CRAN release of 1.1.1. (#31)

.circleci/config.yml

@@ -48,6 +48,50 @@ jobs:
           name: Check coverage
           command: Rscript -e 'library(covr); codecov(quiet = FALSE)'
 
+  Build-for-r4_1_3:
+    docker:
+      - image: rocker/verse:4.1.3
+    resource_class: medium
+
+    steps:
+      - checkout
+      - run:
+          name: Review checkout
+          command: ls -la
+
+      - run:
+          name: Install Linux dependencies
+          command: |
+            sudo apt-get update -y
+            sudo apt-get install -yq texlive-fonts-recommended
+            sudo apt-get install -yq texlive-fonts-extra
+      - run:
+          name: Install R dependencies
+          command: |
+            R -e 'install.packages("BiocManager")'
+            R -e 'BiocManager::install(c("GenomicRanges", "edgeR", "biomaRt"))'
+            R -e 'install.packages("covr")'
+            R -e 'install.packages("conflicted")'
+      - run:
+          name: Session information and installed package versions
+          command: |
+            Rscript -e 'sessionInfo()'
+            Rscript -e 'installed.packages()[, c("Package", "Version")]'
+            Rscript -e 'rmarkdown::pandoc_version()'
+      - run:
+          name: Build package
+          command: R CMD build .
+      - run:
+          name: Check package
+          command: |
+            # Install suggested packages
+            R -e 'install.packages("png")'
+            # Perform package check
+            R CMD check *tar.gz
+      - run:
+          name: Check coverage
+          command: Rscript -e 'library(covr); codecov(quiet = FALSE)'
+
   Build-for-rLATEST:
     docker:
       - image: rocker/verse:latest
@@ -97,4 +141,5 @@ workflows:
   Prepare-All-R-Editions:
     jobs:
       - Build-for-r4_0_5
+      - Build-for-r4_1_3
       - Build-for-rLATEST

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: DGEobj
 Type: Package
 Title: Differential Gene Expression (DGE) Analysis Results Data Object
-Version: 1.1.0
+Version: 1.1.1
 Description: 
     Provides a flexible container to manage and annotate Differential Gene 
     Expression (DGE) analysis results (Smythe et. al (2015) <doi:10.1093/nar/gkv007>).  

DGEobj.Rproj

@@ -18,4 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace,vignette

NEWS.md

@@ -4,11 +4,14 @@
 
 ---
 
+### 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
+
 ### v1.1
 * made GenomicRanges package optional - used only for exon/gene levels
 * added "protein" level data, reviewed/updated isoform data for proper handling
 * added imputationMatrix as a type of metadata
-* reworked reset to resolve issues and remove unneded code
+* reworked reset to resolve issues and remove unneeded code
 * updated tests and documentation
 
 ### v1.0.3

R/addItem.R

@@ -167,7 +167,7 @@ addItem <- function(dgeObj,
 #' @return A DGEobj
 #'
 #' @examples
-#'
+#' \dontrun{
 #'    # Add normalize counts (DGEList) 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")
@@ -179,6 +179,7 @@ addItem <- function(dgeObj,
 #'                       parents = list("counts", "newDgelist")
 #'    )
 #'    inventory(dgeObj)
+#' }
 #'
 #' @importFrom assertthat assert_that
 #'

R/attributes.R

@@ -10,10 +10,12 @@
 #'   "dimnames", "rownames", "colnames", "listData", "objDef")
 #'
 #' @examples
+#' \dontrun{
 #'     # example DGEobj
 #'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
 #'
 #'    showAttributes(exObj)
+#'}
 #'
 #' @export
 showAttributes <- function(dgeObj, skipList = c("dim", "dimnames", "rownames", "colnames", "listData", "objDef")) {

R/reset.R

@@ -11,6 +11,7 @@
 #' @return A DGEobj
 #'
 #' @examples
+#' \dontrun{
 #'     #example object
 #'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
 #'
@@ -19,6 +20,7 @@
 #'
 #'     exObj <- resetDGEobj(exObj)
 #'     dim(exObj)
+#'}
 #'
 #' @importFrom assertthat assert_that
 #'

R/subset.R

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

R/utils.R

@@ -44,10 +44,12 @@ dimnames.DGEobj <- function(x){
 #' @return NULL
 #'
 #' @examples
+#' \dontrun{
 #'     # example DGEobj
 #'     exObj <- readRDS(system.file("exampleObj.RDS", package = "DGEobj"))
 #'
 #'     print(exObj)
+#'}
 #'
 #' @export
 print.DGEobj <- function(x, ..., verbose = FALSE) {
@@ -65,10 +67,12 @@ 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"))
 #'
 #'     inventory(exObj)
+#' }
 #'
 #' @export
 inventory <- function(dgeObj, verbose = FALSE)  {

cran-comments.md

@@ -1,10 +1,8 @@
 ## Comments from Maintainer
 
-* made GenomicRanges package optional - used only for exon/gene levels
-* added "protein" level data, reviewed/updated isoform data for proper handling
-* added imputationMatrix as a type of metadata
-* reworked reset to resolve issues and remove unneeded code
-* updated tests and documentation
+* Resolved CRAN check errors
+* Skipping examples dependent on suggested packages
+* Updated tests so that they do not fail if suggested packages are not available
 
 ---  
 
@@ -20,6 +18,7 @@ CircleCI
 
 * R 4.0.5
 * R 4.1.3
+* rocker/verse:latest
 
 WinBuilder
 
@@ -28,7 +27,8 @@ WinBuilder
 
 RHub
 
-* devtools::check_rhub(interactive = F)
+* devtools::check_rhub(interactive = F,
+                       env_vars    = c("_R_CHECK_DEPENDS_ONLY_"   = "true"))
 
 ---  
 
@@ -54,7 +54,8 @@ revdepcheck::cran_revdeps('DGEobj', bioc = T)
 ```
 
 ```
-revdepcheck:: revdep_report_cran()
+revdepcheck::revdep_report_cran()
+
 ## revdepcheck results
 
 We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.

misc/test_object_creation/create_objects.R

@@ -43,7 +43,9 @@ dge_creation_workflow <- function(counts, gene.data, design, qcdata, contrast_li
     result <- result[result$geneData$gene_biotype == "protein_coding", ]
 
     # Normalize
-    result <- runEdgeRNorm(result, includePlot = FALSE)
+    if (requireNamespace("edgeR", quietly = TRUE)) {
+        result <- runEdgeRNorm(result, includePlot = FALSE)
+    }
 
     # Define Model
     formula          <- '~ 0 + ReplicateGroup'