move some feature-specific pkgs to suggests

DESCRIPTION

@@ -2,7 +2,7 @@ Package: mmgenome2
 Type: Package
 Title: Tools for extracting individual genomes from metagenomes
 Description: mmgenome: a toolbox for extracting individual genomes from metagenomes.
-Version: 2.2.0
+Version: 2.2.1
 Date: 2018-01-01
 Encoding: UTF-8
 Authors@R: c(
@@ -46,29 +46,28 @@ Imports:
     magrittr,
     dplyr,
     Biostrings,
-    rstudioapi,
-    clipr,
+    digest,
     igraph,
     ggrepel,
     tibble,
     tidyr,
     stringr,
-    shiny,
-    rlang
-biocViews:
-    Biostrings
-RoxygenNote: 7.1.1
+    purrr,
+    rlang, 
+    plyr,
+    forcats
+remotes:
+    github::kasperskytte/Rtsne@openmp,
+    bioc::Biostrings
+RoxygenNote: 7.1.2
 VignetteBuilder: knitr
 Suggests:
     testthat,
     knitr,
-    tools,
-    utils,
     vegan,
+    shiny,
     Rtsne,
-    digest,
-    plotly,
-    purrr,
-    plyr,
-    forcats
+    rstudioapi,
+    clipr,
+    plotly
 URL: https://kasperskytte.github.io/mmgenome2

NAMESPACE

@@ -20,7 +20,6 @@ importFrom(Biostrings,readDNAStringSet)
 importFrom(Biostrings,reverseComplement)
 importFrom(Biostrings,width)
 importFrom(Biostrings,writeXStringSet)
-importFrom(clipr,write_clip)
 importFrom(cowplot,plot_grid)
 importFrom(data.table,data.table)
 importFrom(data.table,fread)
@@ -53,21 +52,10 @@ importFrom(igraph,graph.data.frame)
 importFrom(igraph,layout_with_fr)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
+importFrom(plyr,ldply)
+importFrom(purrr,imap)
 importFrom(rlang,quos)
 importFrom(rlang,sym)
-importFrom(rstudioapi,viewer)
-importFrom(shiny,actionButton)
-importFrom(shiny,div)
-importFrom(shiny,fillPage)
-importFrom(shiny,icon)
-importFrom(shiny,observeEvent)
-importFrom(shiny,p)
-importFrom(shiny,plotOutput)
-importFrom(shiny,reactiveValues)
-importFrom(shiny,renderPlot)
-importFrom(shiny,runApp)
-importFrom(shiny,shinyApp)
-importFrom(shiny,stopApp)
 importFrom(sp,point.in.polygon)
 importFrom(stringr,str_remove)
 importFrom(stringr,str_replace_all)

R/internals.R

@@ -1,3 +1,23 @@
+#' @title Check for installed package
+#' @description Returns error if a required package is not installed. Mostly used for checking whether packages listed under the Suggests field in the DESCRIPTION file is installed.
+#'
+#' @param pkg The package to check for, a character of length 1.
+#' @param msg Optionally additional text appended (with \code{paste0}) to the default error message.
+#'
+#' @return Returns error and message if not installed, otherwise \code{invisible(TRUE)}
+#' @author Kasper Skytte Andersen \email{ksa@@bio.aau.dk}
+checkReqPkg <- function(pkg, msg = "") {
+  stopifnot(is.character(pkg), length(pkg) == 1L, nchar(pkg) > 0)
+  if (!requireNamespace(pkg, quietly = TRUE)) {
+    stopifnot(is.character(msg))
+    stop(
+      paste0("Package '", pkg, "' is required but not installed. ", msg),
+      call. = FALSE
+    )
+  }
+  require(pkg, quietly = TRUE, character.only = TRUE)
+}
+
 #' @title Merge mm object with more data
 #'
 #' @description Internal function used in mmload. \code{y} can be a named vector, dataframe, or a list containing any of these types of data to be merged with \code{x}.
@@ -117,15 +137,16 @@ mmmerge <- function(x, y, type) {
 #' @return A data frame with the x/y coordinates of the mousepositions clicked in the ggplot2 plot.
 #'
 #' @import ggplot2
-#' @importFrom shiny actionButton div fillPage icon observeEvent p plotOutput reactiveValues renderPlot runApp shinyApp stopApp
-#' @importFrom clipr write_clip
-#' @importFrom rstudioapi viewer
 #'
 #' @author Kasper Skytte Andersen \email{ksa@@bio.aau.dk}
 #' @author Rasmus Hansen Kirkegaard \email{rhk@@bio.aau.dk}
 #' @author Soren M. Karst \email{smk@@bio.aau.dk}
 #' @author Mads Albertsen \email{MadsAlbertsen85@@gmail.com}
 mmlocator <- function(plot, x_scale = NULL, y_scale = NULL) {
+  checkReqPkg("shiny")
+  checkReqPkg("rstudioapi")
+  checkReqPkg("clipr")
+
   app <- shinyApp(
     ui = fillPage(
       padding = c(5, 5, 50),

R/mmload.R

@@ -29,6 +29,7 @@
 #' @importFrom dplyr mutate_all funs group_by left_join summarise_all
 #' @importFrom stringr str_replace_all str_remove
 #' @importFrom data.table fread
+#' @importFrom tools file_path_sans_ext
 #'
 #' @examples
 #' \dontrun{
@@ -201,7 +202,8 @@ mmload <- function(assembly,
 
   ##### PCA of tetranucleotides #####
   if (isTRUE(kmer_pca)) {
-    checkReqPkgs("vegan")
+    checkReqPkg("vegan")
+
     if (isTRUE(verbose)) {
       message(paste0(
         "Calculating principal components of kmer (k=",
@@ -222,7 +224,7 @@ mmload <- function(assembly,
 
   ##### BH tSNE of tetranucleotides #####
   if (isTRUE(kmer_BH_tSNE)) {
-    checkReqPkgs("Rtsne")
+    checkReqPkg("Rtsne", "To install with support for multithreading run:\n  remotes::install_github('kasperskytte/Rtsne@openmp')\notherwise just install from CRAN.")
     if (isTRUE(verbose)) {
       message(paste0(
         "Calculating Barnes-Hut t-Distributed Stochastic Neighbor Embedding representations of kmer (k=",

R/mmplot_cov_profiles.R

@@ -148,7 +148,7 @@ mmplot_cov_profiles <- function(mm,
 
   # add points to plot and generate plotly hover labels if interactive, return plot
   if (isTRUE(interactive_plot)) {
-    checkReqPkgs(c("plotly", "purrr"))
+    checkReqPkg("plotly")
     data_plotly <- gg %>%
       purrr::imap(~ paste(.y, .x, sep = ": ")) %>%
       as.data.frame() %>%