On 6 Feb 2014, at 9:50, Kevin Owens wrote:

I'm getting, what to me is unexpected behavior, from the command that says "Send Selection/Line to" and in the sub-menu says "R.app & Step" (this is the one that has the default key binding of option+shift+enter. Here is the code in my bundle: […]

First, update to v2.0-alpha.9509 (current nightly build).

Then for the last part, it should be:

if [ "$TM_LINE_NUMBER" != "" ]; then
    "$TM_MATE" -l "$(($TM_LINE_NUMBER+1)):1000000"
elif [[ $TM_SELECTION =~ [1-9][0-9]*:?[0-9]*-([1-9][0-9]*):?[0-9]* ]]; then
    # Regular Selection
    "$TM_MATE" -l "$((${BASH_REMATCH[1]}+1)):1000000"
elif [[ $TM_SELECTION =~ [1-9][0-9]*:?[0-9]*x([1-9][0-9]*):?[0-9]* ]]; then 
    # Block (option) selection
    "$TM_MATE" -l "$((${BASH_REMATCH[1]}+1)):1000000"
else 
    "$TM_MATE"
fi

The command that says ""Send Selection/Document to" in the sub-menu R.app (default keybinding command+option+shift+R) also sends focus to R.app.

For this command, I think you can simply add "$TM_MATE" on a (new) last line.