├── .Rbuildignore ├── .gitattributes ├── .github ├── .gitignore ├── CODE_OF_CONDUCT.md └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ ├── pr-commands.yaml │ └── test-coverage.yaml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── MAINTENANCE.md ├── Makefile ├── NAMESPACE ├── NEWS.md ├── R ├── bioc-standalone.R ├── bioc.R ├── circular.R ├── cran.R ├── dcf.R ├── decompress.R ├── deps.R ├── devel.R ├── download.R ├── git-auth.R ├── git.R ├── github.R ├── install-bioc.R ├── install-bitbucket.R ├── install-cran.R ├── install-dev.R ├── install-git.R ├── install-github.R ├── install-gitlab.R ├── install-local.R ├── install-remote.R ├── install-svn.R ├── install-url.R ├── install-version.R ├── install.R ├── json.R ├── package-deps.R ├── package.R ├── parse-git.R ├── remotes-package.R ├── submodule.R ├── system.R ├── system_requirements.R └── utils.R ├── README.Rmd ├── README.md ├── _pkgdown.yml ├── codecov.yml ├── inst ├── COPYRIGHTS ├── install-github.R └── install-github.Rin ├── install-github.R ├── man ├── available_packages.Rd ├── bioc_install_repos.Rd ├── download.Rd ├── download_version.Rd ├── git_credentials.Rd ├── github_refs.Rd ├── github_remote.Rd ├── gitlab_pat.Rd ├── install_bioc.Rd ├── install_bitbucket.Rd ├── install_cran.Rd ├── install_deps.Rd ├── install_dev.Rd ├── install_git.Rd ├── install_github.Rd ├── install_gitlab.Rd ├── install_local.Rd ├── install_remote.Rd ├── install_svn.Rd ├── install_url.Rd ├── install_version.Rd ├── package_deps.Rd ├── parse-git-repo.Rd ├── remotes-package.Rd ├── standardise_dep.Rd ├── system_requirements.Rd └── update_packages.Rd ├── remotes.Rproj ├── tests ├── testthat.R └── testthat │ ├── Biobase │ └── DESCRIPTION │ ├── MASS │ └── DESCRIPTION │ ├── _snaps │ └── github.md │ ├── archives │ ├── foo.tar │ ├── foo.tar.bz2 │ ├── foo.tar.gz │ ├── foo.tbz │ ├── foo.tgz │ ├── foo.zip │ └── foo │ │ ├── DESCRIPTION │ │ ├── R │ │ └── foo.R │ │ └── configure │ ├── helper.R │ ├── invalidpkg │ └── DESCRIPTION │ ├── noremotes │ └── DESCRIPTION │ ├── submodule │ ├── DESCRIPTION │ └── NAMESPACE │ ├── test-bioc.R │ ├── test-cran.R │ ├── test-dcf.R │ ├── test-decompress.R │ ├── test-deps.R │ ├── test-devel.R │ ├── test-download.R │ ├── test-git.R │ ├── test-github.R │ ├── test-install-bioc.R │ ├── test-install-bitbucket.R │ ├── test-install-cran.R │ ├── test-install-deps.R │ ├── test-install-dev.R │ ├── test-install-git.R │ ├── test-install-github.R │ ├── test-install-gitlab.R │ ├── test-install-local.R │ ├── test-install-remote.R │ ├── test-install-svn.R │ ├── test-install-url.R │ ├── test-install-version.R │ ├── test-install.R │ ├── test-json.R │ ├── test-package-deps.R │ ├── test-package.R │ ├── test-parse-git.R │ ├── test-script.R │ ├── test-submodule.R │ ├── test-system.R │ ├── test-system_requirements.R │ ├── test-utils.R │ ├── urlremotes │ └── DESCRIPTION │ └── withremotes │ └── DESCRIPTION └── vignettes └── dependencies.Rmd /.Rbuildignore: 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