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 = FALSE,
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" "2.5.0" NA
#> GRANCore "GRANCore" "0.2.1" NA
#> GRANstable "GRANstable" "0.10.0" NA
#> deptest "deptest" "1.0" NA
#> switchr "switchr" "0.12.8" NA
#> toyp "toyp" "1.0" NA
#> toypkg "toypkg" "1.0" NA
#> willfail "willfail" "1.0" NA
#> Depends
#> GRANBase "GRANCore, switchr (>= 0.9.28), methods"
#> GRANCore "R (>= 3.1.0), switchr (>= 0.9.28), methods"
#> GRANstable "GRANCore"
#> deptest "toypkg"
#> switchr "methods"
#> toyp NA
#> toypkg NA
#> willfail NA
#> Imports
#> GRANBase "tools, utils, htmlTable (>= 1.11.0), dplyr, sendmailR, covr,\nRCurl, jsonlite, stringi, stats, markdown"
#> GRANCore NA
#> GRANstable NA
#> deptest NA
#> switchr "tools, RJSONIO, RCurl"
#> toyp NA
#> toypkg NA
#> willfail NA
#> LinkingTo Suggests Enhances
#> GRANBase NA "parallel, rmarkdown, hexSticker, knitr" NA
#> GRANCore NA NA NA
#> GRANstable NA NA NA
#> deptest NA NA NA
#> switchr NA "BiocInstaller" NA
#> toyp NA NA NA
#> toypkg NA NA NA
#> willfail NA NA NA
#> License License_is_FOSS License_restricts_use OS_type
#> GRANBase "Artistic-2.0" NA NA NA
#> GRANCore "Artistic-2.0" NA NA NA
#> GRANstable "Artistic-2.0" NA NA NA
#> deptest "Artistic-2.0" NA NA NA
#> switchr "Artistic-2.0" NA NA NA
#> toyp "Artistic-2.0" NA NA NA
#> toypkg "Artistic-2.0" NA NA NA
#> willfail "Artistic-2.0" NA NA NA
#> Archs MD5sum NeedsCompilation File
#> GRANBase NA "d4551a2997b44726b231dcd37b2569fa" "no" NA
#> GRANCore NA "0bccdcd0f242ac3fe940e5e4eb0734c2" "no" NA
#> GRANstable NA "21455eff94d1fc4c70fe6415e2fa1892" "no" NA
#> deptest NA "f3e61d74448b8dae52e3d739064ac8f6" "no" NA
#> switchr NA "06e6c855a35ba5d019bb0bb0e7bb5bff" "no" NA
#> toyp NA "e95d016e23dbc23a03b7935a45da36bd" "no" NA
#> toypkg NA "8c24c6957f8142e09315a36d68961210" "no" NA
#> willfail NA "cdef9616813a49172fee1b9d780e3bce" "no" NA
#> Repository
#> GRANBase "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/repos/stable/src/contrib"
#> GRANCore "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/repos/stable/src/contrib"
#> GRANstable "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/repos/stable/src/contrib"
#> deptest "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/repos/stable/src/contrib"
#> switchr "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/repos/stable/src/contrib"
#> toyp "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/repos/stable/src/contrib"
#> toypkg "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/repos/stable/src/contrib"
#> willfail "file:///var/folders/79/l_n_5qr152d2d9d9xs0591lh0000gn/T/Rtmp9B2Qlw/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:
repo <- makeRepo(file.path(repdir, "stable"), cores=1L)
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.
repo2 <- makeRepo(repo,
build_pkgs = basename(testpkgs)[1],
cores = 1L)
