Merge pull request #211 from grunwaldlab/cran-maintenance-2.8.4

Update unique.MLG documentation for CRAN
grunwaldlab · Feb 13, 2020 · b90f9b7 · b90f9b7
2 parents 60eb0e3 + 4da814f
commit b90f9b7
Show file tree

Hide file tree

Showing 236 changed files with 4,924 additions and 3,235 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -19,3 +19,4 @@
 ^CONTRIBUTING.md$
 ^_pkgdown\.yml$
 ^appveyor\.yml$
+^pkgdown$
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2019-06-14.
-Once it is accepted, delete this file and tag the release (commit a2b31fd4d3).
+This package was submitted to CRAN on 2020-02-12.
+Once it is accepted, delete this file and tag the release (commit d7ae8d2f4e).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 2.8.3
-Date: 2019-06-13
+Version: 2.8.4
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "zkamvar@gmail.com", comment = c(ORCID = "0000-0003-1458-7108")),
     person(c("Javier", "F."), "Tabima", role = "aut",
@@ -66,4 +65,4 @@ Suggests:
     RClone
 License: GPL-2 | GPL-3
 VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+poppr 2.8.4
+===========
+
+CRAN MAINTENANCE
+----------------
+
+* Update documentation for S4 method
+
 poppr 2.8.3
 ===========
 

diff --git a/R/aaaMLGmethods.R b/R/aaaMLGmethods.R
@@ -243,6 +243,7 @@ setGeneric("unique")
 #' 
 #' @rdname unique-methods
 #' @aliases unique,MLG-method
+#' @aliases unique,MLG,ANY-method
 #' @param incomparables vector of values that cannot be compared
 #' @param ... options passed on to the base function \link{unique} or \link{duplicated}.
 #' @export

diff --git a/R/ia_jackknife.R b/R/ia_jackknife.R
@@ -157,7 +157,6 @@ bias.ia <- function(theta_hat, theta_star){
 }
 
 #' @rdname ia
-#' @inheritParams resample.ia
 #' @export
 jack.ia <- function(gid, n = NULL, reps = 999, quiet = FALSE){
   msg <- paste0("jack.ia() is deprecated and will be removed in future versions.\n",

diff --git a/R/poppr.R b/R/poppr.R
@@ -98,9 +98,9 @@
 #' 
 #' Below are descriptions and links to functions found in \pkg{poppr}. Be
 #' aware that all functions in \pkg{\link[adegenet]{adegenet}} are also
-#' available. The functions are documented as:
+#' available. The functions are documented as: 
 #' 
-#' > `function` (data type) - Description
+#' - `function_name()` (data type) - Description
 #' 
 #' Where \sQuote{data type} refers to the type of data that can be used:
 #' \tabular{ll}{
@@ -247,7 +247,7 @@
 #' 
 #' --------- Papers referencing data sets ---------
 #' 
-#' Grunwald, NJ and Hoheisel, G.A. 2006. Hierarchical Analysis of Diversity, 
+#' Grünwald, NJ and Hoheisel, G.A. 2006. Hierarchical Analysis of Diversity, 
 #' Selfing, and Genetic Differentiation in Populations of the Oomycete 
 #' *Aphanomyces euteiches*. Phytopathology 96:1134-1141 doi: 
 #' \href{https://doi.org/10.1094/PHYTO-96-1134}{10.1094/PHYTO-96-1134}

diff --git a/README.md b/README.md
@@ -27,7 +27,7 @@ genind and genlight objects and offers the following implementations:
 or (<img src="https://latex.codecogs.com/gif.latex?%5Cbar%7Br%7D_d" alt = "Standardized index of association">)
 - batch processing on any server that has R (&ge; 2.15.1) installed
 - calculation of Bruvo's distance for microsatellite (SSR) markers (implemented in C for speed)
-- import of data from and export to [GenAlEx](https://biology.anu.edu.au/GenAlEx/Welcome.html "GenAlEx Homepage")
+- import of data from and export to [GenAlEx](https://biology-assets.anu.edu.au/GenAlEx/Welcome.html "GenAlEx Homepage")
 
 ### New in version 2.0:
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,62 +1,23 @@
-# Poppr version 2.8.3
+# Poppr version 2.8.4
 
-This is an attempt at fixing a LaTeX issue with a straddling link [0]
+This is a fix for a warning on CRAN:
 
-[0]: https://hypatia.math.ethz.ch/pipermail/r-package-devel/2019q2/004093.html
+On Wed, Feb 12, 2020 at 6:20 AM Kurt Hornik <Kurt.Hornik@r-project.org> wrote:
+Dear maintainer,
 
+Please see the problems shown on
+<https://cran.r-project.org/web/checks/check_results_poppr.html>.
 
-Thank you for implementing the extra checks for poppr. I really
-appreciate the hard work that goes into maintenance of CRAN. Because
-of the extra checks, I was able to find old code that was poorly
-written and subsequently was fixed.
+Please correct before 2020-02-26 to safely retain your package on CRAN.
 
-This resubmission addresses the following concerns:
-
-> If there are references describing the methods in your package, please
-> add these in the Description field of your DESCRIPTION file in the form
-> authors (year) doi:...
-> authors (year) arXiv:...
-> authors (year, ISBN:...)
-> with no space after 'doi:', 'arXiv:' and angle brackets for auto-linking.
-
-Done.
-
-> Please do not modify the global environment (e.g. by using <<-) in your
-> functions.
-
-Done. There is currently one function that still contains this, but it is
-properly scoped and does not modify the global environment.
-
-> Please always reset the user's options, working directory, ... in your
-> examples (e.g. man/getfile.Rd).
-
-Done.
-
-> Please ensure that your functions do not write by default or in your
-> examples/vignettes/tests in the user's home filespace. That is not allow
-> by CRAN policies. Please only write/save files if the user has specified
-> a directory. In your examples/vignettes/tests you can write to tempdir()
-
-Done.
-
-> Please replace \dontrun{} by \donttest{} or if(interactive()){} in your
-> Rd-file.
-
-I have not done this and am hesitant to do so as several of the examples that
-use \dontrun will have long-running code to show more in-depth examples or have
-code that will fail to show more realistic scenarios for user file interactions.
-Because of the long-running examples, I fear that wrapping them in \donttest
-would cause my package to fail because of their runtime.
-
-I do realize I could wrap these in if (interactive()), but then I would not be
-able to illustrate the longer-running examples on my documentation website 
-(i.e. https://grunwaldlab.github.io/poppr/reference/bitwise.dist.html#examples)
+Best,
+-k
 
 ## Test environments
 
-* local macOS install, R 3.6.0
-* local ubuntu 16.04 install, R 3.6.0
-* ubuntu 14.04 (on travis-ci), devel (2019-06-17 r76705) and R 3.6.0
+* local macOS install, R 3.6.2
+* local ubuntu 16.04 install, R 3.6.2
+* ubuntu 14.04 (on travis-ci), devel (2019-06-17 r76705) and R 3.6.2
 * windows R Under development (unstable) 
 
 ## R CMD check results

diff --git a/docs/404.html b/docs/404.html