Merge pull request #51 from jfisher-usgs/master

Merge with upstream

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: inlmisc
 Title: Miscellaneous Functions for the USGS INL Project Office
-Version: 0.3.4.9000
+Version: 0.3.5
 Authors@R: person(given=c("Jason", "C."), family="Fisher", role=c("aut", "cre"), email="[email protected]")
 Description: A collection of functions for creating high-level graphics,
     performing raster-based analysis, processing MODFLOW-based models, etc.
@@ -35,7 +35,6 @@ Suggests:
     httr,
     maptools,
     parallel,
-    roxygen2,
     testthat
 License: CC0
 Copyright: This software is in the public domain because it contains materials

NEWS.md

@@ -1,6 +1,10 @@
-# inlmisc 0.3.4.9000
+# inlmisc 0.3.5
 
-- ...
+- In `PlotMap` function, fix bug introduced by previous fix of raster range calculation.
+
+- Made `AddCertificate` an 'internal' function.
+
+- Add argument checks using **checkmate** package.
 
 # inlmisc 0.3.4
 

R/CreateWebMap.R

@@ -38,6 +38,8 @@
 
 CreateWebMap <- function(..., collapsed=TRUE) {
 
+  checkmate::assertLogical(collapsed, len=1, any.missing=FALSE)
+
   # establish layers
   basemap <- c("Topo"          = "USGSTopo",
                "Imagery"       = "USGSImageryOnly",

R/FormatPval.R

@@ -37,11 +37,13 @@
 #'
 
 FormatPval <- function(x, digits=max(1, getOption("digits") - 2),
-                       eps=.Machine$double.eps, na.form="NA",
-                       scientific=NA) {
+                       eps=.Machine$double.eps, na.form="NA", scientific=NA) {
 
-  x <- as.numeric(x)
-  scientific <- as.logical(scientific)
+  checkmate::assertNumeric(x)
+  checkmate::assertInt(digits, null.ok=TRUE)
+  checkmate::assertNumber(eps)
+  checkmate::assertCharacter(na.form, len=1)
+  checkmate::assertLogical(scientific, len=1)
 
   p <- format(round(x, digits), nsmall=digits, scientific=FALSE)
 

R/GetDaysInMonth.R

@@ -19,6 +19,9 @@
 #'
 
 GetDaysInMonth <- function(x) {
+
+  checkmate::assertCharacter(x, pattern="^\\d{6}$", any.missing=FALSE)
+
   d <- as.Date(paste0(x, "28"), format="%Y%m%d")
   m <- format(d, format="%m")
   for (i in seq_along(d)) {

R/Grid2Polygons.R

@@ -125,6 +125,16 @@ Grid2Polygons <- function(grd, zcol=1L, level=FALSE, at, cuts=20L,
                           pretty=FALSE, xlim=NULL, ylim=NULL, zlim=NULL,
                           ply=NULL) {
 
+  # check arguments
+  checkmate::qassert(zcol, c("s1", "x1"))
+  checkmate::assertLogical(level, len=1)
+  if (!missing(at)) checkmate::assertNumeric(at, any.missing=FALSE, min.len=2)
+  checkmate::assertInt(cuts, lower=1)
+  checkmate::assertLogical(pretty, len=1)
+  checkmate::assertNumeric(xlim, len=2, sorted=TRUE, null.ok=TRUE)
+  checkmate::assertNumeric(ylim, len=2, sorted=TRUE, null.ok=TRUE)
+  checkmate::assertNumeric(zlim, len=2, sorted=TRUE, null.ok=TRUE)
+
   # check class
   what <- c("RasterLayer", "RasterStack", "RasterBrick",
             "SpatialPixelsDataFrame", "SpatialGridDataFrame")

R/POSIXct2Character.R

@@ -46,6 +46,10 @@
 #'
 
 POSIXct2Character <- function(x, fmt="%Y-%m-%d %H:%M:%OS3") {
+
+  checkmate::assertPOSIXct(x)
+  checkmate::assertCharacter(fmt, any.missing=FALSE, max.len=1)
+
   pos <- gregexpr("%OS[[:digit:]]+", fmt)[[1]]
   if (pos > 0) {
     pos <- pos + c(3L, attr(pos, "match.length"))

R/PlotMap.R

@@ -262,10 +262,10 @@ PlotMap <- function(r, p=NULL, ..., layer=1, att=NULL, n=NULL, breaks=NULL,
   r <- crop(r, extent(e), snap="near")
   if (!is.null(p)) p <- crop(p, extent(e), snap="near")
 
-  zran <- range(r[])
-  if (anyNA(zran)) {
+  if (all(is.na(r[]))) {
     n <- 0
   } else {
+    zran <- range(r[], na.rm=TRUE)
     default.zl <- if (extend.z) range(pretty(zran, n=6)) else zran
     if (raster::is.factor(r)) {
       at1 <- raster::levels(r)[[1]][, "ID"]

