RStudio Package Manager has official support for Bioconductor starting in version 1.2.0-27, please see the below links for further details:
- https://packagemanager.rstudio.com/client/#/repos/3/overview
If you are on an older version and can not upgrade at this time, please use one of the workarounds below.
If you are on an older version and can not upgrade at this time, please use one of the workarounds below.
1) You can download the Bioconductor packages as source tarballs, and then add those tarballs to a local source.
Example:
# Create a source to hold the Bioconductor packages
rspm create source --name=bioc
# For each package: download and add to the source
wget http://bioconductor.org/packages/release/bioc/src/ contrib/BiocGenerics_0.28.0. tar.gz
rspm add --source=bioc --path=BiocGenerics_0.28.0.tar.gz
2) Bioconductor packages live in Git repositories, so you can also use the built-in Git support to automatically pull in the package sources for either a specific release or the bleeding edge development branch. Do this by using creating a git source for each release, and then adding the desired Bioconductor packages to the relevant Git source.
Example:
# Create a git source for the bleeding edge Bioconductor packages
rspm create source --type=git --name=bioc-dev
# Add each package to the source
rspm add --source=bioc-dev --git-url=https://git.bioconductor.org/packages/ BiocGenerics.git
# OR create git source for a specific releases of Bioconductor
rspm create source --name=bioc-3.8
# Add each package to the source using the release branch
rspm add --source=bioc-3.8 --git-url=https://git.bioconductor.org/packages/ BiocGenerics.git --git-branch=RELEASE_3_8
Whether you use Git or a local source, finish by creating a repository to house the Bioconductor sources and then using install.packages, not BiocManager, to install the packages from RStudio Package Manager.
If you wish to use BiocManager to install the packages from RStudio Package manager, follow the instructions at this link. In these instructions, the repository type is set to BioConductor: https://docs.rstudio.com/rspm/admin/getting-started/configuration/#quickstart-bioconductor-repos.
Then, follow these steps to check for success:
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