Error wth Installation BiocManager
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hasmikmd ▴ 10
@hasmikmd-23611
Last seen 13 months ago

Used the code below for installation, but keep getting this error

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

Error: Bioconductor version cannot be validated; no internet connection?

How can this problem can be resolved?

software error • 248 views
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@martin-morgan-1513
Last seen 3 days ago
United States

By default, BiocManager tries to

readLines("https://bioconductor.org/config.yaml")

Please try that. If it fails, it might be that you are behind a 'proxy'; see the 'Setting Proxies' section of ?download.file

It is possible to avoid this online check, but obviously installing packages requires internet access. BiocManager can be used offline as described in the 'Offline use' section of browseVignettes(package="BiocManager")

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Hi, I'm getting the same error when trying to install a package Error: Bioconductor version cannot be validated; no internet connection? 1: In file(con, "r") : URL 'https://bioconductor.org/config.yaml': status was 'Couldn't connect to server' 2: In file(con, "r") : URL 'http://bioconductor.org/config.yaml': status was 'Failure when receiving data from the peer' I'm working behind a proxy, but I didn't had problems installing packages until now. I don't know what can be going wrong. I'm working in VirtualBox with Ubuntu 20.04 distribution, no problems installing R packages in Windows. Any idea?

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Do the links work in an internet browser like chrome?

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Yes, they work fine

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And to be clear, does

readLines("https://bioconductor.org/config.yaml")

work? (or with http://)? If not, then it is definitely a proxy issue, but I am not sure how to tackle this other than pointing to the guidance on ?download.file. Sorry not to be more helpful.

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No, it cannot open the connection. Anyway, thanks for your help. I'll post the answer when I fix it.

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