Rqc package error: "GhostScript was not found"

Question

I'm following the Rqc package documentation so i typed the following :

library(Rqc)
folder <- system.file(package = "ShortRead", "extdata/E-MTAB-1147")
rqc(path = folder, pattern = ".fastq.gz")

but i'm getting the following error :

Error in bitmap(file = filename, width = width, height = height, res = 300) : GhostScript was not found

Answer 1

I'm running the latest version of RStudio (0.99.491). First, make sure you have downloaded GhostScript ( here ). Then, go to the directory where you installed it, and find the path to the executable. Then, do this:

Sys.setenv(R_GSCMD="C:/Program Files/gs/gs9.18/bin/gswin64c.exe")

The path refers to my specific .exe, so yours may be different. Basically, the function that is throwing the error is looking for R_GSCMD to give it a path to run GhostScript. It didn't find one, so it threw an error. By setting R_GSCMD to the path, it now knows where to look.