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-boun...@r-project.org> on behalf of Zuguang Gu <joker...@gmail.com> Date: Tuesday, November 7, 2023 at 3:33 PM To: Cc: Chiagozie Ifeoma Pickens <chiagozie-ono...@northwestern.edu>, bioc-devel@r-project.org <bioc-devel@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()`. [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]]
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