R/ReadCodeChunks.R

@@ -37,14 +37,10 @@
 
 ReadCodeChunks <- function(path) {
 
-  if (!file.exists(path)) stop("file not found")
+  checkmate::assertFileExists(path, extension=c("rnw", "rmd", "r"))
 
   ext <- tools::file_ext(path)
-  if (tolower(ext) %in% c("rnw", "rmd", "r")) {
-    src <- readLines(path)
-  } else {
-    stop("file extension not recognized")
-  }
+  src <- readLines(path)
 
   # extract r code from knitr source documents
   if (tolower(ext) %in% c("rnw", "rmd"))

R/RecreateLibrary.R

@@ -389,3 +389,65 @@ SavePackageDetails <- function(file="R-packages.tsv", lib=.libPaths(), pkg=NULL)
   FUN <- function(i) {system.file(package=i, lib.loc=lib) != ""}
   return(vapply(x, FUN, TRUE))
 }
+
+#' Add X.509 Certificate
+#'
+#' This function adds a \href{https://en.wikipedia.org/wiki/X.509}{X.509} certificate
+#' to your bundle of certificate authority root certificates (CA bundle).
+#' The X.509 certificate is used to authenticate clients and servers.
+#' And the CA bundle is a file that contains root and intermediate certificates.
+#'
+#' @param file 'character'.
+#'   Path (or a complete URL) to the file containing the X.509 certificate.
+#' @param header 'character'.
+#'   Header line to identify the certificate (optional).
+#'
+#' @note This function must be used on Windows and requires access to the \pkg{httr} package.
+#'
+#' @author J.C. Fisher, U.S. Geological Survey, Idaho Water Science Center
+#'
+#' @seealso \code{\link{RecreateLibrary}}
+#'
+#' @keywords internal
+#'
+#' @export
+#'
+#' @examples
+#' # Install the U.S. Department of Interior (DOI) certificate (employees only):
+#' \dontrun{
+#' AddCertificate(file = "http://sslhelp.doi.net/docs/DOIRootCA2.cer",
+#'                header = "DOI Root CA 2")
+#' }
+#'
+
+AddCertificate <- function(file, header=NULL) {
+
+  checkmate::assertOS("windows")
+  checkmate::assertCharacter(header, len=1, any.missing=FALSE, null.ok=TRUE)
+
+  if (!requireNamespace("httr", quietly=TRUE))
+    stop("Requires access to the 'httr' package.", call.=FALSE)
+
+  if (!file.exists(file) & httr::http_error(file))
+    stop("Certificate file doesn't exist or access is denied.", call.=FALSE)
+
+  certificate <- readLines(file)
+
+  bundle <- Sys.getenv("CURL_CA_BUNDLE")
+  if (bundle == "")
+    bundle <- system.file("cacert.pem", package="openssl", mustWork=TRUE)
+  if (!file.exists(bundle))
+    stop("Can't locate CA bundle file.", call.=FALSE)
+
+  if (all(certificate %in% readLines(bundle))) {
+    message("Certificate has already been added to CA bundle.")
+  } else {
+    if (!is.null(header))
+      header <- c(header, paste(rep("=", nchar(header)), collapse=""))
+    certificate <- c("", header, certificate)
+    cat(certificate, file=bundle, sep="\n", append=TRUE)
+    message("Certificate added to CA bundle:\n ", normalizePath(bundle))
+  }
+
+  invisible(NULL)
+}

R/SetPolygons.R

@@ -51,8 +51,10 @@
 #' sp::plot(p, col = "purple", add = TRUE)
 #'
 
-SetPolygons <- function(x, y, cmd=c("gIntersection", "gDifference"),
-                        buffer.width=NA) {
+SetPolygons <- function(x, y, cmd=c("gIntersection", "gDifference"), buffer.width=NA) {
+
+  if (!missing(cmd)) checkmate::assertChoice(cmd, c("gIntersection", "gDifference"))
+  checkmate::assertNumber(buffer.width, na.ok=TRUE, finite=TRUE)
 
   cmd <- match.arg(cmd)
 

R/ToScientific.R

@@ -52,6 +52,14 @@
 ToScientific <- function(x, digits=NULL, type=c("latex", "plotmath"),
                          na=as.character(NA), delimiter="$", scipen=NULL, ...) {
 
+  # check arguments
+  checkmate::assertNumeric(x)
+  checkmate::assertInt(digits, null.ok=TRUE)
+  if (!missing(type)) checkmate::assertChoice(type, c("latex", "plotmath"))
+  checkmate::assertCharacter(na, len=1)
+  checkmate::assertCharacter(delimiter, len=1)
+  checkmate::assertInt(scipen, na.ok=TRUE, null.ok=TRUE)
+
   if (missing(type) && methods::hasArg("lab.type"))
     type <- list(...)$lab.type  # included for backward compatibility
   else

README.md

@@ -1,7 +1,6 @@
 # inlmisc
 
 [![Travis Build Status](https://travis-ci.org/USGS-R/inlmisc.svg?branch=master)](https://travis-ci.org/USGS-R/inlmisc)
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 [![Coverage Status](https://coveralls.io/repos/github/USGS-R/inlmisc/badge.svg?branch=master)](https://coveralls.io/github/USGS-R/inlmisc?branch=master)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/inlmisc)](https://CRAN.R-project.org/package=inlmisc)
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