From 8fe70d56526343fdfd25a322e25e8ab2d430d510 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Mon, 30 Apr 2018 16:24:11 +0200
Subject: [PATCH] Fix Latex PDF error

---
 DESCRIPTION               |  2 +-
 R/clipboard.R             | 24 ++++++++----------------
 man/clipboard.Rd          | 18 +++++-------------
 tests/testthat/test-atc.R | 13 +++++++++++++
 4 files changed, 27 insertions(+), 30 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e032519e..34ae0ab2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
 Version: 0.2.0
-Date: 2018-04-23
+Date: 2018-04-30
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(
diff --git a/R/clipboard.R b/R/clipboard.R
index 03ec6f43..65ca625c 100644
--- a/R/clipboard.R
+++ b/R/clipboard.R
@@ -13,23 +13,15 @@
 #' @importFrom utils read.delim write.table object.size
 #' @details For \code{clipboard_export()}, the reserved clipboard size for exporting will be set to 125\% of the object size of \code{x}. This way, it is possible to export data with thousands of rows as the only limit will be your systems RAM.
 #'
-#'   Example for copying from Excel:
 #'   \if{html}{
+#'      Example for copying from Excel:
 #'     \out{<div style="text-align: left">}\figure{Excel_copy.png}\out{</div>}
-#'   }
-#'   \if{latex}{
-#'     \out{\begin{left}}\figure{Excel_copy.png}\out{\end{left}}
-#'   }
-#'   \cr
-#'   And pasting in R: \cr \cr
-#'   \code{> data <- clipboard_import()} \cr
-#'   \code{> data} \cr
-#'   \if{html}{
+#'     \cr
+#'     And pasting in R: \cr \cr
+#'     \code{> data <- clipboard_import()} \cr
+#'     \code{> data} \cr
 #'     \out{<div style="text-align: left">}\figure{Excel_paste.png}\out{</div>}
 #'   }
-#'   \if{latex}{
-#'     \out{\begin{left}}\figure{Excel_paste.png}\out{\end{left}}
-#'   }
 #' @export
 #' @return data.frame
 clipboard_import <- function(sep = '\t',
@@ -135,14 +127,14 @@ clipboard_export <- function(x,
 }
 
 is_Windows <- function() {
-  Sys.info()['sysname'] %like% "Windows"
+  all(Sys.info()['sysname'] %like% "Windows")
 }
 check_xclip <- function() {
   if (!isTRUE(file.exists(Sys.which("xclip")[1L]))) {
-    if (Sys.info()['sysname'] %like% "Linux") {
+    if (all(Sys.info()['sysname'] %like% "Linux")) {
       stop("Please install Linux package xclip first.")
     } else {
-      stop("Please install package xclip first (use `brew install xclip on macOS`).")
+      stop("Please install package xclip first (use `brew install xclip` on macOS).")
     }
   }
 }
diff --git a/man/clipboard.Rd b/man/clipboard.Rd
index 347da4f0..09607b58 100644
--- a/man/clipboard.Rd
+++ b/man/clipboard.Rd
@@ -46,23 +46,15 @@ These are helper functions around \code{\link{read.table}} and \code{\link{write
 \details{
 For \code{clipboard_export()}, the reserved clipboard size for exporting will be set to 125\% of the object size of \code{x}. This way, it is possible to export data with thousands of rows as the only limit will be your systems RAM.
 
-  Example for copying from Excel:
   \if{html}{
+     Example for copying from Excel:
     \out{<div style="text-align: left">}\figure{Excel_copy.png}\out{</div>}
-  }
-  \if{latex}{
-    \out{\begin{left}}\figure{Excel_copy.png}\out{\end{left}}
-  }
-  \cr
-  And pasting in R: \cr \cr
-  \code{> data <- clipboard_import()} \cr
-  \code{> data} \cr
-  \if{html}{
+    \cr
+    And pasting in R: \cr \cr
+    \code{> data <- clipboard_import()} \cr
+    \code{> data} \cr
     \out{<div style="text-align: left">}\figure{Excel_paste.png}\out{</div>}
   }
-  \if{latex}{
-    \out{\begin{left}}\figure{Excel_paste.png}\out{\end{left}}
-  }
 }
 \keyword{clipboard}
 \keyword{clipboard_export}
diff --git a/tests/testthat/test-atc.R b/tests/testthat/test-atc.R
index 2946446e..d309bbb9 100644
--- a/tests/testthat/test-atc.R
+++ b/tests/testthat/test-atc.R
@@ -29,3 +29,16 @@ test_that("guess_bactid works", {
                               "VISA")),
                rep("STAAUR", 8))
 })
+
+test_that("guess_atc works", {
+  expect_equal(guess_atc(c("J01FA01",
+                           "Erythromycin",
+                           "eryt",
+                           "ERYT",
+                           "ERY",
+                           "Erythrocin",
+                           "Eryzole",
+                           "Pediamycin")),
+               rep("J01FA01", 8))
+
+})