localize: Copy packages, folders, or files to or from google buckets.

In AnVIL: Bioconductor on the AnVIL compute environment

Description

'localize()': recursively synchronizes files from a Google storage bucket ('source') to the local file system ('destination'). This command acts recursively on the 'source' directory, and does not delete files in 'destination' that are not in 'source.

'delocalize()': synchronize files from a local file system ('source') to a Google storage bucket ('destination'). This command acts recursively on the 'source' directory, and does not delete files in 'destination' that are not in 'source'.

'install()': install R / Bioconductor packages, using fast pre-built 'binary' libraries if available.

'repositories()': repositories to search for binary (if available), Bioconductor, and CRAN packages.

'add_libpaths()': Add local library paths to '.libPaths()'.

Usage

localize(source, destination, dry = TRUE)

delocalize(source, destination, unlink = FALSE, dry = TRUE)

install(
  pkgs,
  lib = .libPaths()[1],
  ...,
  version = BiocManager::version(),
  binary_base_url = "https://storage.googleapis.com",
  verbose = getOption("verbose")
)

repositories(
  version = BiocManager::version(),
  binary_base_url = "https://storage.googleapis.com"
)

add_libpaths(paths)

Arguments

source	'character(1)', a google storage bucket or local file system directory location.
destination	'character(1)', a google storage bucket or local file system directory location.
dry	'logical(1)', when 'TRUE' (default), return the consequences of the operation without actually performing the operation.
unlink	'logical(1)' remove (unlink) the file or directory in 'source'. Default: 'FALSE'.
pkgs	'character()' packages to install from binary repository.
lib	'character(1)' library path (directory) in which to install 'pkgs'; defaults to '.libPaths()[1]'.
...	additional arguments, passed to 'install.packages()'.
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.
verbose	'logical(1)' report on package installation progress?
paths	'character()': vector of directories to add to '.libPaths()'. Paths that do not exist will be created.

Details

'repositories()' prepends an additional repository URI to 'BiocManager::repositories()'. The URI is formed by concatenating 'binary_base_url', the environment variables ‘TERRA_R_PLATFORM' and the ’major' and 'minor' components of 'TERRA_R_PLATFORM_BINARY_VERSION' and 'BiocManager::version()'. The URI is only prepended if a CRAN-style repostiory exists at that location, with binary package tar.gz content described by 'src/contrib/PACKAGES.gz'.

Value

'localize()': exit status of function 'gsutil_rsync()'.

'delocalize()': exit status of function 'gsutil_rsync()'

'install()': return value of 'install.packages()'.

'repositories()': character() of binary (if available), Bioconductor, and CRAN repositories.

'add_libpaths()': updated .libPaths(), invisibly.

Examples

## Not run: install(c('BiocParallel', 'BiocGenerics'))

repositories()

## Not run: add_libpaths("/tmp/host-site-library")

AnVIL documentation built on Nov. 8, 2020, 4:57 p.m.