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cnio-bu / beyondcell

Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq and Spatial Transcriptomics data.
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Can beyondcell package be installed under windows system? #68

Closed Phoenix12580 closed 1 year ago

Phoenix12580 commented 1 year ago

Thank you very much for providing such a great tool! I tried to install beyondcell in R 4.2.1 under windows， but failed.

SGMartin commented 1 year ago

Hi @Phoenix12580

Thanks for you kind words. Beyondcell is compiled via bioconda's automatic builder. By default, It targets macOS (non ARM), Linux and Windows, but we don't test the latest extensively. Let us perform a few test and we will get back to you ASAP.

In the meantime, could you paste your 

conda env export

so we may take a closer look at what's actually pulled in your case.

Phoenix12580 commented 1 year ago

Thanks you very much, I am sorry. I did not use bioconda. I tried to install beyondcell in Rstudio.

devtools::install_github("cnio-bu/beyondcell",dependencies = T)

SGMartin commented 1 year ago

Hello @Phoenix12580

We do not recommend installing beyondcell through devtools. As you have noticed, more often than not you will encounter dependency issues. Beyondcell integrates various and sometimes, less than ideally maintained packages and conda protects you againt incompatible R versions and so on.

A beyondcell 2.0 version is coming soon, which will get rid of the worst offenders in terms of package dependencies, but for the time being, I would go with the conda installation as outlayed in the tutorial.

Phoenix12580 commented 1 year ago

Thank you very much for your reply, looking forward to new works.