Preparing to pass CHECK

.Rbuildignore

@@ -1,3 +1,13 @@
+^\./vignettes/resources/dti/dti_bvals\.csv$
+^\./vignettes/resources/dti/dti_example\.nii\.gz$
+^\./vignettes/resources/dti/dti_gradients\.csv$
+^\./vignettes/resources/rsfMRI/anat\.nii\.gz$
+^\./vignettes/resources/rsfMRI/data$
+^\./vignettes/resources/rsfMRI/func\.nii\.gz$
+^\./vignettes/resources/volumetry/bet$
+^\./vignettes/resources/volumetry/input$
+^\./vignettes/resources/volumetry/MNI152_T1_1mm\.nii\.gz$
+^\./vignettes/resources/volumetry/parcellation$
 ^Meta$
 ^doc$
 ^README\.Rmd$

DESCRIPTION

@@ -2,14 +2,15 @@ Package: wf4ni
 Type: Package
 Title: Workflows for Neuroimaging
 Version: 0.1.0
-Date: 2018-01-04
+Date: 2019-04-29
+Author: Domingo López-Rodríguez [aut, cre]
 Authors@R: person("Domingo", "López-Rodríguez", role = c("aut", "cre"), email = "[email protected]")
-Maintainer: Domingo Lopez-Rodriguez <[email protected]>
+Maintainer: Domingo López-Rodríguez <[email protected]>
 Description: The aim of this package is to provide a means to create reproducible workflows specifically designed for Neuroimaging.
 License: GPL (>= 2)
 URL: https://github.com/neuroimaginador/wf4ni
 BugReports: https://github.com/neuroimaginador/wf4ni/issues
-Imports: stringr, styler, devtools, igraph, RCurl, R6, RNifti, neurobase, oro.nifti, scales, zip, crayon, prettyunits, pryr, purrr, methods, utils
+Imports: stringr, styler, devtools, igraph, RCurl, R6, RNifti, neurobase, oro.nifti, scales, zip, crayon, prettyunits, pryr, purrr, methods, utils, Rgraphviz, grid, ANTsRCore, graph
 Suggests: 
     testthat,
     knitr,

NAMESPACE

@@ -4,8 +4,6 @@ export(NIflow)
 export(add)
 export(download_repo)
 export(execute)
-export(get_atlas)
-export(get_dataset)
 export(get_flow)
 export(get_flows_dir)
 export(merge)
@@ -14,14 +12,28 @@ import(crayon)
 import(igraph)
 import(stringr)
 import(zip)
+importFrom(ANTsRCore,antsImageWrite)
 importFrom(R6,R6Class)
 importFrom(RCurl,url.exists)
+importFrom(Rgraphviz,agopen)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,png)
+importFrom(graph,graphAM)
+importFrom(grid,convertX)
+importFrom(grid,convertY)
+importFrom(grid,grid.newpage)
+importFrom(grid,grob)
+importFrom(grid,stringWidth)
+importFrom(grid,unit)
 importFrom(igraph,add_edges)
 importFrom(igraph,add_vertices)
+importFrom(igraph,as_adj)
 importFrom(igraph,make_empty_graph)
 importFrom(igraph,topo_sort)
+importFrom(methods,as)
 importFrom(methods,formalArgs)
 importFrom(neurobase,readnii)
+importFrom(neurobase,writenii)
 importFrom(prettyunits,pretty_bytes)
 importFrom(pryr,object_size)
 importFrom(pryr,partial)

R/flow.R

@@ -3,6 +3,7 @@
 #' @description This internal function provides an environment usable from the class NIflow.
 #'
 #' @param name      (character) Name of the flow
+#' @param work_dir  (character) Path of the temporary folder where to store results
 #' @param inputs    (list of names) List of inputs used in the flow, Default: list()
 #'
 #' @return A NIflow object.

