search

BioPAX / paxtoolsr

The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database
https://bioconductor.org/packages/release/bioc/html/paxtoolsr.html
10 stars 1 forks source link

Downloading new version of Pathway Commons data doesn't work #5

Open TomKellyGenetics opened 6 years ago

TomKellyGenetics commented 6 years ago

Previously, I was able to download Pathway commons data with downloadPc (in October 2015) but this is no longer possible with this package:

> results <- downloadPc2(destDir = ".", verbose=T)
URL:  http://www.pathwaycommons.org/pc2/downloads/ 
Error in strsplit(tmp3, ";") : non-character argument

I believe this is due to an error in which the urls for each version of Pathway Commons (v2-9) available are kept as a vector rather than one being chosen as a character. This is a fundamental issue which means that this package has not been usable due to multiple versions hosted by Pathway Commons since at least January 2016.