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HI all, I have Rstudio version 4.2, and want to download the package mixOmics. As I cannot use Install.packages, I wanted to use BiocManager (version 3.16) to download the package. However I get the problem that I cannot open the URL, see code below.
If I paste the link 'http://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES', I cannot access this indeed. However, the 3.18 packages I can open, so it is not an problem of my browser that I cannot open the 3.16 packages right? I have already added Bioconductor website to the "save" sites in my browser, but still I cannot access the 3.16 packages.
Please help me with suggestions
>install.packages("BiocManager")
>library("BiocManager")
> BiocManager::install("mixOmics")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Warning: unable to access index for repository http://bioconductor.org/packages/3.16/bioc/src/contrib:
cannot open URL 'http://bioconductor.org/packages/3.16/bioc/src/contrib/PACKAGES'
We are aware of some connectivity issues but they seems sporadic. We are working on workarounds.
Hi Vincent, thanks for your answer. Do you mean that it is a server problem from bioconductor? So the website for accessing the packages from 3.16 is not available for anyone?
If so, do you know how long this can take? I have been trying to download packages the whole day already. Or is there a workaround to download the mixOmics package without getting this problem?
I tried to install on an old version of R, and it just hung. So yes, not available for anybody.
The workaround is to install the current version of R and Bioconductor. We don't support old packages, and there have been two update cycles in the interim, so it's in your best interest to use the current versions.
Hi James, I understand. The thing is that I have to work within my institution's workspace (because of sensitive information), but ofcourse the IT-depatrment is lagging, and only Rstudio version 4.2 is available.... Is there maybe another workaround? Manually downloading the packages I need?
Hello, this is a bit of a hard-to-diagnose issue, as it seems the archive is accessible from some but not other networks.
It is definitely somewhat widespread, as we can confirm it can't be accessed from our cloud VMs or GitHub Actions' default runners, but it is still accessible from my home network. Another team member is able to access it on their phone network, but not their home network. While it could be a coincidence, given the selective connectivity and timing overlap, we suspect this might be related (although hard to conclusively diagnose) to the nationwide AT&T outage that seems to be currently happening.
In the meantime, while we wait on more information from the current object store provider, in order to ensure old packages are accessible again more widely, a core team member has rerouted the URL to a backup hosted at another location.
Old packages should now be accessible via BiocManager again, please let us know if you still experience issues.
I just tried this on the Bioconductor 3.16 Docker and it looks to be operational. Thanks all!