Minor changes to please R CMD check --as-cran

satijalab · Jul 20, 2018 · 164208a · 164208a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,16 @@
 Package: sctransform
 Type: Package
-Title: Variance Stabilizing Transformations For Single Cell UMI Data
+Title: Variance Stabilizing Transformations for Single Cell UMI Data
 Version: 0.1.0
-Author: Christoph Hafemeister
-Maintainer: Christoph Hafemeister <chafemeister@nygenome.org>
-Description: Apply a variance stabilizing transformation to single-cell UMI count data. 
-  The transformation is based on a negative binomial regression model with regularized 
-  parameters. 
+Authors@R: person(given = 'Christoph', family = 'Hafemeister', email = 'chafemeister@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-6365-8254'))
+Description: A normalization method for single-cell UMI count data using a 
+  variance stabilizing transformation. The transformation is based on a 
+  negative binomial regression model with regularized parameters. A part of the
+  same regression framework, this package also provides functions for
+  differential gene expression testing, batch correction, and data
+  correction/denoising.
+URL: https://github.com/ChristophH/sctransform
+BugReports: https://github.com/ChristophH/sctransform/issues
 License: GPL-3 | file LICENSE
 Encoding: UTF-8
 LazyData: true

diff --git a/R/denoise.R b/R/denoise.R
@@ -16,7 +16,7 @@
 #'
 smooth_via_pca <- function(x, elbow_th = 0.025, dims_use = NULL, max_pc = 100, do_plot = FALSE,
                            scale. = FALSE) {
-  requireNamespace('irlba')
+  requireNamespace('irlba', quietly = TRUE)
   # perform pca
   if (scale.) {
     scale. <- apply(x, 1, 'sd')

diff --git a/R/vst.R b/R/vst.R
@@ -274,7 +274,7 @@ vst <- function(umi,
       variance = apply(umi, 1, var),
       residual_mean = rowMeans(res)
     )
-    if (requireNamespace('matrixStats')) {
+    if (requireNamespace('matrixStats', quietly = TRUE)) {
       gene_attr$residual_variance = matrixStats::rowVars(res)
     } else {
       message('Consider installing matrixStats package for faster gene attribute calculation.')

diff --git a/README.md b/README.md
@@ -1,3 +1,8 @@
+---
+pagetitle: "README for sctransform R package"
+author: "Christoph Hafemeister"
+---
+
 # sctransform
 R package for modeling single cell UMI expression data using regularized negative binomial regression
 
@@ -19,4 +24,3 @@ Available vignettes:
 [Differential expression](https://rawgit.com/ChristophH/sctransform/master/inst/doc/differential_expression.html)  
 [Batch correction](https://rawgit.com/ChristophH/sctransform/master/inst/doc/batch_correction.html)  
 [Denoising](https://rawgit.com/ChristophH/sctransform/master/inst/doc/denoising.html)  
-