Error: cannot open connection

Hi,
I’m having trouble downloading bioconductor packages - it gives me this error.

BiocManager::install("AnnotationHub")
Error: Bioconductor version cannot be validated; no internet connection?

It does this for every package. It seems that there isn’t a connection through the cluster, what should I do?

Thanks,

Hi, compute nodes don’t have internet access so you’ll have to install your packages from a login node first. Once installed, compute nodes will be able to find any packages you install on the filesystem.

So I’m not able to install bioconductor packages via the interactive mode?

I just tried to install by submitting a job and it still got rejected.

Error: Bioconductor version cannot be validated; no internet connection?
In addition: Warning messages:
1: In file(con, “r”) :
URL ‘https://bioconductor.org/config.yaml’: status was ‘Couldn’t resolve host name’
2: In file(con, “r”) :
URL ‘http://bioconductor.org/config.yaml’: status was ‘Couldn’t resolve host name’

That’s correct, please try on discovery.usc.edu

I’m using discovery.usc.edu. I’m using the compute node while running the interactive session. Then I submitted a batch job to discovery and it still gave me the error, per my reply above.

Thanks,

Compute nodes don’t have internet access, only the login nodes (also called “head nodes”) do. Just install it using the head node

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thank you!