Search
Question: 403 Forbidden During Install
0
gravatar for jjrozewicki
21 days ago by
jjrozewicki0 wrote:

Hello,

In April I became the administrator of an HPC cluster system, and I noticed recently that attempting to access https://bioconductor.org from the cluster system gives a 403 Forbidden HTTP error. Other machines on our university network can access the site fine, but it is not possible within this cluster system.

To get around this problem I created a local BioC mirror here in my lab(rsync mirroring works even though http does not), however the BioC installer still fails when it attempts to access http://bioconductor.org/BiocInstaller.dcf during the BioC install.

From looking at the configuration on this cluster system, it appears as though the previous admin may have configured BioC poorly(on 20-30 machines) in the past which I suspect could have lead to our IP being banned for abuse by the admins of bioconductor.org.

Can this IP ban be lifted or can the BioC installer be modified to pull the BiocInstaller.dcf file from the configured mirror rather than the main bioconductor.org? I would also be interested to e-mail or private message with one of the admins so that I can confirm my cluster system is no longer configured in a way that causes problems.

ADD COMMENTlink modified 20 days ago by Valerie Obenchain ♦♦ 6.4k • written 21 days ago by jjrozewicki0

After looking at the source for the BiocInstaller package I found a variable I can set to work around this, and googling it pulled up this answer:
Offline loading of BiocInstaller or depending packages and connection timeout
 

This workaround seems like it will be okay for the time being, but I still think it would be good if this file were to be loaded from the configured mirror rather than being hardcoded to the main site and only disabled through an undocumented option.

ADD REPLYlink written 21 days ago by jjrozewicki0

It's actually retrieving information from the bioconductor _web_ site, rather than package repository; most local mirrors are of the package repositories. I'll document the option (to use the local DCF) more clearly; it comes with a limitation that after the final build of a release, the local file is necessarily out-of-date.

ADD REPLYlink written 18 days ago by Martin Morgan ♦♦ 21k
0
gravatar for Valerie Obenchain
20 days ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

What is the IP of the cluster being blocked?

Valerie

ADD COMMENTlink modified 20 days ago • written 20 days ago by Valerie Obenchain ♦♦ 6.4k

I have e-mailed this information to you directly because I am not comfortable with posting this information publicly on this site.

ADD REPLYlink written 20 days ago by jjrozewicki0

Thanks for sending the IP and yes, it was blacked for the reasons you describe. It's been removed from the blacklist and you should have access now.

Thanks for fixing the cluster configuration.

Valerie

ADD REPLYlink written 20 days ago by Valerie Obenchain ♦♦ 6.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 424 users visited in the last hour