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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
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Error while parsing "PathwayCommons12.All.hgnc.txt" file using readSifnx #9

Closed Kamalika17 closed 1 year ago

Kamalika17 commented 1 year ago

Hi,

I am trying to get all the pathway information from the PathwayCommons12.All.hgnc.txt file. I am using the paxtoolsr function readSifnx for the same. However, it is throwing the following error:

Error in checkInputFilePc(inputFile) : ERROR: A maximum file size limit of 1GB has been placed on files being read. Reading larger files with this function may be very slow. Please contact package author for workarounds.

Please help me resolve this.

Thanks a lot!

cannin commented 1 year ago

@Kamalika17 please update to the latest version and it should work

setRepositories(ind=1:6)
options(repos="http://cran.rstudio.com/")
if(!require(remotes)) { install.packages("remotes") }
library(remotes) 

remotes::install_github("BioPAX/paxtoolsr")
remotes::install_github("BioPAX/paxtoolsr", args="--no-multiarch") # On Windows, 64-bit
Kamalika17 commented 1 year ago

Thank you very much. That solved the issue.