I've had both of these issues sequentially just as samantha had, and I'm not sure I totally understand the solution.
I was trying to finish an Rmd file with the render command to create an (in my case) Word document of the finished report. The reason I'm using the command render() instead of the Knit button is to manipulate where it stores my output file.
If I have the line render(rmdfile.Rmd) in my Rmd the process will recursively analyze the Rmd over and over again. If I have named chunks, the first error that it will print is the error of duplicate label with whatever the name of my first label is. If I do not have named chunks, it goes through the loop of rendering over and over again until the sink stack is full.
So, how do you write the command line render() if it can't be in your file?
My solution as of now is to comment out the render command, save the file, uncomment it, and then run it. But this seems awfully clunky.
Thanks for your input!