As mentioned in #6, the Bioc-version can be inconsistent with the one requested after the setup-r-dependencies step. I suspect this is due to the use of pak in setup-r-dependencies, which sets its own package repository settings (see pak::repo_get()) and defaults to Bioc-release, thereby ignoring the configuration done by the setup-bioc step.
This PR sets the environment variable R_BIOC_VERSION environment variable during the setup-bioc step, to ensure that pak will use the requested Bioc-version in subsequent installation steps.
As mentioned in #6, the Bioc-version can be inconsistent with the one requested after the
setup-r-dependenciesstep. I suspect this is due to the use of pak insetup-r-dependencies, which sets its own package repository settings (seepak::repo_get()) and defaults to Bioc-release, thereby ignoring the configuration done by thesetup-biocstep.This PR sets the environment variable
R_BIOC_VERSIONenvironment variable during thesetup-biocstep, to ensure that pak will use the requested Bioc-version in subsequent installation steps.See also https://github.com/r-lib/pak/issues/309#issuecomment-876202541