I know this package is out-dated. I just want to report this error.
I was using cufflinks 2.2.1. Every thing was fine.
I wanted to used cummeRbund (v 2.24.0) to visualize the results. I had tried cummeRbund on expdata of package and there was no error.
Then I tried it on my data. The error lied in readCufflinks.
Specifically, the error occured at this line:
The warning and error message were:
Aggregation function missing: defaulting to length Error in dim(ordered) <- ns : dims [product 23544] do not match the length of object 
I looked into my data, I found this line caused error:
XLOC_002304 - - XLOC_002304 ZnT35C TSS2720,TSS2721 2L:15228728-15247832 - - 1.64092 0 3.29494 OK 2.00419 0 4.17461 OK
If I deleted this line, there was no error while calling readCufflinks.
But it was not this line per se that caused the error. If I deleted the line above, the error also disappeared.