replace BiocInstaller biocLite mentions with BiocManager

benjjneb · Aug 30, 2018 · e1f7ff1 · e1f7ff1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -8,7 +8,7 @@ Description: The dada2 package infers exact amplicon sequence variants (ASVs) fr
     removing substitution and chimera errors. Taxonomic classification is available
     via a native implementation of the RDP naive Bayesian classifier, and genus-species
     assignment by exact matching.
-Version: 1.9.0
+Version: 1.9.1
 Date: 2018-1-30
 Maintainer: Benjamin Callahan <benjamin.j.callahan@gmail.com>
 Author: Benjamin Callahan <benjamin.j.callahan@gmail.com>, Paul McMurdie, Susan

diff --git a/R/misc.R b/R/misc.R
@@ -266,8 +266,9 @@ is.list.of <- function(x, ctype) {
 
 #' @keywords internal
 bcinstall <- function(pkg="dada2", suppressUpdates=TRUE) {
-  source("https://bioconductor.org/biocLite.R")
-  biocLite(pkg, suppressUpdates=suppressUpdates)
+  if (!requireNamespace("BiocManager", quietly=TRUE))
+      install.packages("BiocManager")
+  BiocManager::install(pkg, suppressUpdates=suppressUpdates)
 }
 
 #' @keywords internal

diff --git a/README.md b/README.md
@@ -11,8 +11,9 @@ The dada2 package binaries are available through Bioconductor:
 
 ```S
 ## try http:// if https:// URLs are not supported
-source("https://bioconductor.org/biocLite.R")
-biocLite("dada2")
+if (!requireNamespace("BiocManager", quietly=TRUE))
+    install.packages("BiocManager")
+BiocManager::install("dada2")
 ```
 
 In order to install dada2 from source (and get the latest and greatest new features) see our [installation from source instructions](https://benjjneb.github.io/dada2/dada-installation.html).