Please do not try to copy-paste the code from the article into an R
session - rather, please use the code provided with the package
"ccTutorial", which is for example available from
http://www.bioconductor.o...

The code is in the "vignettes" subdirectory of the package, in the file
ccTutorial.Rnw. You can use the R function "Stangle" to extract the R
code only from this combined document.

The code chunks shown in the article use funny quotation marks, have
spaces in the wrong places, and the "+" character for line continuation
will confuse the R parser.

Let us know how it goes.