Question: Bioconductor IP addresses for whitelist
gravatar for jdshih
11 weeks ago by
jdshih10 wrote:

The higher-ups at our institution (MD Anderson Cancer Center) have made the decision to disable Internet access on our computing cluster, and only allow incoming access to specific IP addresses.

In order to install Bioconductor packages, we need a list of stable IP addresses for Bioconductor that we can whitelist. However, the IP address for does not appear to be stable (currently, pointing to an Amazon server).

This question was asked before, but the provided answer is no longer applicable, as the recommended stable IP address is no longer hosting a Bioconductor mirror (; Fred Hutch).

I suppose one solution is to whitelist all of AWS's IP ranges... but this might not be acceptable to the higher-ups.

Does anyone have other solutions to this firewall problem?


As Martin indicates below, has a stable IP of and is serving packages. Perhaps options(BioC_mirror=""); biocLite("DNAcopy") will work once is whitelisted on our network.

Will it be acceptable to Bioconductor for us to bypass load balancing and use as the sole IP address for downloading packages on our Internet-disabled computing cluster?

ip firewall • 119 views
ADD COMMENTlink modified 10 weeks ago • written 11 weeks ago by jdshih10
Answer: Bioconductor IP addresses for whitelist
gravatar for Martin Morgan
11 weeks ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote: is in the Amazon cloud, but is a static (elastic) IP address; it is stable.

An alternative is to clone, using rsync, the Bioconductor (and/or CRAN) repository and arrange for your cluster to point to the local repository (via R.home("etc/"), for instance, with options(Bioc_mirror = ...), see ?setRepositories).

Many clusters have a 'head' node that has access to outside IP addresses; the requirement then is to install packages on the head node.

ADD COMMENTlink written 11 weeks ago by Martin Morgan ♦♦ 23k

Unfortunately, our new cluster will not have a head node with Internet access; the admins will have temporary Internet access on special nodes until a unspecified date. The cluster will be a dead zone once Information Security is done with it...

I'll look into mirroring the Bioconductor repository, but space is very limited for both my workstation and my allocation on the cluster.

I'll ask request that be whitelisted... hopefully this will solve our problem.

I mistakenly thought that and were the same.

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by jdshih10
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