Merge branch 'dev'

* dev: Bump version to 0.2.11 Add mockery to Suggests Update docs Add tests to improve code coverage minor cleanup misc cleanup Mock without using mockery or testthat::with_mock More mocking experiments mockery(>= 0.4.0) Depends on mockery >= 0.4.0 #107 stub one level less deep Rebuild vignettes Use mocking to speed up tests #107 Remove magrittr dependency
andrie · Jan 15, 2018 · 77eace6 · 77eace6
2 parents 7b62d23 + 5075147
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,11 @@
 Package: miniCRAN
+Date: 2018-01-15
+Version: 0.2.11
 Authors@R: c(person("Microsoft Corporation", role="cph"), person("Andrie", "de
-    Vries", role=c("aut", "cre"), email="[email protected]"),
+    Vries", role=c("aut", "cre", "cph"), email="[email protected]"),
     person("Alex", "Chubaty", role="ctb", email="[email protected]"))
 License: GPL-2
-Copyright: Microsoft Corporation
+Copyright: Microsoft Corporation, Andrie de Vries
 Title: Create a Mini Version of CRAN Containing Only Selected Packages
 Description: Makes it possible to create an internally consistent
     repository consisting of selected packages from CRAN-like repositories.
@@ -12,29 +14,27 @@ 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: 2017-12-19
-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
     requirements on `libxml2-devel`, `libcurl-devel` and `openssl-devel`.
 Imports:
     graphics,
     httr,
-    magrittr,
     methods,
     stats,
     tools,
     utils,
     XML,
-    igraph
+    igraph,
 Suggests:
     devtools,
     knitr,
     rmarkdown,
     testthat(>= 0.9),
     covr,
-    withr
+    withr,
+    mockery
 LazyData: true
 LazyLoad: true
 VignetteBuilder: knitr

diff --git a/NAMESPACE b/NAMESPACE
@@ -28,14 +28,15 @@ importFrom(igraph,V)
 importFrom(igraph,get.edge.attribute)
 importFrom(igraph,graph.data.frame)
 importFrom(igraph,plot.igraph)
-importFrom(magrittr,'%>%')
 importFrom(methods,is)
 importFrom(stats,reshape)
 importFrom(stats,setNames)
 importFrom(tools,write_PACKAGES)
+importFrom(utils,available.packages)
 importFrom(utils,chooseCRANmirror)
 importFrom(utils,compareVersion)
 importFrom(utils,download.file)
+importFrom(utils,download.packages)
 importFrom(utils,flush.console)
 importFrom(utils,installed.packages)
 importFrom(utils,select.list)
diff --git a/NEWS b/NEWS
@@ -1,9 +1,14 @@
-miniCRAN v0.2.11.9000 (Release date: in development)
+miniCRAN v0.2.11 (Release date: in development)
 ================
 
 New features: 
 
-* Used `pkgdown` to build documentation site
+* None
+
+Other changes:
+
+* Use `pkgdown` to build documentation site
+* Speed up unit testing by mocking internal functions
 
 
 miniCRAN v0.2.10.9000

diff --git a/R/addPackages.R b/R/addPackages.R
@@ -98,7 +98,7 @@ addPackage <- function(pkgs = NULL, path = NULL, repos = getOption("repos"),
       dupes <- with(curr.df, package[duplicated(package)])
       if (length(dupes)) {
         to_remove <- lapply(dupes, findPrevPackage)
-        if(length(unlist(to_remove))){
+        if (length(unlist(to_remove))) {
           file.remove(prev[unlist(to_remove)])
         }
       }
@@ -156,7 +156,7 @@ addOldPackage <- function(pkgs = NULL, path = NULL, vers = NULL,
   if (!file.exists(pkgPath)) dir.create(pkgPath, recursive = TRUE)
 
   do_one <- function(x) {
-    result <- utils::download.file(x, destfile = file.path(pkgPath, basename(x)),
+    result <- download.file(x, destfile = file.path(pkgPath, basename(x)),
                                    method = "auto", mode = "wb", quiet = quiet)
     if (result != 0) warning("error downloading file ", x)
   }
@@ -179,22 +179,14 @@ addOldPackage <- function(pkgs = NULL, path = NULL, vers = NULL,
 #' @rdname listFiles
 #' @docType methods
 #'
-#' @importFrom magrittr '%>%'
-#'
 #' @examples
 #' \dontrun{
 #'  .listFiles('path/to/my/packages', type = "source")
 #' }
 #'
 .listFiles <- function(pkgs, path, type) {
   stopifnot(dir.exists(path))
-  pattern <- switch(type,
-                    mac.binary = ".tgz",
-                    mac.binary.leopard = ".tgz",
-                    mac.binary.mavericks = ".tgz",
-                    source = ".tar.gz",
-                    win.binary = ".zip",
-                    stop("Type ", type, "not recognised."))
+  pattern <- pkgFileExt(type)
 
