Code formatting

.Rbuildignore

@@ -3,3 +3,5 @@ LICENSE.md
 .travis.yml
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^docs$
+^_pkgdown\.yml$

DESCRIPTION

@@ -12,8 +12,8 @@ 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 (or zero) Internet access.
-Date: 2017-11-15
-Version: 0.2.10.9000
+Date: 2017-12-19
+Version: 0.2.11.9000
 URL: https://github.com/andrie/miniCRAN
 BugReports: https://github.com/andrie/miniCRAN/issues
 SystemRequirements: Imports the `curl` and `XML` packages. These have system

NEWS

@@ -1,3 +1,11 @@
+miniCRAN v0.2.11.9000 (Release date: in development)
+================
+
+New features: 
+
+* Used `pkgdown` to build documentation site
+
+
 miniCRAN v0.2.10.9000
 =====================
 

README.md

@@ -11,16 +11,18 @@ Create a mini version of CRAN containing only selected packages
 
 ## Introduction
 
-At the end of 2014, CRAN consisted of more than 6,000 packages.  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 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.
 
-`miniCRAN` 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.  
+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.  
 
 ## Important functions:
 
-* Find package dependencies: `pkgDep()`
-* Make repository (with or without downloading packages): `makeRepo()`
-* Add additonal packages (and their dependencies) to existing repository: `addPackage()`
-* Update the versions of packages currently in the repository: `updatePackages()`
+Function           | Use it for
+--------------     | ------------------------------------------
+`pkgDep()`         | Find package dependencies
+`makeRepo()`       | Make repository (with or without downloading packages)
+`addPackage()`     | Add additonal packages (and their dependencies) to existing repository
+`updatePackages()` | Update the versions of packages currently in the repository
 
 ## Installation:
 
@@ -33,7 +35,7 @@ library("miniCRAN")
 
 ### Development version
 
-Get the latest stable development version from github:
+Get the latest development version from github:
 
 ```r
 # Use `devtools` to install directly from github
@@ -43,19 +45,19 @@ install_github("andrie/miniCRAN")
 
 ### System requirements
 
-The `miniCRAN` package itself doesn't introduce any system dependencies.  However, the package imports [`curl`](https://cran.r-project.org/package=curl) and `XML` packages. These have system requirements on `libxml2-devel`, `libcurl-devel` and `openssl-devel`.
+The `miniCRAN` package itself doesn't introduce any system dependencies.  However, the package imports the  [`curl`](https://cran.r-project.org/package=curl) and [`XML`](https://cran.r-project.org/package=XML) packages. These have system requirements on `libxml2-devel`, `libcurl-devel` and `openssl-devel`.
 
-On systems with the `rpm` package manager (Red Hat, CentOS) try:
+* On systems with the `rpm` package manager (Red Hat, CentOS) try:
 
-```bash
-yum install libcurl-devel libxml2-devel openssl-devel
-```
+    ```sh
+    yum install libcurl-devel libxml2-devel openssl-devel
+    ```
 
-On systems with the `aptitude` package manager (Debian, Ubuntu) try:
+* On systems with the `aptitude` package manager (Debian, Ubuntu) try:
 
-```bash
-apt-get install libcurl4-openssl-dev libxml2-devel openssl-devel
-```
+    ```sh
+    apt-get install libcurl4-openssl-dev libxml2-devel openssl-devel
+    ```
 
 
 ## Example:
@@ -65,7 +67,7 @@ apt-get install libcurl4-openssl-dev libxml2-devel openssl-devel
 
 library("miniCRAN")
 pkgs <- c("ggplot2", "plyr", "reshape2")
-makeRepo(pkgDep(pkgs), path=file.path(tempdir(), "miniCRAN"), download=TRUE)
+makeRepo(pkgDep(pkgs), path = file.path(tempdir(), "miniCRAN"))
 ```
 
 ## Supported by Microsoft

inst/doc/miniCRAN-dependency-graph.rmd

@@ -2,10 +2,7 @@
 title:  "Using miniCRAN to identify package dependencies"
 author: "Andrie de Vries"
 date:   "`r as.character(format(Sys.Date(), format='%B %d, %Y'))`"
-output:
-  html_document:
-    self_contained: yes
-    toc: yes
+output: rmarkdown::html_vignette
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Using miniCRAN to identify package dependencies}

inst/doc/miniCRAN-introduction.R

@@ -2,11 +2,12 @@
 library("miniCRAN")
 
 # use Revolution Analytics CRAN mirror
-revolution <- c(CRAN="http://cran.microsoft.com")
+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 <- pkgDep(pkgs, repos = revolution, type = "source", suggests = FALSE, 
+                  availPkgs = cranJuly2014)
 pkgList
 
