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kharchenkolab / Baysor

Bayesian Segmentation of Spatial Transcriptomics Data
https://kharchenkolab.github.io/Baysor/
MIT License
152 stars 31 forks source link

Installation Issue as Julia Package #135

Closed marsdenl closed 1 month ago

marsdenl commented 1 month ago

Hi there,

I've been trying to install Baysor to run segmentation via SOPA on a MERSCOPE dataset. Using the Julia package installation method on a VM windows desktop, the installation has been paused it seems (or has been running for quite some time > 60mn). I have GCC and Julia installed and my code for the installation is: julia -e "using Pkg; Pkg.add(PackageSpec(url=\"https://github.com/kharchenkolab/Baysor.git\")); Pkg.build()"

The pausing occurs at: Resolving package versions... No Changes to C:\Users\user\.julia\environments\v1.10\Project.toml No Changes to C:\Users\user\.julia\environments\v1.10\Manifest.toml Precompiling project... 309 dependencies successfully precompiled in 198 seconds. 9 already precompiled. 1 dependency had output during precompilation: ┌ Formatting │ ┌ Warning: DEPRECATION NOTICE │ │ │ │ Formatting.jl has been unmaintained for a while, with some serious │ │ correctness bugs compromising the original purpose of the package. As a result, │ │ it has been deprecated - consider using an alternative, such as │ │ Format.jl (https://github.com/JuliaString/Format.jl) or the Printf stdlib directly. │ │ │ │ If you are not using Formatting.jl as a direct dependency, please consider │ │ opening an issue on any packages you are using that do use it as a dependency. │ │ From Julia 1.9 onwards, you can query ]why Formatting to figure out which │ │ package originally brings it in as a dependency. │ └ @ Formatting C:\Users\user.julia\packages\Formatting\3VxOt\src\Formatting.jl:12 └ Building HDF5 ──→ C:\Users\user\.julia\scratchspaces\44cfe95a-1eb2-52ea-b672-e2afdf69b78f\114e20044677badbc631ee6fdc80a67920561a29\build.log Building Baysor → C:\Users\user\.julia\scratchspaces\44cfe95a-1eb2-52ea-b672-e2afdf69b78f\69139e6b79413cf8d068d520ebc69f987e633c98\build.log Progress [====================> ] 1/2

Do you know why that might be the case? Any help would be greatly appreciated thank you.

Luc

VPetukhov commented 1 month ago

Hi Luc, on my laptop it may take ~30 minute single-thread, as the process compiles a lot of packages. You can parallelize it using JULIA_NUM_THREADS=13 julia -e "using Pkg; Pkg.add(PackageSpec(url="[https://github.com/kharchenkolab/Baysor.git\](https://github.com/kharchenkolab/Baysor.git%5C)")); Pkg.build()". I will add this to the readme.

Please, let me know if this doesn't work!

marsdenl commented 1 month ago

It worked, in the end, thanks for your help @VPetukhov :)