R/plot.R

@@ -1,18 +1,21 @@
-
 ##%######################################################%##
 #                                                          #
 ####                      PLOTTING                      ####
 #                                                          #
 ##%######################################################%##
 
 # Auxiliary function for plotting
+#' @importFrom grid unit stringWidth convertX convertY grob
+#' @importFrom graph graphAM
+#' @importFrom methods as
+#' @importFrom igraph as_adj
+#' @importFrom Rgraphviz agopen
+#'
 .plot_flow <- function(flow,
                        to_file = "") {
 
   nWi <- function(labels, margin) {
 
-    library(grid)
-
     result <- unit(0, "inch")
     for (label in labels) result <- result + stringWidth(label) +
         unit(margin$rl * 2, "inch")
@@ -25,8 +28,6 @@
 
   nHi <- function(labels, margin) {
 
-    library(grid)
-
     result <- unit(1, "lines") + unit(margin$tb * 2, "inch")
     if (length(labels) > 1)
       result <- result + unit(margin$otb * 2, "inch")
@@ -36,8 +37,8 @@
 
   stopifnot(inherits(flow, "NIflow"))
 
-  suppressPackageStartupMessages(library(grid))
-  suppressPackageStartupMessages(library(Rgraphviz))
+  requireNamespace("grid", quietly = TRUE)
+  requireNamespace("Rgraphviz", quietly = TRUE)
 
   # Define color of each node as its type
   # num_types <- length(unique(V(flow$graph)$type))
@@ -119,17 +120,18 @@
 #' @description This function plots a flow using \link{igraph} plotting capabilities.
 #'
 #' @param flow           (a NIflow object) The flow.
+#' @param to_file        (character) Path to a file to save the graph. If not present, plots the flow to the screen. Otherwise, it is stored in a PNG file with the given name.
 #'
 #' @return Nothing
 #'
-#' @seealso
-#'  \code{\link[threejs]{graphjs}}
-
-#'  \code{\link[igraph]{layout_with_sugiyama}}
-
-#'  \code{\link[scales]{alpha}},\code{\link[scales]{hue_pal}}
 #' @import igraph
 #' @importFrom scales alpha hue_pal
+#' @importFrom grid unit stringWidth convertX convertY grob grid.newpage
+#' @importFrom graph graphAM
+#' @importFrom methods as
+#' @importFrom igraph as_adj
+#' @importFrom Rgraphviz agopen
+#' @importFrom grDevices dev.off png
 #'
 plot <- function(flow,
                  to_file = "") {

R/save_result.R

@@ -1,23 +1,30 @@
 # Save an object to the temp folder.
+#' @importFrom neurobase writenii
+#' @importFrom ANTsRCore antsImageWrite
+#'
 .save_result <- function(value, name, folder = tempdir()) {
 
   if (inherits(value, "nifti") | inherits(value, "niftiImage")) {
 
+    requireNamespace("neurobase", quietly = TRUE)
+
     my_file <- file.path(folder, paste0(name, ".nii.gz"))
 
-    neurobase::writenii(nim = value,
-                        filename = my_file)
+    writenii(nim = value,
+             filename = my_file)
 
     return(invisible(TRUE))
 
   }
 
   if (inherits(value, "antsImage")) {
 
+    requireNamespace("ANTsRCore", quietly = TRUE)
+
     my_file <- file.path(folder, paste0(name, ".nii.gz"))
 
-    ANTsRCore::antsImageWrite(image = value,
-                              filename = my_file)
+    antsImageWrite(image = value,
+                   filename = my_file)
 
     return(invisible(TRUE))
 

README.Rmd

@@ -68,7 +68,7 @@ In `wf4ni`, a _flow_ is an ordered collection of processes that convert inputs i
 
 By defining the appropriate functions, one can model the pipeline in the correct order and obtain a flow as the one depicted in the following figure:
 
-![A sample workflow](img/flow.png)
+![A sample workflow](vignettes/img/flow.png)
 
 Original inputs in the _flow_ are _I1_, _I2_ and _I3_ (in blue). Other nodes represent the output of a given function, using the incident nodes as inputs for that function.
 

README.md

@@ -114,7 +114,7 @@ By defining the appropriate functions, one can model the pipeline in the
 correct order and obtain a flow as the one depicted in the following
 figure:
 
-![A sample workflow](img/flow.png)
+![A sample workflow](vignettes/img/flow.png)
 
 Original inputs in the *flow* are *I1*, *I2* and *I3* (in blue). Other
 nodes represent the output of a given function, using the incident nodes