RSuite (version 0.37-253)

repo_upload_bioc_package: Loads package from the Bioconductor repository.

Description

It will download Bioconductor repository, build package into package file and will upload it into the repository. It will search dependencies in provided project's repositories.

Usage

repo_upload_bioc_package(repo_manager, repo, ..., prj = NULL,
  pkg_type = .Platform$pkgType, with_deps = FALSE,
  skip_build_steps = NULL, keep_sources = FALSE)

Arguments

repo_manager

repo manager to use for uploading. (type: rsuite_repo_manager)

repo

repository address in format [username:password@][release/]repo[#revision]. See devtools::install_bioc for more information.

...

Bioconductor specific parameters passed to devtools::install_bioc.

prj

project object to use. If not passed will init project from working directory. (type: rsuite_project, default: NULL)

pkg_type

type of packages to upload (type: character, default: platform default)

with_deps

If TRUE will include pkgs dependencies while uploading into the repository. Packages in repository satisfying pkgs requirements will not be included. (type: logical, default: FALSE)

skip_build_steps

character vector with steps to skip while building project packages. Can contain following entries:

specs

Process packages specifics

docs

Try build documentation with roxygen

imps

Perform imports validation

tests

Run package tests

rcpp_attribs

Run rppAttribs on the package

vignettes

Build package vignettes

(type: character(N), default: NULL).

keep_sources

if TRUE downloaded package sources will not be removed after building. (type: logical, default: FALSE)

Details

Logs all messages onto rsuite logger. Use logging::setLevel to control logs verbosity.

See Also

Other in repository management: repo_mng_init, repo_mng_list, repo_mng_remove, repo_mng_start, repo_mng_stop, repo_upload_ext_packages, repo_upload_github_package, repo_upload_package_files, repo_upload_pkgzip, repo_upload_prj_packages

Examples

# NOT RUN {
  # create exemplary project base folder
  prj_base <- tempfile("example_")
  dir.create(prj_base, recursive = TRUE, showWarnings = FALSE)

  # start project
  prj <- prj_start("my_project", skip_rc = TRUE, path = prj_base)

  # set it to use in project repository and CRAN
  prj_config_set_repo_adapters(c("Dir", "CRAN"), prj = prj)

  # start managing in project repository
  rmgr <- repo_mng_start("Dir", prj = prj, ix = 1)

  # upload logging package from cran repository
  repo_upload_bioc_package(rmgr, repo = "BiocGenerics",
                           prj = prj, pkg_type = "source")

  # list available packages
  repo_mng_list(rmgr, pkg_type = "source")

  # stop repository management
  repo_mng_stop(rmgr)
# }
# NOT RUN {
# }