diff --git a/DESCRIPTION b/DESCRIPTION index 26f588d2eca11bca7b9a821ea130c78c914cebc8..7ce0ae1ee0f38baccac5352952a2e1626ca2b8e1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: splatter Type: Package Title: Simple Simulation of Single-cell RNA Sequencing Data -Version: 1.5.3 +Version: 1.5.4 Date: 2018-08-20 Author: Luke Zappia Authors@R: diff --git a/README.md b/README.md index b53a44dbe29bb8b3596a7019fc7277eec8ae0023..9d9ae2a3c52613274a447d3f62117e032f1305d6 100644 --- a/README.md +++ b/README.md @@ -30,14 +30,15 @@ If you have this installed Splatter can be installed from Bioconductor using `biocLite`: ```{r} -source("https://bioconductor.org/biocLite.R") -biocLite("splatter") +if (!requireNamespace("BiocManager", quietly=TRUE)) + install.packages("BiocManager") +BiocManager::install("splatter") ``` If you wish to build a local version of the vignette use: ```{r} -biocLite("splatter", build_vignettes=TRUE) +BiocManager::install("splatter", build_vignettes=TRUE) ``` This will also build the vignette and install all suggested dependencies (which diff --git a/index.md b/index.md index 90cfdc6369d87c00d275d3d441b1f04cbca521f9..85c210205736a132e29fc9e21553ae5f0003cccb 100644 --- a/index.md +++ b/index.md @@ -34,14 +34,15 @@ If you have these installed Splatter can be installed from Bioconductor using `biocLite`: ```{r} -source("https://bioconductor.org/biocLite.R") -biocLite("splatter") +if (!requireNamespace("BiocManager", quietly=TRUE)) + install.packages("BiocManager") +BiocManager::install("splatter") ``` If you wish to build a local version of the vignette use: ```{r} -biocLite("splatter", build_vignettes=TRUE) +BiocManager::install("splatter", build_vignettes=TRUE) ``` This will also build the vignette and install all suggested dependencies (which @@ -55,11 +56,11 @@ If you want to try the [development version][devel] this can also be installed from Bioconductor: ```{r} -library(BiocInstaller) +library(BiocManager) useDevel() biocValid() # checks for out of date packages -biocLite() # (optional) updates out of date packages -biocLite("splatter") +BiocManager::install() # (optional) updates out of date packages +BiocManager::install("splatter") ``` Depending on the current release cycle you may also need to install the diff --git a/vignettes/splatter.Rmd b/vignettes/splatter.Rmd index 0301b122f0b28e83fca312145c8155e8955b5104..efaa1e7d48f8ecd1d44ba14e8802f9b632bb37ad 100644 --- a/vignettes/splatter.Rmd +++ b/vignettes/splatter.Rmd @@ -29,14 +29,15 @@ introduction to Splatter's functionality. Splatter can be installed from Bioconductor: ```{r install, eval = FALSE} -source("https://bioconductor.org/biocLite.R") -biocLite("splatter") +if (!requireNamespace("BiocManager", quietly=TRUE)) + install.packages("BiocManager") +BiocManager::install("splatter") ``` To install the most recent development version from Github use: ```{r install-github, eval = FALSE} -biocLite("Oshlack/splatter", dependencies = TRUE, +BiocManager::install("Oshlack/splatter", dependencies = TRUE, build_vignettes = TRUE) ```