 ## ----make-repo-2, eval=FALSE---------------------------------------------
@@ -18,11 +19,11 @@ pkgList
 
 ## ----make-repo-3, eval=FALSE---------------------------------------------
 #  # List all files in miniCRAN
-#  list.files(pth, recursive=TRUE, full.names=FALSE)
+#  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)]
+#  pkgAvail(repos = pth, type = "win.binary")[, c(1:3, 5)]
 
 ## ----make-repo-5, eval=FALSE---------------------------------------------
 #  install.packages(pkgs,
@@ -31,22 +32,24 @@ pkgList
 
 ## ----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)]
+#  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)
+#  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$version, repos=revolution, type="source")
+#  addOldPackage(pkgList, path = pth, vers = oldVers$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")
+#  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
@@ -55,21 +58,21 @@ pkgList
 #  file.remove(pkgVersionsSrc[c(2,4,6)])
 #  
 #  # rebuild the package index after removing duplicate package versions
-#  updateRepoIndex(pth, type=c("source", "win.binary"))
+#  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
+#  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
+#  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
+#  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

inst/doc/miniCRAN-introduction.rmd

@@ -2,10 +2,7 @@
 title: "Using miniCRAN to create a local CRAN repository"
 author: "Andrie de Vries and Alex Chubaty"
 date:   "`r as.character(format(Sys.Date(), format='%B %d, %Y'))`"
-output:
-  html_document:
-    self_contained: yes
-    toc: yes
+output: rmarkdown::html_vignette
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Using miniCRAN to create and maintain a local CRAN repository}
@@ -28,7 +25,8 @@ 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 <- pkgDep(pkgs, repos = revolution, type = "source", suggests = FALSE, 
+                  availPkgs = cranJuly2014)
 pkgList
 ```
 
@@ -39,7 +37,7 @@ Next, create a repository with the function `makeRepo()`.  In this example, get
 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"))
+makeRepo(pkgList, path=pth, repos=revolution, type=c("source", "win.binary"))
 ```
 
 
@@ -91,9 +89,11 @@ To add a specific version of a package from CRAN (or another CRAN-like repositor
 
 ```{r 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)
+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")
@@ -143,7 +143,7 @@ oldPackages(path = pth, repos = revolution, type = "win.binary")[, 1:3] # should
 ```
 
 
-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 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.
 
 ```{r update-repo-2, eval=FALSE}
 # Update available packages

inst/doc/miniCRAN-non-CRAN-repos.R

@@ -1,9 +1,9 @@
 ## ----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)
+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]
 }
 
@@ -27,7 +27,7 @@ index <- function(url, type="source", filters=NULL, head=5, cols=c("Package", "V
 #  bioc <- local({
 #    env <- new.env()
 #    on.exit(rm(env))
-#    evalq(source("http://bioconductor.org/biocLite.R", local=TRUE), env)
+#    evalq(source("http://bioconductor.org/biocLite.R", local = TRUE), env)
 #    biocinstallRepos()
 #  })
 #  

inst/doc/miniCRAN-non-CRAN-repos.rmd

@@ -1,11 +1,8 @@
 ---
 title:  "Using repositories other than CRAN with miniCRAN"
 author: "Andrie de Vries"
-date:   "`r as.character(format(Sys.Date(), format='%B %d, %Y'))`"
-output:
-  html_document:
-    self_contained: yes
-    toc: yes
+date:   "`r as.character(format(Sys.Date(), format = '%B %d, %Y'))`"
+output: rmarkdown::html_vignette
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Using repositories other than CRAN with miniCRAN}
@@ -24,9 +21,9 @@ To simplify the code to show the salient features, we use a little helper functi
 ```{r 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)
+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]
 }
  
@@ -71,7 +68,7 @@ Although BioConductor has a different preferred install mechanism, the underlyin
 bioc <- local({
   env <- new.env()
   on.exit(rm(env))
-  evalq(source("http://bioconductor.org/biocLite.R", local=TRUE), env)
+  evalq(source("http://bioconductor.org/biocLite.R", local = TRUE), env)
   biocinstallRepos()
 })
  

vignettes/miniCRAN-dependency-graph.rmd

@@ -2,10 +2,7 @@
 title:  "Using miniCRAN to identify package dependencies"
 author: "Andrie de Vries"
 date:   "`r as.character(format(Sys.Date(), format='%B %d, %Y'))`"
-output:
-  html_document:
-    self_contained: yes
-    toc: yes
+output: rmarkdown::html_vignette
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteIndexEntry{Using miniCRAN to identify package dependencies}