   # get a list of all files in pkgPaths directory matching pattern
   f <- list.files(path, pattern = pattern)
@@ -204,15 +196,19 @@ addOldPackage <- function(pkgs = NULL, path = NULL, vers = NULL,
 
   if (length(f)) {
     # if multiple versions present, always use latest
-    fp <- strsplit(f, "_") %>%
-      sapply(., `[[`, 1)
-
-    fv <- strsplit(f, "_") %>%
-      sapply(., `[[`, 2) %>%
-      strsplit(., pattern) %>%
-      sapply(., `[[`, 1) %>%
-      as.numeric_version()
-
+    fp <- local({
+      x <- strsplit(f, "_")
+      sapply(x, `[[`, 1)
+    })
+
+    fv <- local({
+      x <- strsplit(f, "_")
+      x <- sapply(x, `[[`, 2)
+      x <- strsplit(x, pattern)
+      x <- sapply(x, `[[`, 1)
+      as.numeric_version(x)
+    })
+
     fout <- sapply(fp, function(x) {
       ids.p <- which(fp %in% x)
 
@@ -221,11 +217,10 @@ addOldPackage <- function(pkgs = NULL, path = NULL, vers = NULL,
       id.v <- which(fv == max(fv[ids.p]))
 
       f[id.v]
-    }) %>% unique()
-
-    return(fout)
+    })
+    unique(fout)
   } else {
-    return(character())
+    character()
   }
 }
 
@@ -326,5 +321,5 @@ addLocalPackage <- function(pkgs = NULL, pkgPath = NULL, path = NULL,
   # write package index for each folder:
   index <- updateRepoIndex(path = path, type = type, Rversion = Rversion)
 
-  return(invisible(index))
+  invisible(index)
 }
diff --git a/R/getCranDescription.R b/R/getCranDescription.R
@@ -2,7 +2,7 @@
 #' @importFrom XML readHTMLTable
 oldGetCranDescription <- function(pkg, repos = getOption("repos"),
                                   type = "source",
-                                  pkgs = pkgDep(pkg, repos = repos, type = type)){
+                                  pkgs = pkgDep(pkg, repos = repos, type = type)) {
   getOne <- function(package) {
     repos <- repos[[1]]
     if(!grepl("/$", repos)) repos <- paste0(repos, "/")
@@ -42,9 +42,9 @@ oldGetCranDescription <- function(pkg, repos = getOption("repos"),
 #' @example /inst/examples/example_getCranDescription.R
 getCranDescription <- function(pkg, repos = getOption("repos"),
                                type = "source",
-                               pkgs = pkgDep(pkg, repos = repos, type = type)){
+                               pkgs = pkgDep(pkg, repos = repos, type = type)) {
 
-  if (getRversion() >= "3.4.1"){
+  if (getRversion() >= "3.4.1") {
     pdb <- tools::CRAN_package_db()
     pdb[match(pkgs, pdb$Package), ]
   } else {

diff --git a/R/github-functions.R b/R/github-functions.R
@@ -11,27 +11,28 @@ pkgFileExt <- function(type) {
 }
 
 
-
 getPkgVersFromFile <- function(file) {
   file <- grep("\\.(tar\\.gz|zip|tgz)$", basename(as.character(file)), value = TRUE)
   if (length(file)) {
     file <- sapply(strsplit(file, "\\.tar\\.gz"), "[[", 1)
     file <- sapply(strsplit(file, "\\.zip"), "[[", 1)
     file <- sapply(strsplit(file, "\\.tgz"), "[[", 1)
-    pkg <- sapply(strsplit(file, "_"), "[[", 1)
+    pkg  <- sapply(strsplit(file, "_"), "[[", 1)
     vers <- sapply(strsplit(file, "_"), "[[", 2)
-    df <- data.frame(package = pkg, version = vers, stringsAsFactors = FALSE)
-    return(df[order(df$package),])
+    df <- data.frame(package = pkg, version = vers, stringsAsFactors = FALSE, row.names = NULL)
+    df <- df[order(df$package),]
+    row.names(df) <- seq_len(nrow(df))
+    df
   } else {
-    return(NULL)
+    data.frame(package = character(0), version = character(0))
   }
 }
 
