can't open mghp.osn.xsede.org
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15753563659 ▴ 60
@558fa874
Last seen 10 months ago
United States

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

GenomeInfoDbData genomeinfodbdata • 1.7k views
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A good question should have at least one line of code, the error messages and a sessionInfo.

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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'.'

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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:

- https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.9.tar.gz
- https://bioconductor.org/packages/3.16/data/annotation/src/contrib/GenomeInfoDbData_1.2.9.tar.gz
- https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.9_src_all.tar.gz
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Mike Smith ★ 6.5k
@mike-smith
Last seen 17 hours ago
EMBL Heidelberg

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.

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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

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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.

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Because I used the old version of the R package installed by conda, there is no way to choose the mirror. so sad. But thank you for your kind reply

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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.

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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?

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I believe Mike Smith already answered this question.

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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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