From d39fe552dfc0612373dc6d5d1aa828fff9b0df15 Mon Sep 17 00:00:00 2001
From: Luke Zappia <lazappi@users.noreply.github.com>
Date: Thu, 29 Dec 2016 14:38:39 +1100
Subject: [PATCH] Tidy up and bump version
---
DESCRIPTION | 4 ++--
NAMESPACE | 1 -
NEWS.md | 6 ++++++
R/SCDDParams-methods.R | 6 ++----
R/scDD-estimate.R | 3 +--
appveyor.yml | 6 ++++++
6 files changed, 17 insertions(+), 9 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 991c035..7fed680 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: splatter
Type: Package
Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.99.5
-Date: 2016-12-28
+Version: 0.99.6
+Date: 2016-12-29
Author: Luke Zappia
Authors@R:
c(person("Luke", "Zappia", role = c("aut", "cre"),
diff --git a/NAMESPACE b/NAMESPACE
index 9d8ff06..0bfc62e 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -90,5 +90,4 @@ importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,rpois)
importFrom(stats,runif)
-importFrom(utils,data)
importFrom(utils,head)
diff --git a/NEWS.md b/NEWS.md
index 66bfb92..b09c356 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# 0.99.6
+
+* Add installation to vignette
+* Add detail about counts matrix to vignette
+* Replace 1:x with seq_len/seq_along
+
# 0.99.5
* Set R_TESTS environment
diff --git a/R/SCDDParams-methods.R b/R/SCDDParams-methods.R
index 57eb760..2ff8543 100644
--- a/R/SCDDParams-methods.R
+++ b/R/SCDDParams-methods.R
@@ -1,15 +1,13 @@
#' @rdname newParams
-#' @importFrom utils data
#' @importFrom methods new
#' @export
newSCDDParams <- function(...) {
if (!requireNamespace("scDD", quietly = TRUE)) {
- stop("The scDD simulation requires the 'scDD' package. ",
- "See https://github.com/kdkorthauer/scDD for installation.")
+ stop("The scDD simulation requires the 'scDD' package.")
}
- data("scDatEx", package = "scDD", envir = environment())
+ utils::data("scDatEx", package = "scDD", envir = environment())
params <- new("SCDDParams", SCdat = scDatEx)
diff --git a/R/scDD-estimate.R b/R/scDD-estimate.R
index a4e9fa8..8f9a5c2 100644
--- a/R/scDD-estimate.R
+++ b/R/scDD-estimate.R
@@ -38,8 +38,7 @@ scDDEstimate.SCESet <- function(counts, conditions, params = newSCDDParams()) {
scDDEstimate.matrix <- function(counts, conditions, params = newSCDDParams()) {
if (!requireNamespace("scDD", quietly = TRUE)) {
- stop("The scDD simulation requires the 'scDD' package. ",
- "See https://github.com/kdkorthauer/scDD for installation.")
+ stop("The scDD simulation requires the 'scDD' package.")
}
checkmate::assertClass(params, "SCDDParams")
diff --git a/appveyor.yml b/appveyor.yml
index 6ae614c..af7524c 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -12,6 +12,12 @@ install:
# Adapt as necessary starting from here
+environment:
+ matrix:
+ - R_VERSION: devel
+
+ - R_VERSION: release
+
build_script:
- travis-tool.sh install_bioc_deps
--
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