 
 
 readDescription <- function(file) {
   stopifnot(file.exists(file))
-  trimSpaces <- function(x){
+  trimSpaces <- function(x) {
     gsub("^\\s+|\\s+$", "", x)
   }
 
@@ -77,7 +78,7 @@ addPackageListing <- function(pdb = pkgAvail(), dcf, warnings = TRUE) {
 # Possible to override the blocking of a package's (re-)installation after it has been required/loaded?
 
 #' @importFrom httr GET stop_for_status content
-readDescriptionGithub <- function(repo, username, branch = "master", quiet = TRUE){
+readDescriptionGithub <- function(repo, username, branch = "master", quiet = TRUE) {
   if (!missing(username) && !is.null(username)) repo <- paste(username, repo, sep = "/")
   pkg <- sprintf("https://github.com/%s/raw/%s/DESCRIPTION", repo, branch)
   ff <- tempfile()

diff --git a/R/helpers.R → R/internal.R b/R/helpers.R → R/internal.R
@@ -1,5 +1,5 @@
 #' Get the path to the repo directory containing the package files.
-#' 
+#'
 #' @note Not all versions of R are compatible with with all package types (e.g., `mac.binary.el-capitan` is only valid for R > 3.4.0).
 #'
 #' @param Rversion Version of R. Can be specified as a character string with the two digit R version, e.g. "3.1".  Defaults to [R.version]
@@ -45,13 +45,13 @@
 #'
 repoPrefix <- function(type, Rversion) {
   Rversion <- twodigitRversion(Rversion)
-  
+
   if ((type == "mac.binary.el-capitan") && (numeric_version(Rversion) < "3.4")) {
     warning("Type mac.binary.el-capitan only valid for R >= 3.4")
   } else if ((type == "mac.binary.mavericks") && (numeric_version(Rversion) >= "3.4")) {
     warning("Type mac.binary.mavericks only valid for R < 3.4")
   }
-  
+
   switch(
     type,
     "source" = "src/contrib",
@@ -67,12 +67,10 @@ repoPrefix <- function(type, Rversion) {
 #' Construct path to full binary location
 #' @inheritParams makeRepo
 #' @inheritParams repoPrefix
-repoBinPath <- function(path, type, Rversion){
+repoBinPath <- function(path, type, Rversion) {
   normalizePath(file.path(path, repoPrefix(type, Rversion)), mustWork = FALSE, winslash = "/")
 }
 
-
-
 #' Get a two-digit version of the R version
 #'
 #' @param R Either a list of the format [R.version], a character string (e.g., `"3.1.2"`), or a numeric version of the type [R_system_version()].
@@ -81,12 +79,12 @@ repoBinPath <- function(path, type, Rversion){
 #'
 #' @importFrom methods is
 #'
-twodigitRversion <- function(R=R.version){
+twodigitRversion <- function(R = R.version) {
   if ("simple.list" %in% is(R)) {
     paste(R$major, strsplit(R$minor, ".", fixed = TRUE)[[1L]][1L], sep = ".")
   } else if ("R_system_version" %in% is(R)) {
-    paste(strsplit(as.character(R), ".", fixed=TRUE)[[1L]][1L:2L], collapse=".")
+    paste(strsplit(as.character(R), ".", fixed = TRUE)[[1L]][1L:2L], collapse = ".")
   } else if (is.character(R)) {
-    paste(strsplit(R, ".", fixed=TRUE)[[1L]][1L:2L], collapse=".")
+    paste(strsplit(R, ".", fixed = TRUE)[[1L]][1L:2L], collapse = ".")
   }
 }
diff --git a/R/makeDepGraph.R b/R/makeDepGraph.R
@@ -6,7 +6,7 @@ fastdf <- function (list) {
   list
 }
 
