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Hi, I'm curious if anyone has tried to clone or fork the fgsea package on the latest version of R?
How can I reproduce the scripts to run locally?
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Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R. Currently R 4.3 is paired with Bioconductor release 3.18 and R 4.4 alpha is paired with Bioconductor devel 3.19. If you have a version of R installed, you can follow the installation instructions on fgsea landing page and then should be able to run any of the code in the documentation
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with
devtools::install_github("ctlab/fgsea")For What its worth BiocManager should also be able to install the github remotes
BiocManager::install("ctlab/fgsea")Thanks for the reply.
I want to replicate the fgsea source code on my local machine. I don't intend to install the package. I want to run the r source code directly on my local machine. So, I tried to fork the git repo to run it on my machine locally. In plain terms, I downloaded the zip folder of the fgsea source code from the GitHub repo and tried to run it on my machine. The package works when I install it, but I don't want to install the package, I want to run the r source code on my machine. I hope this is clearer.
Installing the package allows you to run the R source code on your machine. You need R to run the R code, so it's not clear in what way 'run the r source code on my machine` could be accomplished that doesn't involve using R to run the code.
In addition
fgseaincludes C++ code that gets compiled as part of the installation process. Having the .R files from the GitHub repo isn't sufficient, because you also need the compiled binaries.Also, this support site is meant to help people with questions about how to use the packages as intended. You apparently don't want to use the package as intended, which is fine - it's Open Source code after all - but you shouldn't expect to get any help in your endeavors. If you want to do your own thing, it's up to you to figure out how to do that.