransformations [02fcd773] log:
 ├─possible versions are: 0.2.0-0.10.0 or uninstalled
 ├─restricted by compatibility requirements with Colors [5ae59095] to versions: 0.8.1-0.10.0 or uninstalled
 │ └─Colors [5ae59095] log:
 │   ├─possible versions are: 0.9.0-0.12.10 or uninstalled
 │   └─restricted to versions 0.12 by Baysor [cc9f9468], leaving only versions 0.12.0-0.12.10
 │     └─Baysor [cc9f9468] log:
 │       ├─possible versions are: 0.6.2 or uninstalled
 │       └─Baysor [cc9f9468] is fixed to version 0.6.2
 ├─restricted by compatibility requirements with Images [916415d5] to versions: 0.9.0-0.9.5
 │ └─Images [916415d5] log:
 │   ├─possible versions are: 0.17.3-0.26.0 or uninstalled
 │   ├─restricted to versions * by CellScopes [708d50d9], leaving only versions 0.17.3-0.26.0
 │   │ └─CellScopes [708d50d9] log:
 │   │   ├─possible versions are: 0.1.0 or uninstalled
 │   │   └─CellScopes [708d50d9] is fixed to version 0.1.0
 │   └─restricted by compatibility requirements with ImageMorphology [787d08f9] to versions: 0.25.0-0.25.3 or uninstalled, leaving only versions: 0.25.0-0.25.3
 │     └─ImageMorphology [787d08f9] log:
 │       ├─possible versions are: 0.1.0-0.4.5 or uninstalled
 │       └─restricted to versions 0.3 by Baysor [cc9f9468], leaving only versions 0.3.0-0.3.2
 │         └─Baysor [cc9f9468] log: see above
 └─restricted by compatibility requirements with Augmentor [02898b10] to versions: 0.5.0-0.8.13 — no versions left
   └─Augmentor [02898b10] log:
     ├─possible versions are: 0.6.0-0.6.6 or uninstalled
     └─restricted to versions * by CellScopes [708d50d9], leaving only versions 0.6.0-0.6.6
       └─CellScopes [708d50d9] log: see above

As I am not that familiar with Julia I'm not sure how to get it to work

Hope you can help

Hi @ddcham, I'm curious which operating system were you installing Julia and CellScopes on? Linux, Windows, or Mac? And also, did you start from a brand new Julia environment? Or your Julia environment has other packages installed previously?

[ddcham]

Hey @BuilderPie,

I am running Linux on a dedicated server and this was a fresh Julia installation

[BuilderPie]

Hey @BuilderPie,

I am running Linux on a dedicated server and this was a fresh Julia installation

Hi @ddcham, could you compare your installation process with my notes for installing Julia 1.9.4 and CellScopes on a Linux server? Here is the link to my notes:

https://builderpie.github.io/CellScopes_test/docs/installation/linux/julia1.9.4/CellScopes_for_julia1.9

[ddcham]

@BuilderPie,

I did exactly as you did in your notes. After installing CellScopes and importing, once I am then try to install Baysor through: using Pkg;Pkg.add(PackageSpec(url="https://github.com/kharchenkolab/Baysor.git")); Pkg.build() it gives me the Error outlined above.

However I dont even get to the point where I need baysor in the xenium analysis anymore as it throws another error while doing @time brain = cs.read_xenium(xenium_dir; min_gene = 0, min_cell = 0, prefix = "brain")

Here I get a never ending string of:

 SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}, SparseArrays.SparseVector{Float64, Int64}).
This might be caused by recursion over very long tuples or argument lists.

[dchauss]

I get the same error if installing Baysor first before CellScopes, and also the other way around.

julia> Pkg.add(url="https://github.com/TheHumphreysLab/CellScopes.jl") Updating git-repo https://github.com/TheHumphreysLab/CellScopes.jl Resolving package versions... ERROR: Unsatisfiable requirements detected for package ImageTransformations [02fcd773]: ImageTransformations [02fcd773] log: ├─possible versions are: 0.2.0-0.10.1 or uninstalled ├─restricted by compatibility requirements with Compat [34da2185] to versions: 0.5.0-0.10.1 or uninstalled

etc..