prepare cran submission

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: valr
 Type: Package
 Title: Genome Interval Arithmetic in R
-Version: 0.3.0.9000
+Version: 0.3.1
 Authors@R: c(
     person('Jay', 'Hesselberth', role = c('aut', 'cre'), email = '[email protected]'),
     person('Kent', 'Riemondy', role = c('aut'), email = '[email protected]')
@@ -40,7 +40,6 @@ Suggests:
     GenomicRanges,
     IRanges,
     S4Vectors,
-BiocViews:
 VignetteBuilder: knitr
 RoxygenNote: 6.0.1
 URL: http://github.com/rnabioco/valr, http://rnabioco.github.io/valr

NEWS.md

@@ -1,7 +1,9 @@
-# valr 0.3.0.9000
+# valr 0.3.1
 
 ## Enhancements
 
+* A manuscript describing valr has been published in [F1000Research](https://f1000research.com/articles/6-1025/v1).
+
 * New S3 generic `as.tbl_interval()` converts `GenomicRanges::GRanges` objects to `tbl_interval`.
 
 * New `create_tss()` for creating transcription start sites.

cran-comments.md

@@ -2,15 +2,13 @@
 
 * This is a new minor version (see NEWS.md).
 
-* This version incorporates changes to be compatible with the new version of dplyr (v0.7.0).
-
 ## Test environments
 
-* Windows Server 2012 R2 x64 (on appveyor), R 3.4.0
+* Windows Server 2012 R2 x64 (on appveyor), R 3.4.1
 * win-builder (devel and release)
-* local OS X install, R 3.4.0
-* OS X (on travis-ci), R 3.4.0
-* ubuntu 14.04 (on travis-ci), R 3.4.0
+* local OS X install, R 3.4.1
+* OS X (on travis-ci), R 3.4.1
+* ubuntu 14.04 (on travis-ci), R 3.4.1
 
 ## R CMD check results
 
@@ -21,23 +19,14 @@
 
 * on win-builder
 
-  Status: WARNING
-  0 errors | 1 warnings | 0 notes
-
-  This warning is caused by an issue with pandoc, which I understand CRAN is already aware of.
+  Status: OK
+  0 errors | 0 warnings | 0 notes
 
-  * checking top-level files ... WARNING
-Conversion of 'README.md' failed:
-pandoc.exe: Could not fetch https://img.shields.io/codecov/c/github/rnabioco/valr/master.svg
-TlsExceptionHostPort (HandshakeFailed Error_EOF) "img.shields.io" 443
-
 * on OS X 
 
   Status: OK
   0 errors | 0 warnings | 0 notes
 
-  valr builds cleanly on my local machine. valr fails on travis-ci because the binary dplyr v0.7.0 is not available on CRAN due to an ERROR with its build. This will be fixed in a forthcoming patch release of dplyr (https://github.com/tidyverse/dplyr/commit/0b40356fe22bc33fc9ba38bac22aa898c1c40480).
-
 * on ubuntu
 
   Status: 1 NOTE