Conflict with rtracklayer

[AlohaPropolis]

Install rtracklayer separate from BSgenome using the following method instead of loading it from BSgenome.

library(devtools) library(roxygen2)

Create directory RTRACKLAYER move to that directory and run

create_package(“rtracklayer”)

This will create the directory called rtracklayer with one file and an empty R directory. Replace all of the contents of this directory with the files and directories in the rtracklayer found in the GitHub repository. Now from the RTRACKLAYER directory run

document(rtracklayer)

This will rebuild the folder with the correct “namespace”. Load the new package

library(rtracklayer)

Then install the “new coded”BSgenome package which does not attempts to load rtracklayer.

[hpages]

Doesn't work for me:

> document('rtracklayer')
ℹ Updating rtracklayer documentation
ℹ Loading rtracklayer
Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Warning messages:
1: roxygen2 requires Encoding: "UTF-8"
ℹ Current encoding is NA 
2: Skipping NAMESPACE
✖ It already exists and was not generated by roxygen2. 

Also I don't know what the “new coded”BSgenome package is.

Also I don't understand the purpose of all the acrobatics with creating RTRACKLAYER, running create_package(“rtracklayer”) in it, replacing all of the contents of that with the files and directories etc.. etc.. when you can simply run document() from within a git clone of the rtracklayer package. Am I missing something?

[hpages]

No answer. I guess all is good then. Shall we close this?