I want to analyse my RSQ lite data (generated in Galaxy)  in R. But I keep getting this error. Could someone pelase help me sort this out?

> source("http://bioconductor.org/biocLite.R")

Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("cummeRbund")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
Installing package(s) ‘cummeRbund’
trying URL 'https://bioconductor.org/packages/3.4/bioc/bin/windows/contrib/3.3/cummeRbund_2.16.0.zip'
Content type 'application/zip' length 7436796 bytes (7.1 MB)
downloaded 7.1 MB

package ‘cummeRbund’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Efraim Culfa\AppData\Local\Temp\RtmpucYSiN\downloaded_packages
> cuff_data<-readCufflinks('D:\\AAA-PengZhou\\R-3.0.1\\library\\AAAAAA')
Error: could not find function "readCufflinks"

You have a number of issues, but importantly you are installing Bioconductor at the top of your script, which is unnecessary. But if you don't have Bioconductor installed, do it like this:

source("https://bioconductor.org/biocLite.R")
biocLite()

I aways restart R after this with Ctl-Shift-0 or Cmd-Shift-0, if using RStudio.

Then you can install and use cummeRbund like so:

BiocInstaller::biocLite("cummeRbund")
cummeRbund::readCufflinks("whateverFileYouWant")

Or this syntax will do the same:

library(BiocInstaller)
biocLite("cummeRbund")
library(cummeRbund)
readCufflinks("whateverFileYouWant")