This allows bioconductor packages to be installed and cleans up some of
the steps from the workflows to make them a bit more readable.
A new function is added to bin/dependencies.R called use_bioc_repos() that will
set "repos" option to the ones used by BioConductor and returns a function that
resets it to the user-set repository options.
BiocManager has been added to the default packages added.
One of the things we want to pay attention to: renv::dependencies() does not list hidden (recursive) dependencies, so when we create the DESCRIPTION file, I have updated it to create it based on the output of remotes::dev_package_deps(), and at that, only the ones that have changed. This way, when we call remotes::system_requirements(), it can install the requirements for these dependencies that are not explicitly listed.
This allows bioconductor packages to be installed and cleans up some of the steps from the workflows to make them a bit more readable.
A new function is added to bin/dependencies.R called use_bioc_repos() that will set "repos" option to the ones used by BioConductor and returns a function that resets it to the user-set repository options.
BiocManager has been added to the default packages added.
One of the things we want to pay attention to:
renv::dependencies()does not list hidden (recursive) dependencies, so when we create the DESCRIPTION file, I have updated it to create it based on the output ofremotes::dev_package_deps(), and at that, only the ones that have changed. This way, when we callremotes::system_requirements(), it can install the requirements for these dependencies that are not explicitly listed.