i started to read and use the tutorial for the BioNet package for the functional analysis of biological networks(http://www.bioconductor.org/packages/release/bioc/vignettes/BioNet/inst/doc/Tutorial.pdf), in order to implemented afterwards for finding interesting functional modules in my colon cancer microarray data analysis DE genes. More specifically, in page 15 of the vignette i used instead of the command ”heinz.py -e ALL edges 001.txt -n ALL nodes 001.txt -N True -E False” the runHeinz command :
runHeinz(heinz.folder="heinz_1.67", heinz.e.file="ALL_edges_001", heinz.n.file="ALL_nodes_001", N=TRUE, E=FALSE, diff=-1, n=1)
where heinz_1.67 is the name of the heinz folder, but i got the following warning:
running command 'cd heinz_1.67;heinz.py -e ALL_edges_001 -n ALL_nodes_001 -N True -E False -d -1 -s 1' had status 127
Afterwards the tutorial continued without error, but
datadir <- file.path(.path.package("BioNet"), "extdata")
Error: '.path.package' is defunct.
Use 'path.package' instead.
And when i used datadir <- file.path(path.package("BioNet"), "extdata")
it didnt showed an error. These are some bugs with Bioconductor ? i have also downloaded CPLEX and installed it.