[Bioc-devel] Unable to install Bioconductor despite multiple attempts and troubleshooting

[Martin Morgan]

Using setRepositories()does not give the correct repositories for all Bioconductor releases. For instance, the R-4-3 version might be associated with Bioconductor 3.17 (the �previous� release) or 3.18 (the �current� release). R thinks Bioc 3.17 is appropriate (not wrong, just not correct)

> utils:::.BioC_version_associated_with_R_version()
[1] '3.17'

Whereas BiocManager::version() knows best

> BiocManager::version()
[1] '3.18'

BiocManager knows best because it�s consulted config.yaml, the problem file!

Likely, Chiagozie is behind a proxy, and visting https://bioconductor.org/config.yaml �works� because the browser resolves the proxy. But I�d bet `readLines()` on the same url fails.

I *think* the solution is in ?download.file searching for �proxy�.

Martin Martin

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Zuguang Gu <jokergoo using gmail.com>
Date: Tuesday, November 7, 2023 at 3:33 PM
To:
Cc: Chiagozie Ifeoma Pickens <Chiagozie-Ononye using northwestern.edu>, bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Unable to install Bioconductor despite multiple attempts and troubleshooting
An alternative way is to first set `setRepositories(ind = 1:4)`. This will
add Bioconductor repos to the default repos in your R session.
Then you can use `install.packages()` instead of `BiocManager::install()`.

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