/usr/lib/R/site-library/Gviz/scripts/sourcePackage.R is in r-bioc-gviz 1.14.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ##library(methods)
library(grid)
library(IRanges)
library(rtracklayer)
library(GenomicRanges)
library(lattice)
library(biomaRt)
library(RColorBrewer)
library(Biobase)
library(grid)
library(AnnotationDbi)
## options(error=recover)
removeAndSource <- function(file, remove=FALSE){
if(remove){
exp <- parse(file)
sapply(exp, function(x){
x <- as.character(x)
if(x[[1]]=="setMethod")
suppressWarnings(try(removeMethod(x[[2]], ifelse(length(grep("\\(", x[3]))>0, eval(parse(text=x[3])), x[3]))))
if(x[[1]]=="setReplaceMethod")
suppressWarnings(try(removeMethod(paste(x[[2]], "<-", sep=""), ifelse(length(grep("\\(", x[3]))>0, eval(parse(text=x[3])), x[3]))))
if(x[[1]]=="setAs")
suppressWarnings(try(removeMethod("coerce", x[2:3])))
})
}
source(file)
}
path <- "~/Rpacks/Gviz/R"
files <- c("Gviz.R", "AllGenerics.R", "AllClasses.R", "Gviz-methods.R")
sapply(file.path(path, files), removeAndSource)
## dtTrack <- DataTrack(start=seq(1,1000, len=100), width=10, data=matrix(runif(400), nrow=4), chromosome=1, genome="mm9", name="random data")
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