Merge pull request #310 from thibautjombart/cran-release-2021-07

prepare for CRAN release

.github/workflows/R-CMD-check.yaml

@@ -65,6 +65,10 @@ jobs:
 
       - name: Install dependencies
         run: |
+          options(repos = c(
+            `r-spatial` = "https://r-spatial.r-universe.dev/",
+            CRAN = "https://cloud.r-project.org/"
+          ))
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}

CRAN-RELEASE

@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-05-09.
-Once it is accepted, delete this file and tag the release (commit 7a1141592d).
+This package was submitted to CRAN on 2021-07-17.
+Once it is accepted, delete this file and tag the release (commit f728a41).

ChangeLog

@@ -1,3 +1,10 @@
+			CHANGES IN ADEGENET VERSION 2.1.4
+
+DOCUMENTATION
+
+  - `snapclust()` documentation has been updated to be not so scary
+	(@thibautjombart, #287)
+
 			CHANGES IN ADEGENET VERSION 2.1.3
 
 BUG FIX

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: adegenet
 Title: Exploratory Analysis of Genetic and Genomic Data
-Version: 2.1.3
+Version: 2.1.4
 Authors@R: 
     c(person(given = "Thibaut",
              family = "Jombart",

R/snapclust.R

@@ -11,7 +11,7 @@
 #'
 #' @details The method is described in Beugin et al (2018) A fast likelihood
 #'   solution to the genetic clustering problem. Methods in Ecology and
-#'   Evolution \url{https://doi.org/10.1111/2041-210X.12968}. A dedicated
+#'   Evolution \doi{10.1111/2041-210X.12968}. A dedicated
 #'   tutorial is available by typing \code{adegenetTutorial("snapclust")}.
 #'
 #' @seealso The function \code{\link{snapclust.choose.k}} to investigate the optimal

R/snapclust.choose.k.R

@@ -10,7 +10,7 @@
 #' 
 #' @details The method is described in Beugin et al (2018) A fast likelihood
 #'   solution to the genetic clustering problem. Methods in Ecology and
-#'   Evolution \url{https://doi.org/10.1111/2041-210X.12968}. A dedicated
+#'   Evolution \doi{10.1111/2041-210X.12968}. A dedicated
 #'   tutorial is available by typing \code{adegenetTutorial("snapclust")}.
 #' 
 #' @author Thibaut Jombart \email{thibautjombart@@gmail.com}

README.md

@@ -1,15 +1,13 @@
-  <!-- badges: start -->
-  [![R-CMD-check](https://github.com/thibautjombart/adegenet/workflows/R-CMD-check/badge.svg)](https://github.com/thibautjombart/adegenet/actions)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/thibautjombart/adegenet/workflows/R-CMD-check/badge.svg)](https://github.com/thibautjombart/adegenet/actions)
 
 [![Build status](https://ci.appveyor.com/api/projects/status/l7a9k1saqnshakk9/branch/master?svg=true)](https://ci.appveyor.com/project/thibautjombart/adegenet/branch/master)
 
-[![CRAN Status Badge](http://www.r-pkg.org/badges/version/adegenet)](https://cran.r-project.org/package=adegenet)
+[![CRAN Status Badge](https://www.r-pkg.org/badges/version/adegenet)](https://cran.r-project.org/package=adegenet)
 
 [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/adegenet)](https://cran.r-project.org/package=adegenet)
 
-[![Downloads from Rstudio mirror](https://cranlogs.r-pkg.org/badges/grand-total/adegenet)](http://www.r-pkg.org/pkg/adegenet)
-
-[![Research software impact](http://depsy.org/api/package/cran/adegenet/badge.svg)](http://depsy.org/package/r/adegenet)
+[![Downloads from Rstudio mirror](https://cranlogs.r-pkg.org/badges/grand-total/adegenet)](https://cran.r-project.org/package=adegenet)
 
   <!-- badges: end -->
 

cran-comments.md

@@ -1,8 +1,8 @@
-This is largely a maintenance update. 
- 
+This is a maintenance update and fixes the urls giving 301 codes 
+
 ## Test environments
-* local OS X install, R 4.0.0
-* ubuntu 14.04 (on travis-ci), R 4.0.0
+* local OS X install, R 4.0.1
+* ubuntu 20.04 (on GitHub Actions), R 4.0.1
 * win-builder (devel and release)
 
 ## R CMD check results