-addDepType <- function(p, type = c("Imports", "Depends", "LinkingTo", "Suggests"), pdb){
+addDepType <- function(p, type = c("Imports", "Depends", "LinkingTo", "Suggests"), pdb) {
   if (!p %in% rownames(pdb)) {
     fastdf(list(
       dep = character(0),
@@ -35,9 +35,9 @@ addDepType <- function(p, type = c("Imports", "Depends", "LinkingTo", "Suggests"
 #' @importFrom igraph graph.data.frame
 #' @export
 #' @family dependency functions
-#' 
+#'
 #' @seealso [pkgDep()] to extract package dependencies
-#' 
+#'
 #' @example /inst/examples/example_makeDepGraph.R
 makeDepGraph <- function(
   pkg, availPkgs, repos = getOption("repos"), type = "source",
@@ -109,4 +109,3 @@ makeDepGraph <- function(
   attr(ret, "pkgs") <- pkg_orig
   ret
 }
-
diff --git a/R/makeRepo.R b/R/makeRepo.R
@@ -52,17 +52,19 @@
 #' @export
 #' @family update repo functions
 #'
+#' @importFrom utils download.packages
+#'
 #' @example /inst/examples/example_makeRepo.R
 makeRepo <- function(pkgs, path, repos = getOption("repos"), type = "source",
                      Rversion = R.version, download = TRUE, writePACKAGES = TRUE, quiet = FALSE) {
   if (!file.exists(path)) stop("Download path does not exist")
 
   downloaded <- lapply(type, function(t) {
     pkgPath <- repoBinPath(path = path, type = t, Rversion = Rversion)
-    if(!file.exists(pkgPath)) {
+    if (!file.exists(pkgPath)) {
       result <- dir.create(pkgPath, recursive = TRUE, showWarnings = FALSE)
-      if(result) {
-        if(!quiet) message("Created new folder: ", pkgPath)
+      if (result) {
+        if (!quiet) message("Created new folder: ", pkgPath)
       } else {
         stop("Unable to create repo path: ", pkgPath)
       }
@@ -71,21 +73,21 @@ makeRepo <- function(pkgs, path, repos = getOption("repos"), type = "source",
     pdb <- pkgAvail(repos = repos, type = t, Rversion = Rversion)
 
     if (download) {
-      utils::download.packages(pkgs, destdir = pkgPath, available = pdb, repos = repos,
-                               contriburl = contribUrl(repos, t, Rversion),
-                               type = t, quiet = quiet)
+      download.packages(pkgs, destdir = pkgPath, available = pdb, repos = repos,
+                        contriburl = contribUrl(repos, t, Rversion),
+                        type = t, quiet = quiet)
     }
   })
 
   if (download) {
     downloaded <- downloaded[[1]][, 2]
-    
+
     ## allow for more than one repo
     fromLocalRepos <- grepl("^file://", repos)
-    
-    if(any(fromLocalRepos)){
+
+    if (any(fromLocalRepos)) {
       # need to copy files to correct folder
-      if (sum(fromLocalRepos) > 1) 
+      if (sum(fromLocalRepos) > 1)
         warning("More than one local repos provided. Only the first listed will be used.")
       pat <- ifelse(Sys.info()["sysname"] == "Windows", "^file:///", "^file://")
       repoPath <- gsub(pat, "", repos[fromLocalRepos][1])
@@ -110,10 +112,10 @@ updateRepoIndex <- function(path, type = "source", Rversion = R.version) {
   n <- lapply(type, function(t) {
     pkgPath <- repoBinPath(path = path, type = t, Rversion = Rversion)
     if (grepl("mac.binary", t)) t <- "mac.binary"
-    tools::write_PACKAGES(dir = pkgPath, type = t)
+    write_packages(dir = pkgPath, type = t)
   })
   names(n) <- type
-  return(n)
+  n
 }
 
 
@@ -122,14 +124,8 @@ updateRepoIndex <- function(path, type = "source", Rversion = R.version) {
 #'
 #' @inheritParams makeRepo
 #' @export
-makeLibrary <- function(pkgs, path, type = "source"){
+makeLibrary <- function(pkgs, path, type = "source") {
   .Deprecated("makeRepo")
   NULL
-  #   if(!file.exists(path)) stop("Download path does not exist")
-  #   wd <- getwd()
-  #   on.exit(setwd(wd))
-  #   setwd(normalizePath(path))
-  #   message(getwd())
-  #   download.packages(pkgs, destdir = path, type = type)
 }