[ADAM-1783] Resolve check issues that block pushing to CRAN.

Resolves #1783. Cleans up a host of documentation issues that would cause
warnings when submitting to CRAN.

adam-r/bdgenomics.adam/DESCRIPTION

@@ -5,17 +5,17 @@ Title: R Frontend for Big Data Genomics/ADAM
 Description: ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark and Parquet.
 Author: Big Data Genomics
 Maintainer: Frank Austin Nothaft <fnothaft@alumni.stanford.edu>
-Authors@R: c(person("Frank", "Nothaft", role = c("aut", "cre"),
+Authors@R: c(person("Frank Austin", "Nothaft", role = c("aut", "cre"),
                     email = "fnothaft@alumni.stanford.edu"),
              person(family = "Big Data Genomics", role = c("aut", "cph")))
 License: Apache License (== 2.0)
 URL: http://www.bdgenomics.org https://github.com/bigdatagenomics/adam
 BugReports: https://github.com/bigdatagenomics/adam/issues
 Imports:
-    methods
-Depends:
-    R (>= 3.0),
+    methods,
     SparkR (>= 2.1.0)
+Depends:
+    R (>= 3.0)
 Suggests:
     testthat
 Collate:

adam-r/bdgenomics.adam/NAMESPACE

@@ -1,6 +1,40 @@
 # Generated by roxygen2: do not edit by hand
 
 export(ADAMContext)
+export(aggregatedCoverage)
+export(collapse)
+export(countKmers)
+export(coverage)
+export(createADAMContext)
+export(flankAdjacentFragments)
+export(flatten)
+export(loadAlignments)
+export(loadContigFragments)
+export(loadCoverage)
+export(loadFeatures)
+export(loadFragments)
+export(loadGenotypes)
+export(loadVariants)
+export(markDuplicates)
+export(pipe)
+export(realignIndels)
+export(recalibrateBaseQualities)
+export(save)
+export(saveAsParquet)
+export(saveAsSam)
+export(saveAsVcf)
+export(sort)
+export(sortLexicographically)
+export(sortReadsByReferencePosition)
+export(sortReadsByReferencePositionAndIndex)
+export(toCoverage)
+export(toDF)
+export(toFeatures)
+export(toFragments)
+export(toReads)
+export(toVariantContexts)
+export(transform)
+export(transmute)
 exportClasses(ADAMContext)
 exportClasses(AlignmentRecordRDD)
 exportClasses(CoverageRDD)
@@ -45,3 +79,8 @@ exportMethods(toReads)
 exportMethods(toVariantContexts)
 exportMethods(transform)
 exportMethods(transmute)
+importFrom(SparkR,sparkR.callJMethod)
+importFrom(SparkR,sparkR.callJStatic)
+importFrom(SparkR,sparkR.newJObject)
+importFrom(SparkR,sparkR.session)
+importFrom(methods,new)

adam-r/bdgenomics.adam/R/adam-context.R

@@ -23,10 +23,32 @@ setOldClass("jobj")
 #' @description The ADAMContext provides helper methods for loading in genomic
 #'              data into a Spark RDD/Dataframe.
 #' @slot jac Java object reference to the backing JavaADAMContext.
+#'
+#' @rdname ADAMContext
+#' 
 #' @export
 setClass("ADAMContext",
          slots = list(jac = "jobj"))
 
+#' Creates an ADAMContext by creating a SparkSession.
+#'
+#' @return Returns an ADAMContext.
+#' 
+#' @importFrom SparkR sparkR.session
+#'
+#' @export
+createADAMContext <- function() {
+    ADAMContext(sparkR.session())
+}
+
+#' Creates an ADAMContext from an existing SparkSession.
+#'
+#' @param ss The Spark Session to use to create the ADAMContext.
+#' @return Returns an ADAMContext.
+#'
+#' @importFrom SparkR sparkR.callJMethod sparkR.newJObject
+#' @importFrom methods new
+#'
 #' @export
 ADAMContext <- function(ss) {
     ssc = sparkR.callJMethod(ss, "sparkContext")
@@ -36,6 +58,7 @@ ADAMContext <- function(ss) {
     new("ADAMContext", jac = jac)
 }
 
+#' @importFrom SparkR sparkR.callJStatic
 javaStringency <- function(stringency) {
     stringency <- sparkR.callJStatic("htsjdk.samtools.ValidationStringency",
                                      "valueOf",
@@ -62,6 +85,8 @@ javaStringency <- function(stringency) {
 #' @param stringency The validation stringency to apply. Defaults to STRICT.
 #' @return Returns an RDD containing reads.
 #'
+#' @importFrom SparkR sparkR.callJMethod
+#'
 #' @export
 setMethod("loadAlignments",
           signature(ac = "ADAMContext", filePath = "character"),
@@ -85,6 +110,8 @@ setMethod("loadAlignments",
 #' @param filePath The path to load the file from.
 #' @return Returns an RDD containing sequence fragments.
 #'
+#' @importFrom SparkR sparkR.callJMethod
+#'
 #' @export
 setMethod("loadContigFragments",
           signature(ac = "ADAMContext", filePath = "character"),
@@ -109,6 +136,8 @@ setMethod("loadContigFragments",
 #' @param stringency The validation stringency to apply. Defaults to STRICT.
 #' @return Returns an RDD containing sequence fragments.
 #'
+#' @importFrom SparkR sparkR.callJMethod
+#'
 #' @export
 setMethod("loadFragments",
           signature(ac = "ADAMContext", filePath = "character"),
@@ -141,6 +170,8 @@ setMethod("loadFragments",
 #' @param stringency The validation stringency to apply. Defaults to STRICT.
 #' @return Returns an RDD containing features.
 #'
+#' @importFrom SparkR sparkR.callJMethod
+#'
 #' @export
 setMethod("loadFeatures",
           signature(ac = "ADAMContext", filePath = "character"),
@@ -174,6 +205,8 @@ setMethod("loadFeatures",
 #' @param stringency The validation stringency to apply. Defaults to STRICT.
 #' @return Returns an RDD containing coverage.
 #'
+#' @importFrom SparkR sparkR.callJMethod
+#'
 #' @export
 setMethod("loadCoverage",
           signature(ac = "ADAMContext", filePath = "character"),
@@ -196,6 +229,8 @@ setMethod("loadCoverage",
 #' @param stringency The validation stringency to apply. Defaults to STRICT.
 #' @return Returns an RDD containing genotypes.
 #'
+#' @importFrom SparkR sparkR.callJMethod
+#'
 #' @export
 setMethod("loadGenotypes",
           signature(ac = "ADAMContext", filePath = "character"),
@@ -218,6 +253,8 @@ setMethod("loadGenotypes",
 #' @param stringency The validation stringency to apply. Defaults to STRICT.
 #' @return Returns an RDD containing variants.
 #'
+#' @importFrom SparkR sparkR.callJMethod
+#'
 #' @export
 setMethod("loadVariants",
           signature(ac = "ADAMContext", filePath = "character"),