duplicate rownames not allowed => change error notification?

[AMChalkie]

duplicate rownames not allowed caused by input with Gene ID, name not in first columns. Would be more robust to not rely on the order being correct, but find Gene ID column and put it first.

Alternatively, a better error message thown: "Gene ID expected as first column of input".

I expect a bunch of additional format checks of the input would be useful including parts to strip potentially malicious code from the input file.

[AMChalkie]

Suggest using fread or similar for reading input in R. Works nicely and much more verbose in error messaging.

[drpowell]

I can't reproduce this error?
I didn't think we had a requirement for a unique gene id anywhere in degust.

We do format cleaning for the input fields to avoid malicious code from leaking into R or js.