I would like to install R packages. But I failed. I suspect it has something to do with my inability to log in to https://mghp.osn.xsede.org/. It took me a whole day to solve the problem. Looking forward to your reply
It looks like the site that hosts the archived versions of Bioconductor packages is currently down (https://mghp.osn.xsede.org/).
You could try the function chooseBiocMirror() and select an alternative. In my experience option 2 (Germany (Gottingen) [https]) often works well.
Alternatively (and probably recommended), you can update to using R 4.3 and Bioconductor 3.17. Then the packages will come from a different site, and you'll be getting the most up-to-date versions.
Thank you very much for your reply. Will this website (https://mghp.osn.xsede.org/) return to normal? I really need an old version of the R package
I assume it will come back, but it's not something I have control over and can't suggest a timeframe.
Did you try selecting a mirror using the function above? Many of the mirrors include packages going back to very early versions of Bioconductor, so you can install from their instead.
Installing via Conda is a thing you can do, but that's out of our control as well. I don't know of a compelling reason to use Conda for R/Bioconductor (it's not Python after all). You will be better off if you just install the current versions of R and Bioconductor directly.
Thank you very much for your reply. But I found that the URL for downloading the R package of the old version (Bioconductor 3.16) cannot be logged in. I still want to use older versions of R packages (eg genomeinfodbdata version 1.2.9). May I ask when will the server https://mghp.osn.xsede.org/ that stores the old version work normally?
Seeing this issue today, now with the R 4.3 + Bioc 3.18 version of this package. It is the Bioconductor servers that redirect to this unreliable mirror, as illustrated by a direct wget request:
$ wget https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
--2024-05-22 20:43:05-- https://bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
Resolving bioconductor.org (bioconductor.org)... 13.225.63.129, 13.225.63.75, 13.225.63.67, ...
Connecting to bioconductor.org (bioconductor.org)|13.225.63.129|:443... connected.
HTTP request sent, awaiting response... 302 Moved Temporarily
Location: https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz [following]
--2024-05-22 20:43:05-- https://mghp.osn.xsede.org/bir190004-bucket01/archive.bioconductor.org/packages/3.18/data/annotation/src/contrib/GenomeInfoDbData_1.2.11.tar.gz
Resolving mghp.osn.xsede.org (mghp.osn.xsede.org)... 192.69.103.247, 192.69.103.246, 192.69.103.248
Connecting to mghp.osn.xsede.org (mghp.osn.xsede.org)|192.69.103.247|:443... failed: Operation timed out.
The crippling thing about this in my case is that this is for a Conda environment that is part of a Snakemake pipeline - this is not interactive installation and the option to switch to Bioc 3.19 is non-existent. It seems that there should be something server-side that Bioconductor can do to address this.
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version 2.3.6
A good question should have at least one line of code, the error messages and a sessionInfo.
Code:
conda install -c bioconda bioconductor-genomeinfodbdata=1.2.9
Error messages:
ERROR conda.core.link:_execute(945):An error occurred while installing package 'bioconductor-genomeinfodbdata-1.2.9-r42hdfd78af_0'.'
All three of the sites where genomeinfodbdata R packages are stored appear to be down. package: name: bioconductor-genomeinfodbdata version: 1.2.9 source: md5: 7cc138cfb74665fdfa8d1c244eac4879 url: