Start by creating the recursive dependency tree for your target packages.
For example, imagine a scenario where you want to create a repository that consists of the package foreach and its dependencies.
Start by creating the dependency list:
library("miniCRAN")
# use Revolution Analytics CRAN mirror
revolution <- c(CRAN="http://cran.revolutionanalytics.com")
# Specify list of packages to download
pkgs <- c("foreach")
pkgList <- pkgDep(pkgs, repos=revolution, type="source", suggests = FALSE, )
pkgList
## [1] "foreach" "codetools" "iterators"
Next, create a repository with the function makeRepo(). In this example, get the required files for source packages as well as windows binaries:
# Create temporary folder for miniCRAN
dir.create(pth <- file.path(tempdir(), "miniCRAN"))
# Make repo for source and win.binary
makeRepo(pkgList, path=pth, repos=revolution, type="source")
## Created new folder: C:/Users/ANDRIE~1/AppData/Local/Temp/RtmpcRONMK/miniCRAN/src/contrib
## [[1]]
## [1] 3
makeRepo(pkgList, path=pth, repos=revolution, type="win.binary")
## Created new folder: C:/Users/ANDRIE~1/AppData/Local/Temp/RtmpcRONMK/miniCRAN/bin/windows/contrib/3.2
## Warning in utils::download.packages(pkgs, destdir = pkgPath, available =
## pdb, : no package 'codetools' at the repositories
## [[1]]
## [1] 2
Investigate the repository file structure:
# List all files in miniCRAN
list.files(pth, recursive=TRUE, full.names=FALSE)
## [1] "bin/windows/contrib/3.2/foreach_1.4.2.zip"
## [2] "bin/windows/contrib/3.2/iterators_1.0.7.zip"
## [3] "bin/windows/contrib/3.2/PACKAGES"
## [4] "bin/windows/contrib/3.2/PACKAGES.gz"
## [5] "src/contrib/codetools_0.2-11.tar.gz"
## [6] "src/contrib/foreach_1.4.2.tar.gz"
## [7] "src/contrib/iterators_1.0.7.tar.gz"
## [8] "src/contrib/PACKAGES"
## [9] "src/contrib/PACKAGES.gz"
Use pkgAvail to list available packages in your repository:
# Check for available packages
pkgAvail(repos=pth, type="win.binary")[, c(1:3, 5)]
## Package Version Priority Imports
## foreach "foreach" "1.4.2" NA "codetools, utils, iterators"
## iterators "iterators" "1.0.7" NA NA
To install packages from a local repository, you need to use the URI convention file:/// to point to your file lcoation.
install.packages(pkgs,
repos = paste0("file:///", pth),
type = "source")
After creating a local miniCRAN repository, additional packages and their dependencies can easily be added. This mechanism can also be used to re-add an existing package to the miniCRAN repo.
# Add new packages (from CRAN) to the miniCRAN repo
addPackage("Matrix", path=pth, repos=revolution, type="source")
The value that is returned via addPackage is the number of packages written to the index file, i.e., the total number of packages in the repo of that type.
To add a specific version of a package from CRAN (or another CRAN-like repository), we can easily download the source packages from the CRAN archives. Dependencies for old package versions cannot be determined automatically and must be specified by the user.
Note: in order to to add binaries of older packages, you will need to download the source and build the binaries on the intended platform yourself. You will need the appropriate R development tools installed in order to build package binaries from source.
# create a data frame with the package and version info
oldVers <- data.frame(package=c("foreach", "codetools", "iterators"),
version=c("1.4.0", "0.2-7", "1.0.5"),
stringsAsFactors=FALSE)
# download old source package version and create repo index
addOldPackage(pkgList, path=pth, vers=oldVers$version, repos=revolution, type="source")
You will get a warning whenever there are multiple versions of a package saved in the repository. Currently, you need to manually remove duplicate versions before rebuilding the repository's package index.
Note: This last step is important, otherwise you may end up with a repo in an inconsistent state.
# List package versions in the miniCRAN repo (produces warning about duplicates)
pkgVersionsSrc <- checkVersions(pkgList, path=pth, type="source")
## Warning in checkVersions(pkgList, path = pth, type = "source"): Duplicate
## package(s): foreach, codetools, iterators
pkgVersionsBin <- checkVersions(pkgList, path=pth, type="win.binary")
# After inspecting package versions, remove old versions
basename(pkgVersionsSrc) # duplicate versions
## [1] "foreach_1.4.0.tar.gz" "foreach_1.4.2.tar.gz"
## [3] "codetools_0.2-11.tar.gz" "codetools_0.2-7.tar.gz"
## [5] "iterators_1.0.5.tar.gz" "iterators_1.0.7.tar.gz"
basename(pkgVersionsBin)
## [1] "foreach_1.4.2.zip" "iterators_1.0.7.zip"
file.remove(pkgVersionsSrc[c(2,4,6)])
## [1] TRUE TRUE TRUE
# rebuild the package index after removing duplicate package versions
updateRepoIndex(pth, type=c("source", "win.binary"))
## [[1]]
## [1] 7
##
## [[2]]
## [1] 2
To see the updated list of packages available in the miniCRAN repo:
pkgAvail(pth, type="source")[, c(1:3, 5)] # contains the old versions
## Package Version Priority
## codetools "codetools" "0.2-11" "recommended"
## expm "expm" "0.99-1.1" NA
## foreach "foreach" "1.4.0" NA
## iterators "iterators" "1.0.5" NA
## lattice "lattice" "0.20-30" "recommended"
## MASS "MASS" "7.3-40" "recommended"
## Matrix "Matrix" "1.1-5" "recommended"
## Imports
## codetools NA
## expm NA
## foreach "codetools, utils, iterators"
## iterators NA
## lattice "grid, grDevices, graphics, stats, utils"
## MASS NA
## Matrix "graphics, grid, stats, utils, lattice"
pkgAvail(pth, type="win.binary")[, c(1:3, 5)] # contains the current versions
## Package Version Priority Imports
## foreach "foreach" "1.4.2" NA "codetools, utils, iterators"
## iterators "iterators" "1.0.7" NA NA
This feature will be implemented in a future release.
Checking for updated versions of the packages currently stored in the miniCRAN repository:
# Check if updated packages are available
oldPackages(path=pth, repos=revolution, type="source")[, 1:3] # should need update
## Package LocalVer ReposVer
## foreach "foreach" "1.4.0" "1.4.2"
## iterators "iterators" "1.0.5" "1.0.7"
oldPackages(path=pth, repos=revolution, type="win.binary")[, 1:3] # should be current
## Package LocalVer ReposVer
Update the versions of the packages currently stored in the miniCRAN repository. By default, a prompt is given to confirm the update for each package. This prompt can be suppressed using ask=FALSE, which will update all packages. Be careful using this option if you want to keep certain packages at an older version.
# Update available packages
updatePackages(path=pth, repos=revolution, type="source", ask=FALSE) # should need update
updatePackages(path=pth, repos=revolution, type="win.binary", ask=FALSE) # should be current