Update docs

README.md

@@ -11,7 +11,7 @@ Create a mini version of CRAN containing only selected packages
 
 ## Introduction
 
-At the end of 2014, CRAN consisted of more than 6,000 packages. By then end of 2017, the number of packages doubled to more than 12,000.  Many organisations need to maintain a private mirror of CRAN, but with only a subset of packages that are relevant to them.
+At the end of 201, CRAN consisted of more than 6,000 packages, and by 2017 this number doubled to more than 12,000.  Many organisations need to maintain a private mirror of CRAN, but with only a subset of packages that are relevant to them.
 
 The `miniCRAN` package makes it possible to create an internally consistent repository consisting of selected packages from CRAN-like repositories.  The user specifies a set of desired packages, and `miniCRAN` recursively reads the dependency tree for these packages, then downloads only this subset.  
 
@@ -49,15 +49,15 @@ The `miniCRAN` package itself doesn't introduce any system dependencies.  Howeve
 
 * On systems with the `rpm` package manager (Red Hat, CentOS) try:
 
-    ```sh
-    yum install libcurl-devel libxml2-devel openssl-devel
-    ```
+        ```
+        yum install libcurl-devel libxml2-devel openssl-devel
+        ```
 
 * On systems with the `aptitude` package manager (Debian, Ubuntu) try:
 
-    ```sh
-    apt-get install libcurl4-openssl-dev libxml2-devel openssl-devel
-    ```
+        ```
+        apt-get install libcurl4-openssl-dev libxml2-devel openssl-devel
+        ```
 
 
 ## Example:

docs/articles/miniCRAN-dependency-graph.R

@@ -0,0 +1,20 @@
+## ----init----------------------------------------------------------------
+library("miniCRAN")
+
+## ----pkgdep--------------------------------------------------------------
+tags <- "chron"
+pkgDep(tags, availPkgs = cranJuly2014)
+
+## ----makeDepGraph, warning=FALSE-----------------------------------------
+dg <- makeDepGraph(tags, enhances = TRUE, availPkgs = cranJuly2014)
+set.seed(1)
+plot(dg, legendPosition = c(-1, 1), vertex.size = 20)
+
+## ----so-tags, warning=FALSE, fig.width=10, fig.height=10-----------------
+tags <- c("ggplot2", "data.table", "plyr", "knitr", "shiny", "xts", "lattice")
+pkgDep(tags, suggests = TRUE, enhances = FALSE, availPkgs = cranJuly2014)
+
+dg <- makeDepGraph(tags, enhances = TRUE, availPkgs = cranJuly2014)
+set.seed(1)
+plot(dg, legendPosition = c(-1, -1), vertex.size = 10, cex = 0.7)
+

docs/articles/miniCRAN-introduction.R

@@ -0,0 +1,80 @@
+## ----make-repo-1---------------------------------------------------------
+library("miniCRAN")
+
+# use Revolution Analytics CRAN mirror
+revolution <- c(CRAN = "http://cran.microsoft.com")
+
+# Specify list of packages to download
+pkgs <- c("foreach")
+pkgList <- pkgDep(pkgs, repos = revolution, type = "source", suggests = FALSE, 
+                  availPkgs = cranJuly2014)
+pkgList
+
+## ----make-repo-2, eval=FALSE---------------------------------------------
+#  # 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=c("source", "win.binary"))
+
+## ----make-repo-3, eval=FALSE---------------------------------------------
+#  # List all files in miniCRAN
+#  list.files(pth, recursive = TRUE, full.names = FALSE)
+
+## ----make-repo-4, eval=FALSE---------------------------------------------
+#  # Check for available packages
+#  pkgAvail(repos = pth, type = "win.binary")[, c(1:3, 5)]
+
+## ----make-repo-5, eval=FALSE---------------------------------------------
+#  install.packages(pkgs,
+#                   repos = paste0("file:///", pth),
+#                   type = "source")
+
+## ----addto-repo-new-1, eval=FALSE----------------------------------------
+#  # Add new packages (from CRAN) to the miniCRAN repo
+#  addPackage("Matrix", path = pth, repos = revolution, type = c("source", "win.binary"))
+#  pkgAvail(repos = pth, type = "win.binary")[, c(1:3, 5)]
+
+## ----addto-repo-old-1, eval=FALSE----------------------------------------
+#  # 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")
+
+## ----addto-repo-old-2, eval=FALSE----------------------------------------
+#  # List package versions in the miniCRAN repo (produces warning about duplicates)
+#  pkgVersionsSrc <- checkVersions(pkgList, path = pth, type = "source")
+#  pkgVersionsBin <- checkVersions(pkgList, path = pth, type = "win.binary")
+#  
+#  # After inspecting package versions, remove old versions
+#  basename(pkgVersionsSrc) # duplicate versions
+#  basename(pkgVersionsBin)
+#  
+#  file.remove(pkgVersionsSrc[c(2,4,6)])
+#  
+#  # rebuild the package index after removing duplicate package versions
+#  updateRepoIndex(pth, type = c("source", "win.binary"))
+
+## ----addto-repo-old-3, eval=FALSE----------------------------------------
+#  pkgAvail(pth, type = "source")[, c(1:3, 5)] # contains the old versions
+#  pkgAvail(pth, type = "win.binary")[, c(1:3, 5)] # contains the current versions
+
+## ----update-repo-1, eval=FALSE-------------------------------------------
+#  # Check if updated packages are available
+#  oldPackages(path = pth, repos = revolution, type = "source")[, 1:3] # should need update
+#  oldPackages(path = pth, repos = revolution, type = "win.binary")[, 1:3] # should be current
+
+## ----update-repo-2, eval=FALSE-------------------------------------------
+#  # 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
+
+## ----cleanup, include=FALSE, eval=FALSE----------------------------------
+#  # Delete temporary folder
+#  unlink(pth, recursive = TRUE)
+

docs/articles/miniCRAN-non-CRAN-repos.R

@@ -0,0 +1,39 @@
+## ----setup---------------------------------------------------------------
+# Wrapper around available.packages ---------------------------------------
+
+index <- function(url, type = "source", filters = NULL, head = 5, cols = c("Package", "Version")) {
+  contribUrl <- contrib.url(url, type = type)
+  p <- available.packages(contribUrl, type = type, filters = filters)
+  p[1:head, cols]
+}
+
+
+## ----CRAN, eval=FALSE----------------------------------------------------
+#  CRAN <- "http://cran.r-project.org"
+#  index(CRAN)
+
+## ----revo, eval=FALSE----------------------------------------------------
+#  revoStable <- "http://packages.revolutionanalytics.com/cran/3.1/stable"
+#  index(revoStable)
+#
+#  revoMirror <- "http://cran.revolutionanalytics.com"
+#  index(revoMirror)
+
+## ----rforge, eval=FALSE--------------------------------------------------
+#  rforge <- "http://r-forge.r-project.org"
+#  index(rforge)
+
+## ----bioc, eval=FALSE----------------------------------------------------
+#  bioc <- local({
+#    env <- new.env()
+#    on.exit(rm(env))
+#    evalq(source("http://bioconductor.org/biocLite.R", local = TRUE), env)
+#    biocinstallRepos()
+#  })
+#
+#  bioc
+#  bioc[grep("BioC", names(bioc))]
+#
+#
+#  index(bioc["BioCsoft"])
+