BiocManager
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Bioconductor
CRAN Package For Managing Bioconductor Packages
Suppose we want to establish the version of Bioconductor in a new session, but we want to use the AnVIL-oriented binary repository for Bioconductor packages. It seems reasonable to try...
The vignette suggests to use: https://github.com/Bioconductor/BiocManager/blob/ff48728b9a3bcc00e4013c9d2ec9e7e0d1c97b96/vignettes/BiocManager.Rmd#L248 to launch `R` with `R_LIBS_USER` set that way. Not sure if you've already explored it, but `R` on Windows actually supports the following: ```...
The vignette mentions `CRAN_mirror`; https://github.com/Bioconductor/BiocManager/blob/ce4586155ec7f59bffb6d040321bb569713ce2ac/vignettes/BiocManager.Rmd#L284-L287 Is that `CRAN_mirror` meant to be `CRAN` that R recognizes? FWIW, contrary to `BioC_manager`, `CRAN_mirror` is _not_ something R itself is aware of. I searched...
The change in 1fed5289f00871b8b4d42736c7c329378da21627 is causing emission of annoying messages in all packages that `Import` **BiocManager**. For example, **BiocStyle** imports **BiocManager**, and this is causing all my vignettes and reports...
A user trying to update a package that has been installed under an unwritable (e.g., windows Administrator) account is told that the package could not be updated. This could be...
Unless I've missed something, you have to use an alternative like `devtools::install('.', dependencies=TRUE, build_vignettes=TRUE, repos = BiocManager::repositories())` to install a local package normally or in Dockerfiles, taking us away from...
So we have a bunch of failures on the BioC 3.10 report today because BiocManager is complaining with: ``` unknown Bioconductor version '3.10'; see https://bioconductor.org/install` ``` That's because the build...
remotes::install_github() converts warnings about dependencies that cannot be installed (e.g., because of missing binaries) into errors. This is different from the install.packages() behavior in non-github installations by BiocManager. This can...
BiocManager delegates to remotes::install_github() to install github packages. The remotes package offers to update Bioc-hosted packages to their github version, which is counter to the BiocManager goal of providing a...
Hi Martin, @mtmorgan Here is a draft PR to re-direct `CI=TRUE` environments to low-cost egress services via the `BioC_mirror` option. cc: @almahmoud @vjcitn
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CRAN Package For Managing Bioconductor Packages