Introduction
GRANBase is an open source set of tools for testing and deploying R packages as package repositories for both general deployment and result reproduction. It is based on the switchr framework, and allows users to deploy package manifests as validated repositories.It is centered around the R repository mechanism for pacakge distribution. GRANBase provides three major areas of functionality:
- The ability to create one or more
R repositories by pulling and testing packages from diverse locations (scm, local directory), in a manner conducive to continuous integration
- Tools for recreating specific environments based on sessionInfos, and for creating lightweight virtual repositories which serve the exact package versions specified in the sessoinInfo
- Tools for assessing the potential impact of upgrading a package, to assist administrators in keeping systems up-to-date while protecting reproducibility and comparability of results in long-running core applications.
Creating GRANBase repositories
GRANBase relies on the GRANCore framework for repository management, which in turn is based on package manifests (PkgManifest or SeedingManifest objects from the switchr framework).
Given a manifest, initial construction and rebuilding of individual GRANBase repositories (referred to as subrepositories because GRANBase supports a form of branched deployment) is performed via the makeRepo function. For example:
testpkgs <- list.files(system.file("testpkgs", package = "GRANBase"),
full.names = TRUE)
man <- PkgManifest(name = basename(testpkgs),
url = testpkgs, type = "local")
repdir <- file.path(tempdir(), "repos")
if(!file.exists(repdir)) dir.create(repdir)
repo <- makeRepo(man,
repo_name= "stable",
basedir = repdir,
destination = repdir,
cores = 1L,
install_test = TRUE,
check_test = FALSE)
NOTE: In the above code, we disabled the installation and R CMD check-related tests due to not playing well with the CRAN build system. In most cases, these should be TRUE in order to create a validated package repository. Also note that in the output below, the willfail package appears in the repository. This would not be the case if the check test was turned on, as it is engineered as a test case to fail check.
available.packages(repo, type="source")
#> Package Version Priority
#> GRANBase "GRANBase" "2.6.19" NA
#> GRANCore "GRANCore" "0.2.6" NA
#> GRANstable "GRANstable" "0.10.0" NA
#> deptest "deptest" "1.0" NA
#> switchr "switchr" "0.14.1" NA
#> toyp "toyp" "1.0" NA
#> toypkg "toypkg" "1.0" NA
#> Depends
#> GRANBase "GRANCore, switchr (>= 0.13.4), methods"
#> GRANCore "R (>= 3.1.0), switchr (>= 0.9.28), methods"
#> GRANstable "GRANCore"
#> deptest "toypkg"
#> switchr "methods"
#> toyp NA
#> toypkg NA
#> Imports
#> GRANBase "tools, utils, htmlTable (>= 1.11.0), dplyr, sendmailR, covr,\nRCurl, jsonlite, stringi, stats, markdown, desc"
#> GRANCore NA
#> GRANstable NA
#> deptest NA
#> switchr "tools, RJSONIO, RCurl"
#> toyp NA
#> toypkg NA
#> LinkingTo Suggests
#> GRANBase NA "parallel, rmarkdown, hexSticker, knitr, DT (>= 0.2)"
#> GRANCore NA NA
#> GRANstable NA NA
#> deptest NA NA
#> switchr NA NA
#> toyp NA NA
#> toypkg NA NA
#> Enhances License License_is_FOSS License_restricts_use
#> GRANBase NA "Artistic-2.0" NA NA
#> GRANCore NA "Artistic-2.0" NA NA
#> GRANstable NA "Artistic-2.0" NA NA
#> deptest NA "Artistic-2.0" NA NA
#> switchr NA "Artistic-2.0" NA NA
#> toyp NA "Artistic-2.0" NA NA
#> toypkg NA "Artistic-2.0" NA NA
#> OS_type Archs MD5sum
#> GRANBase NA NA "593efb233c1f2aff37aa9acb22bed944"
#> GRANCore NA NA "50d07fd01d9cdd1475cd6630d2eb3fcb"
#> GRANstable NA NA "e741036d4d9c8f263775d6cfd7f106fc"
#> deptest NA NA "2f8d8daf7a2d812fc19ad3a0e68f0471"
#> switchr NA NA "9990925259a3d0e29b87a447b3906e0d"
#> toyp NA NA "9b884923688483153538c7e722a9111f"
#> toypkg NA NA "e6512421fcf88ed9d8189c37e9ee7deb"
#> NeedsCompilation File
#> GRANBase "no" NA
#> GRANCore "no" NA
#> GRANstable "no" NA
#> deptest "no" NA
#> switchr "no" NA
#> toyp "no" NA
#> toypkg "no" NA
#> Repository
#> GRANBase "file:///var/folders/14/z0rjkn8j0n5dj1lkdd4ng1600000gn/T/RtmppqoEKc/repos/stable/src/contrib"
#> GRANCore "file:///var/folders/14/z0rjkn8j0n5dj1lkdd4ng1600000gn/T/RtmppqoEKc/repos/stable/src/contrib"
#> GRANstable "file:///var/folders/14/z0rjkn8j0n5dj1lkdd4ng1600000gn/T/RtmppqoEKc/repos/stable/src/contrib"
#> deptest "file:///var/folders/14/z0rjkn8j0n5dj1lkdd4ng1600000gn/T/RtmppqoEKc/repos/stable/src/contrib"
#> switchr "file:///var/folders/14/z0rjkn8j0n5dj1lkdd4ng1600000gn/T/RtmppqoEKc/repos/stable/src/contrib"
#> toyp "file:///var/folders/14/z0rjkn8j0n5dj1lkdd4ng1600000gn/T/RtmppqoEKc/repos/stable/src/contrib"
#> toypkg "file:///var/folders/14/z0rjkn8j0n5dj1lkdd4ng1600000gn/T/RtmppqoEKc/repos/stable/src/contrib"
Note that the repository contains the package GRANstable. This was generated automatically, and exports a defaultGRAN() function which the switchr package will use when the package is loaded to incorporate our package into the set of default repositories.
GRANBase represents (sub)repositories as GRANRepository objects, which come from the GRANCore package. These objects contain all the information required to build and deploy the repository.
Once a repository is created, its GRANRepository object is saved within the created directory structure as the repo.R file. This allows future builds to be invoked by the simpler syntax of passing a GRANRepository object or path to a created repository to makeRepo() directly:
The makeRepo() function also accepts a build_pkgs argument, which will cause only the specified packages (and their reverse dependencies) to be rebuilt, regardless of changes in version number.
