Open tsvvas opened 11 months ago
HaojiaWu
commented
11 months ago @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
commented
10 months ago 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
commented
10 months ago 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
commented
9 months ago 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
commented
8 months ago 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 aboveAs I am not that familiar with Julia I'm not sure how to get it to work
Hope you can help
BuilderPie
commented
8 months ago 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 aboveAs 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
commented
8 months ago Hey @BuilderPie,
I am running Linux on a dedicated server and this was a fresh Julia installation
BuilderPie
commented
8 months ago 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:
ddcham
commented
8 months ago @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
commented
4 months ago 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..
Hello CellScopes team,
I have encountered a dependency error while installing the CellScope package – Unsatisfiable requirements for package ImageTransformations. Here is the traceback:
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