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buenrostrolab / FigR

Functional Inference of Gene Regulation
https://buenrostrolab.github.io/FigR/
MIT License
32 stars 10 forks source link

About installation #7

Closed pocession closed 1 year ago

pocession commented 1 year ago

Hi, Thanks for providing this wonderful tool.

I encountered an error showing ERROR: dependencies 'chromVAR', 'motifmatchr', 'ComplexHeatmap', 'BuenColors', 'BSgenome.Hsapiens.UCSC.hg19' are not available for package 'FigR. I am wondering does this mean I need to install all the above packages before installing FigR? It looks not the case, since I installed two of these packages and the same error message was still showing up.

I used R4.2.1.

Best,

Tsunghan (post doc in Radboud University)

vkartha commented 1 year ago

Hi there - yes, the package internally uses chromVAR, motifmatchr, ComplexHeatmap and BuenColors. The BSgenome one is only because we need a default genome to use, if you want hg38 or mm10 you have to install those yourself separately. Some of those are installed via BioConductor (BSgenome, motifmatchr, ComplexHeatmap), whereas the others can be installed from github (e.g. see https://github.com/caleblareau/BuenColors). Usually FigR will autoinstall all required dependencies, but given these are from alternative sources, it might not be doing that automatically. Please let us know if you are able to load FigR after installing these dependencies, R4.2.1 should be OK.

pocession commented 1 year ago

Hi vkartha,

Thanks for your reply. I installed all the packages and FigR runs well.