Modify all vignettes and examples to assume that neither github nor C…

…RAN are available. #63

DESCRIPTION

@@ -14,7 +14,7 @@ Description: Makes it possible to create an internally consistent
     subset. The user can then install packages from this repository directly, 
     rather than from CRAN.  This is useful in production settings, e.g. server 
     behind a firewall, or remote locations with slow broadband access.
-Version: 0.2.2
+Version: 0.2.4
 URL: https://github.com/RevolutionAnalytics/miniCRAN
 BugReports: https://github.com/RevolutionAnalytics/miniCRAN/issues
 Date: 2015-03-26

inst/doc/miniCRAN-dependency-graph.R

@@ -3,18 +3,18 @@ library("miniCRAN")
 
 ## ----pkgdep--------------------------------------------------------------
 tags <- "chron"
-pkgDep(tags)
+pkgDep(tags, availPkgs = cranJuly2014)
 
 ## ----makeDepGraph, warning=FALSE-----------------------------------------
-dg <- makeDepGraph(tags, enhances=TRUE)
+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)
+pkgDep(tags, suggests = TRUE, enhances=FALSE, availPkgs = cranJuly2014)
 
-dg <- makeDepGraph(tags, enhances=TRUE)
+dg <- makeDepGraph(tags, enhances=TRUE, availPkgs = cranJuly2014)
 set.seed(1)
 plot(dg, legendPosition = c(-1, -1), vertex.size=10, cex=0.7)
 

inst/doc/miniCRAN-dependency-graph.rmd

@@ -49,14 +49,14 @@ library("miniCRAN")
 
 ```{r pkgdep}
 tags <- "chron"
-pkgDep(tags)
+pkgDep(tags, availPkgs = cranJuly2014)
 ```
 
 
 To create an igraph plot of the dependencies, use the function `makeDepGraph()` and plot the results: 
 
 ```{r makeDepGraph, warning=FALSE}
-dg <- makeDepGraph(tags, enhances=TRUE)
+dg <- makeDepGraph(tags, enhances=TRUE, availPkgs = cranJuly2014)
 set.seed(1)
 plot(dg, legendPosition = c(-1, 1), vertex.size=20)
 ```
@@ -72,9 +72,9 @@ As a final example, create a dependency graph of seven very popular R packages:
 
 ```{r 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)
+pkgDep(tags, suggests = TRUE, enhances=FALSE, availPkgs = cranJuly2014)
 
-dg <- makeDepGraph(tags, enhances=TRUE)
+dg <- makeDepGraph(tags, enhances=TRUE, availPkgs = cranJuly2014)
 set.seed(1)
 plot(dg, legendPosition = c(-1, -1), vertex.size=10, cex=0.7)
 ```

inst/doc/miniCRAN-introduction.R

@@ -6,72 +6,72 @@ 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 <- pkgDep(pkgs, repos=revolution, type="source", suggests = FALSE, availPkgs = cranJuly2014)
 pkgList
 
-## ----make-repo-2---------------------------------------------------------
-# Create temporary folder for miniCRAN
-dir.create(pth <- file.path(tempdir(), "miniCRAN"))
+## ----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="source")
+#  makeRepo(pkgList, path=pth, repos=revolution, type="win.binary")
 
-# Make repo for source and win.binary
-makeRepo(pkgList, path=pth, repos=revolution, type="source")
-makeRepo(pkgList, path=pth, repos=revolution, type="win.binary")
+## ----make-repo-3, eval=FALSE---------------------------------------------
+#  # List all files in miniCRAN
+#  list.files(pth, recursive=TRUE, full.names=FALSE)
 
-## ----make-repo-3---------------------------------------------------------
-# List all files in miniCRAN
-list.files(pth, recursive=TRUE, full.names=FALSE)
-
-## ----make-repo-4---------------------------------------------------------
-# Check for available packages
-pkgAvail(repos=pth, type="win.binary")[, c(1:3, 5)]
+## ----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----------------------------------------------------
-# Add new packages (from CRAN) to the miniCRAN repo
-addPackage("Matrix", path=pth, repos=revolution, type="source")
-
-## ----addto-repo-old-1----------------------------------------------------
-# 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----------------------------------------------------
-# 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----------------------------------------------------
-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-------------------------------------------------------
-# 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-------------------------------------------------------
-# 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----------------------------------------------
-# Delete temporary folder
-unlink(pth, recursive = TRUE)
+## ----addto-repo-new-1, eval=FALSE----------------------------------------
+#  # Add new packages (from CRAN) to the miniCRAN repo
+#  addPackage("Matrix", path=pth, repos=revolution, type="source")
+
+## ----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)