rGREAT Service Unavailable: Operation timed out

[apblair]

Hello, I'm running into a service unavailable error when trying to run rGREAT. The site appears to be down too: http://great.stanford.edu/ Please let me know if I can provide any additional information. Thanks, Andrew

[jokergoo]

Yeah, I can also see the GREAT server is down. I am not the maintainer of GREAT server. If you use the online GREAT analysis, you have to wait.

Or you can use the "local GREAT" analysis with the function great(). You need to install it from GitHub and you can find the usage of this new function in the vignette.

[gene-drive]

Hi, I tried to use local GREAT, but I'm getting this message:

Error in great(test, "GO:BP", "GREAT:$mm10") : 
  could not find function "great"

How can I fix this?

Edit: Figured it out. I needed to install the latest version of rGREAT. Also, I needed to remove the $ above. However, it returned the error:

Error in read.table(system.file("extdata", paste0("GREATv4.genes.", genome,  :
no lines available in input
In addition: Warning message:
In file(file, "rt") :
file("") only supports open = "w+" and open = "w+b": using the former

I then decided to use RefSeq instead of GREAT as the TSS source.

[jokergoo]

It seems some platforms do not support directly reading gzfiles. I just updated the code. Can you update the package from GitHub and try again?