Cran 1.1.2 Version Release (#32)

.gitignore

@@ -5,7 +5,6 @@
 *-Ex.R
 /*.Rcheck/
 .Rproj.user/
-vignettes/*.html
 .httr-oauth
 /*_cache/
 /cache/
@@ -28,4 +27,7 @@ revdep
 vignettes/*.html
 vignettes/*.R
 vignettes/*.log
+
 !vignettes/precompiled_vignettes.R
+!inst/exampleObj.RDS
+!inst/miniObj.RDS

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DGEobj
 Type: Package
 Title: Differential Gene Expression (DGE) Analysis Results Data Object
-Version: 1.1.1
+Version: 1.1.2
 Description: 
     Provides a flexible container to manage and annotate Differential Gene 
     Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>).  
@@ -29,15 +29,15 @@ Imports:
     stringr,
     utils
 Suggests: 
+    biomaRt,
     conflicted,
     dplyr,
+    edgeR,
+    GenomicRanges,
     glue,
     knitr,
     rmarkdown,
-    testthat,
-    biomaRt,
-    edgeR,
-    GenomicRanges
+    testthat
 biocViews:
 RoxygenNote: 7.1.2
 VignetteBuilder: knitr

NEWS.md

@@ -4,6 +4,12 @@
 
 ---
 
+### v1.1.2
+* Made all Bioconductor packages optional (suggested)
+* Added a new, minimal "mini" example object that has no internal Bioconductor-based features (ie normalization, analysis) to allow 
+for clean, simple examples that do not depend on suggested packages
+* Testing updated so that when Bioconductor suggested packages are unavailable the tests will not be run
+
 ### v1.1.1
 * Updated tests and examples so that when suggested packages are unavailable the examples and/or tests dependent on them are not run
 

R/addItem.R

@@ -16,10 +16,10 @@
 #' \dontrun{
 #'    myFunArgs <- match.call()  #  Capture calling function and arguments
 #'
-#'    myDGEobj <- addItem(myDGEobj, item = MyCounts,
+#'    myDGEobj <- addItem(myDGEobj, item     = MyCounts,
 #'                                  itemName = "counts",
 #'                                  itemType = "counts",
-#'                                  funArgs = myFunArgs)
+#'                                  funArgs  = myFunArgs)
 #' }
 #'
 #' @importFrom assertthat assert_that
@@ -168,7 +168,9 @@ addItem <- function(dgeObj,
 #'
 #' @examples
 #' \dontrun{
-#'    # Add normalize counts (DGEList) and log2CPM as additional "assay" items in the DGEobj
+#'    # NOTE: Requires the edgeR package
+#'
+#'    # Add normalized counts and log2CPM as additional "assay" items in the DGEobj
 #'    dgeObj  <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
 #'    dgeList <- edgeR::calcNormFactors(edgeR::DGEList(dgeObj$counts), method="TMM")
 #'    log2cpm <- edgeR::cpm(dgeList, log = TRUE)

R/annotate.R

@@ -16,19 +16,21 @@
 #' @return A DGEobj
 #'
 #' @examples
-#'    MyDgeObj <- system.file("exampleObj.RDS", package = "DGEobj")
+#'    MyDgeObj <- system.file("miniObj.RDS", package = "DGEobj")
 #'
 #' \dontrun{
 #'    #using a text file file of key=value pairs
 #'    annotationFile <- "/location/to/myAnnotations.txt"
 #'    MyDgeObj <- annotateDGEobj(MyDgeObj, annotationFile)
-#'}
+#' }
+#'
 #'    #using a named list of key/values
 #'    annotations <- list(Title     = "Rat Liver Slices from Bile Duct Ligation animals",
 #'                        Organism  = "Rat",
 #'                        GeneModel = "Ensembl.R89")
 #'    MyDgeObj <- annotateDGEobj(MyDgeObj, annotations)
 #'
+#'
 #' @import magrittr
 #' @importFrom stringr str_remove_all str_locate
 #' @importFrom utils read.delim

R/attributes.R

@@ -10,12 +10,10 @@
 #'   "dimnames", "rownames", "colnames", "listData", "objDef")
 #'
 #' @examples
-#' \dontrun{
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'    showAttributes(exObj)
-#'}
 #'
 #' @export
 showAttributes <- function(dgeObj, skipList = c("dim", "dimnames", "rownames", "colnames", "listData", "objDef")) {
@@ -57,7 +55,7 @@ showAttributes <- function(dgeObj, skipList = c("dim", "dimnames", "rownames", "
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     # Assign attributes to a DGEobj
 #'     MyAttributes <- list(Platform       = "RNA-Seq",
@@ -107,7 +105,7 @@ setAttributes <- function(dgeObj, attribs){
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     getAttributes(exObj)
 #'
@@ -132,7 +130,7 @@ getAttributes <- function(dgeObj,
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     showMeta(exObj)
 #'

R/get.R

@@ -7,7 +7,7 @@
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     myList <- getItems(exObj, list("counts", "geneData"))
 #'     names(myList)
@@ -17,7 +17,6 @@
 #'
 #' @export
 getItems <- function(dgeObj, itemNames){
-
     assertthat::assert_that(!missing(dgeObj),
                             !missing(itemNames),
                             msg = "Specify both a DGEobj and at least one itemName to retrieve.")
@@ -52,7 +51,7 @@ getItems <- function(dgeObj, itemNames){
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     MyCounts <- getItem(exObj, "counts")
 #'
@@ -85,7 +84,7 @@ getItem <- function(dgeObj, itemName){
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     MyRawData      <- getType(exObj, type = list("counts", "design", "geneData"))
 #'
@@ -119,7 +118,7 @@ getType <- function(dgeObj, type, parent){
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     Assays <- getBaseType(exObj, baseType = "assay")
 #'     AssaysAndMeta <- getBaseType(exObj, c("assay", "meta"))

