[BioC] CummeRbund Error

[john herbert]

Hi,
I have downloaded/installed cummeRbund vis biocLite and have run it on
2 sets of samples.

I have 2 sets of cuffdiff 1.3.0 results and they both load fine into
cummeRbund as follows.

library(cummeRbund)

setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_blad_1_3_0/diff_blad_1_3_0")

cuff<-readCufflinks()

dens<-csDensity(genes(cuff))
dens

# This works fine and displays a density plot. But, if I run all this
again on a different set of samples, I get this.

library(cummeRbund)
setwd("C:/Users/mark/Documents/Cross/cufflinks_data/diff_colon_1_3_0/diff_colon_1_3_0")
cuff<-readCufflinks()
dens<-csDensity(genes(cuff))
dens

Error: attempt to apply non-function

Any ideas how I can fix this; looks like there is a difference in
results somewhere but all files present in both sets of data.

Thank you.