error in cuffcompare

Question

[collinsagho]

cuffcompare command in Linux is giving error of "not available, check new version, go to the website .....", but the cuffmerge is working. What should I do? I want to use it to identify novel transcript.

[Kevin Blighe]

What is the output of:

which cuffcompare 
which cuffmerge

Also say how you installed both programs, and how you typically execute them. Please show all commands that you use, state all versions, and display all output messages. Also state the type of machine that you use.