unable to execute phantomjs from within my CI3 app

Your chmod command is wrong. You are in ~/rst/RST/app/vendor/koolreport/export/bin and then you then you try to change permission of a file in app/vendor/koolreport/export/bin/phantomjs. The OS is right, it doesn't exist. Try sudo chmod +x phantomjs.

...but the question remains, since when a javascript file needs to be executable? This doesn't make any sense. It's not a binary file containing an executable program, it's just a text file. I should be readable by the web server, not executable. That's an unnecessary security risk.