I noticed there is a bug in a function from a package I want to use. An issue has been made on GitHub, but the creator hasn't adressed this yet, and I need the function as soon as possible.
Therefore I want to edit the code. Apparently this is possible by editing the source, repacking and installing the entire package, I can rewrite the function and reassign the namespace, but also possibly by just editing the function in the current session using trace().
I already found out I can do:
as.list(body(package:::function_inside_function))
The line I want to edit is located in the second step of the function.
Specifically, it is this line in the code I need to edit. I have to change ignore.case to ignore.case=TRUE. An example in case the link dies:
functionx(){if{...} else if(grepl("miRNA", data.type, ignore.case)) {...}}
I haven't really found a practical example on how to proceed from here, so can anyone show me an example of how to do this, or lead me to a practical example of using trace? Or perhaps reassigning the function to the namespace?
For your specific case, you could probably indeed work around it using trace.
From the link you provide I don't know why you speak of a function inside a function, but this should work:
# example
trace("grepl", tracer = quote(ignore.case <- TRUE))
grepl("hi", "Hi")
## Tracing grepl("hi", "Hi") on entry
## [1] TRUE
# your case (I assume)
trace("readTranscriptomeProfiling", tracer = quote(ignore.case <- TRUE))
Note that this would be more complicated if the argument ignore.case that you want to fix wasn't already at the right position in the call.