Trouble with DESeq2

[Mauricio Cuello]

Can you check on DESeq2 module. I have been using since a while ago but this weekend it is not working. 

Constantly it appears stderr.txt saying 

Error in library(getopt) : there is no package called ‘getopt’ Calls: suppressMessages -> withCallingHandlers Execution halted

getopt is missing in the library

Thanks for taking care of this issue or explaining how to solve in GenePattern

[Ted Liefeld]

Hi

DESeq2 should be working again now, we are sorry for the inconvenience.  The problem was that for a while it was unable to connect to the CRAN repository.  This is a problem we see periodically and some of the old R modules (including this one) need to do some installations at the start of their runs.  We will add creating a custom docker container for this module to our queue of work, but I cannot give any idea of an ETA at the moment.  If this happens again you just need to wait a few hours for the CRAN repository to become available again, after which you can re-run your jobs.

Thanks for your patience,

Ted