R/init.R

@@ -20,18 +20,17 @@
 #' @return A DGEobj
 #'
 #' @examples
-#'
-#'    dgeObj   <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'    dgeObj   <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'    MyCounts <- dgeObj$counts
 #'    geneinfo <- dgeObj$geneData
 #'    sampinfo <- dgeObj$design
 #'
 #'   myDgeObj <- initDGEobj(primaryAssayData = MyCounts,
-#'                          rowData = geneinfo,
-#'                          colData = sampinfo,
-#'                          level = "gene",
-#'                          customAttr = list (Genome = "Rat.B6.0",
-#'                                             GeneModel = "Ensembl.R89"))
+#'                          rowData          = geneinfo,
+#'                          colData          = sampinfo,
+#'                          level            = "gene",
+#'                          customAttr       = list (Genome = "Rat.B6.0",
+#'                                                GeneModel = "Ensembl.R89"))
 #'
 #' @import magrittr
 #' @importFrom assertthat assert_that

R/reset.R

@@ -11,16 +11,14 @@
 #' @return A DGEobj
 #'
 #' @examples
-#' \dontrun{
 #'     #example object
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     # subset to first 10 rows to show reset functionality
 #'     exObj <- exObj[c(1:10), ]
 #'
 #'     exObj <- resetDGEobj(exObj)
 #'     dim(exObj)
-#'}
 #'
 #' @importFrom assertthat assert_that
 #'

R/rmItem.R

@@ -7,7 +7,7 @@
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     exObj <- rmItem(exObj, "design")
 #'

R/subset.R

@@ -11,12 +11,10 @@
 #' @return A DGEobj
 #'
 #' @examples
-#' \dontrun{
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     exObj <- subset(exObj, 1:10, 5:50)
-#'}
 #'
 #' @importFrom assertthat assert_that
 #' @importFrom stringr str_c

R/types.R

@@ -7,7 +7,7 @@
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     baseType(exObj, type = "DGEList")
 #'
@@ -43,7 +43,7 @@ baseType <- function(dgeObj, type){
 #'     baseTypes()
 #'
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     # Basetypes from a specific DGEobj
 #'     baseTypes(exObj)
@@ -65,7 +65,7 @@ baseTypes <- function(dgeObj){
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     showTypes(exObj)
 #'
@@ -98,7 +98,7 @@ showTypes <- function(dgeObj){
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     exObj <- newType(exObj,
 #'                      itemType   = "AffyRMA",

R/utils.R

@@ -44,12 +44,10 @@ dimnames.DGEobj <- function(x){
 #' @return NULL
 #'
 #' @examples
-#' \dontrun{
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     print(exObj)
-#'}
 #'
 #' @export
 print.DGEobj <- function(x, ..., verbose = FALSE) {
@@ -67,12 +65,10 @@ print.DGEobj <- function(x, ..., verbose = FALSE) {
 #' @return A data.frame summarizing the data contained in the DGEobj
 #'
 #' @examples
-#' \dontrun{
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     inventory(exObj)
-#' }
 #'
 #' @export
 inventory <- function(dgeObj, verbose = FALSE)  {
@@ -122,7 +118,7 @@ inventory <- function(dgeObj, verbose = FALSE)  {
 #'
 #' @examples
 #'     # example DGEobj
-#'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
+#'     exObj <- readRDS(system.file("miniObj.RDS", package = "DGEobj"))
 #'
 #'     mylist <- as.list(exObj)
 #'

cran-comments.md

@@ -1,8 +1,16 @@
 ## Comments from Maintainer
 
-* Resolved CRAN check errors
-* Skipping examples dependent on suggested packages
-* Updated tests so that they do not fail if suggested packages are not available
+* There is one outstanding note - we updated this package recently in an attempt to resolve the issues with noSuggests
+however unfortunately it uncovered a different package dependency problem that wasn't caught on the 3 standard RHub platform
+configurations.  We have now combed over the entire package and extensively checked all RHub and local platforms to try to 
+ensure the suggested packages are just that, suggested!  We also made sure we now have a very small example object to use
+that was not made using any of the suggested packages as well.
+
+* We appreciate your consideration of this package update, here is what we have done for this release:
+  * Resolved CRAN check errors, including the noSuggests issues
+  * Added a new example object so that as many examples can be run as possible without suggested packages
+  * Bioconductor packages in suggests are required for testing, now we will not run tests if any are missing
+  * Also updated our process to check ALL available/usable RHub platforms prior to submission
 
 ---  
 
@@ -13,6 +21,7 @@ RStudio Server Pro (ubuntu 18.04.2)
 * R 3.6.3
 * R 4.0.5
 * R 4.1.3
+* R 4.2.0
 
 CircleCI
 
@@ -28,7 +37,9 @@ WinBuilder
 RHub
 
 * devtools::check_rhub(interactive = F,
-                       env_vars    = c("_R_CHECK_DEPENDS_ONLY_"   = "true"))
+                       platforms   = c(rhub::platforms()$name),
+                       env_vars    = c("_R_CHECK_DEPENDS_ONLY_"   = "true",
+                                       "_R_CHECK_FORCE_SUGGESTS_" = "false"))
 
 ---