Installation of rtracklayer

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.

For reasons unknown it is necessary to run document(“./rtracklayer”) every time in order to library(“rtracklayer”). This must be done each time a new R session is started. There seems to be something in the rtracklayer package that retains a “fixed namespace”.

When starting rtracklayer is this manner you get a warning,

1: roxygen2 requires Encoding: “UTF-8”

: Current encoding is NA

2: Skipping NAMESPACE

x It already exists and was generated by roxygen2.
———————

Now the library rtracklayer loads without errors.

Problem solved

I changed my working directory to

/Library/Frameworks/R.framework/Versions/4.2/Resources/library

and then ran install_github(“lawremi/rtracklayer”)

Thanks for listening

John

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