AnVIL-defunct: Defunct functions in package 'AnVIL'

In Bioconductor/AnVIL: Bioconductor on the AnVIL compute environment

Defunct functions in package ‘AnVIL’

Description

These functions are provided for compatibility with older versions of ‘AnVIL’ only, and will be defunct at the next release.

install() is deprecated in favor of BiocManager::install().

repository() is deprecated in favor of BiocManager::containerRepository().

repositories() is deprecated in favor of BiocManager::repositories().

Usage

avworkflow_configuration(
  configuration_namespace,
  configuration_name,
  namespace = avworkspace_namespace(),
  name = avworkspace_name()
)

avworkflow_import_configuration(
  config,
  namespace = avworkspace_namespace(),
  name = avworkspace_name()
)

Gen3Fence()

Gen3Indexd()

Gen3Sheepdog()

Gen3Peregrine()

install(
  pkgs = character(),
  ...,
  version = BiocManager::version(),
  binary_base_url = BINARY_BASE_URL
)

repository(version = BiocManager::version(), binary_base_url = BINARY_BASE_URL)

repositories(
  version = BiocManager::version(),
  binary_base_url = BINARY_BASE_URL
)

Arguments

configuration_namespace	character(1).
configuration_name	character(1).
namespace	character(1).
name	character(1).
config	avworkflow_configuration object.
pkgs	character() packages to install from binary repository.
...	additional arguments. install() passes additional arguments to BiocManager::install(). print.repository_stats() ignores the additional arguments.
version	character(1) or package_version Bioconductor version, e.g., "3.12".
binary_base_url	character(1) host and base path for binary package 'CRAN-style' repository; not usually required by the end-user.

Details

The following functions are defunct and will be deleted after the next Bioconductor release of ‘AnVIL’. Use the replacement indicated below:

• avworkflow_configuration(): avworkflow_configuration_get

• avworkflow_import_configuration(): avworkflow_configuration_set

Value

⁠gen3_*⁠ APIs are not fully implemented, because a service endpoint has not been identified.

Gen3Fence() returns the authentication API at https://raw.githubusercontent.com/uc-cdis/fence/master/openapis/swagger.yaml

Gen3Indexd() returns the indexing service API documented at https://raw.githubusercontent.com/uc-cdis/indexd/master/openapis/swagger.yaml

Gen3Sheepdog returns the submission services API at https://raw.githubusercontent.com/uc-cdis/sheepdog/master/openapi/swagger.yml

Gen3Peregrine returns the graphQL query services API at https://raw.githubusercontent.com/uc-cdis/peregrine/master/openapis/swagger.yaml

Bioconductor/AnVIL documentation built on April 12, 2024, 6:41 p.m.