Error: cannot open connection

Discovery Cluster
1

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,

2

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.

3

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

4

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’

5

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

7

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,

8

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

1 Like
9

thank you!