diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index fada210..2c939ac 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.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} diff --git a/CRAN-RELEASE b/CRAN-RELEASE index db33ddf..2f6756e 100644 --- a/CRAN-RELEASE +++ b/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). diff --git a/ChangeLog b/ChangeLog index 3cd3ca4..c4836d1 100644 --- a/ChangeLog +++ b/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 diff --git a/DESCRIPTION b/DESCRIPTION index ba6fd97..a4b0ea8 100644 --- a/DESCRIPTION +++ b/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", diff --git a/R/snapclust.R b/R/snapclust.R index 0a83e4d..b10058e 100644 --- a/R/snapclust.R +++ b/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 diff --git a/R/snapclust.choose.k.R b/R/snapclust.choose.k.R index b1f135f..4eaca59 100644 --- a/R/snapclust.choose.k.R +++ b/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} diff --git a/README.md b/README.md index 958c0b8..7086d1e 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,13 @@ - - [![R-CMD-check](https://github.com/thibautjombart/adegenet/workflows/R-CMD-check/badge.svg)](https://github.com/thibautjombart/adegenet/actions) + +[![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) diff --git a/cran-comments.md b/cran-comments.md index 5e109d6..a2cc64b 100644 --- a/cran-comments.md +++ b/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 diff --git a/man/snapclust.Rd b/man/snapclust.Rd index 32f9bfb..1903ed2 100644 --- a/man/snapclust.Rd +++ b/man/snapclust.Rd @@ -97,7 +97,7 @@ tutorial which can be accessed using \code{adegenetTutorial("snapclust")}. \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")}. } \examples{ diff --git a/man/snapclust.choose.k.Rd b/man/snapclust.choose.k.Rd index 26b3922..c717f46 100644 --- a/man/snapclust.choose.k.Rd +++ b/man/snapclust.choose.k.Rd @@ -32,7 +32,7 @@ accessed using \code{adegenetTutorial("snapclust")}. \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{