Question

Error wth Installation BiocManager

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hasmikmd ▴ 10

@hasmikmd-23611

Last seen 5.5 years 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 • 8.8k views

ADD COMMENT • link updated 3.8 years ago by weiran • 0 • written 5.5 years ago by hasmikmd ▴ 10

score 0 · Answer 1 · 2020-05-28

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Martin Morgan 25k

@martin-morgan-1513

Last seen 10 months 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")

ADD COMMENT • link 5.5 years ago Martin Morgan 25k

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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?

ADD REPLY • link 4.5 years ago beaferbl • 0

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Do the links work in an internet browser like chrome?

ADD REPLY • link 4.5 years ago Martin Morgan 25k

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Yes, they work fine

ADD REPLY • link 4.5 years ago beaferbl • 0

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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.

ADD REPLY • link 4.5 years ago Martin Morgan 25k

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

ADD REPLY • link 4.5 years ago beaferbl • 0

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hi, have you fix this problem? I have also met this problem. Thank you very much.

ADD REPLY • link 3.8 years ago weiran • 0