Merge branch 'issue-25':

These commits fix issues related to the use of a new, default, RNG method
in R-devel (to be 3.6.x), which was causing failures in unit tests and
differences in outputs of examples/vignettes etc. This is fixed temporarily
here. A broader fix might be to require R >= 3.6.0 when it is released.
Closes #25

.travis.yml

@@ -1,9 +1,10 @@
 language: r
 cache: packages
 
-r:
-  - release
-  - devel
+matrix:
+  include:
+  - r: devel
+  - r: release
 
 sudo: false
 
@@ -22,7 +23,7 @@ r_binary_packages:
   - htmltools
 
 r_github_packages:
-  - jimhester/covr
+  - r-lib/covr
 
 after_success:
   - Rscript -e 'covr::codecov()'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: permute
 Title: Functions for Generating Restricted Permutations of Data
-Version: 0.9-4
-Date: 2016-08-08
+Version: 0.9-5
+Date: 2019-03-10
 Authors@R: c(person(given = "Gavin L.", family = "Simpson",
                     email = "[email protected]",
                     role = c("aut", "cph", "cre"),

man/nobs.Rd

@@ -42,6 +42,8 @@
 }
 \author{Gavin Simpson}
 \examples{
+\dontshow{suppressWarnings(RNGversion("3.5.0"))}
+set.seed(1)
 ## numeric vector
 len <- sample(1:10, 1)
 v <- as.numeric(sample(1:100, len))

man/shuffle-utils.Rd

@@ -75,6 +75,7 @@ shuffleStrata(strata, type, mirror = FALSE, start = NULL, flip = NULL,
   wrapper to these functions.}
 
 \examples{
+\dontshow{suppressWarnings(RNGversion("3.5.0"))}
 set.seed(3)
 
 ## draw 1 value at random from the set 1:10

man/shuffle.Rd

@@ -63,6 +63,7 @@ permute(i, n, control)
   permutation scheme described by \code{\link{how}}.}
 
 \examples{
+\dontshow{suppressWarnings(RNGversion("3.5.0"))}
 set.seed(1234)
 
 ## unrestricted permutations

man/shuffleSet.Rd

@@ -111,6 +111,8 @@ shuffleSet(n, nset, control = how(), check = TRUE, quietly = FALSE)
   \code{\link{how}} for setting up permutation designs.
 }
 \examples{
+\dontshow{suppressWarnings(RNGversion("3.5.0"))}
+set.seed(1)
 ## simple random permutations, 5 permutations in set
 shuffleSet(n = 10, nset = 5)
 

tests/Examples/permute-Ex.Rout.save

@@ -1,6 +1,6 @@
 
-R version 3.3.0 Patched (2016-05-12 r70603) -- "Supposedly Educational"
-Copyright (C) 2016 The R Foundation for Statistical Computing
+R version 3.5.3 beta (2019-02-28 r76174) -- "Great Truth"
+Copyright (C) 2019 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -23,6 +23,7 @@ Type 'q()' to quit R.
 > library('permute')
 > 
 > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
+> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
 > cleanEx()
 > nameEx("allPerms")
 > ### * allPerms
@@ -643,6 +644,10 @@ Permutation details:
 > 
 > ### ** Examples
 > 
+> ## Don't show: 
+> suppressWarnings(RNGversion("3.5.0"))
+> ## End(Don't show)
+> set.seed(1)
 > ## numeric vector
 > len <- sample(1:10, 1)
 > v <- as.numeric(sample(1:100, len))
@@ -768,6 +773,9 @@ Permutation details:
 > 
 > ### ** Examples
 > 
+> ## Don't show: 
+> suppressWarnings(RNGversion("3.5.0"))
+> ## End(Don't show)
 > set.seed(3)
 > 
 > ## draw 1 value at random from the set 1:10
@@ -809,6 +817,9 @@ Permutation details:
 > 
 > ### ** Examples
 > 
+> ## Don't show: 
+> suppressWarnings(RNGversion("3.5.0"))
+> ## End(Don't show)
 > set.seed(1234)
 > 
 > ## unrestricted permutations
@@ -1001,6 +1012,10 @@ mean in group Group 1 mean in group Group 2
 > 
 > ### ** Examples
 > 
+> ## Don't show: 
+> suppressWarnings(RNGversion("3.5.0"))
+> ## End(Don't show)
+> set.seed(1)
 > ## simple random permutations, 5 permutations in set
 > shuffleSet(n = 10, nset = 5)
 No. of Permutations: 5
@@ -1155,9 +1170,10 @@ p4 5 1 2 3 4 10  6  7  8  9 15 11 12 13 14 20 16 17 18 19
 > 
 > ### * <FOOTER>
 > ###
+> cleanEx()
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  4.459 0.081 4.542 0 0 
+Time elapsed:  3.78 0.067 3.873 0 0 
 > grDevices::dev.off()
 null device 
           1 

tests/testthat/test-shuffle.R

@@ -30,6 +30,8 @@ test_that("shuffle() works for non-contigous blocks of samples", {
     CTRL <- how(plots = Plots(strata = Plot, type = "free"),
                 within = Within(type = "none"))
     n <- 20
+    ## FIXME Temporary fix related to #25
+    suppressWarnings(RNGversion("3.5.0"))
     set.seed(2)
     result <- shuffle(n, CTRL)
     out1 <- as.integer(c( 3, 2, 1, 4,

vignettes/permutations.Rnw

@@ -49,6 +49,7 @@
 <<preliminary,results=hide,echo=false>>=
 options("prompt" = "R> ", "continue" = "+  ")
 options(useFancyQuotes="UTF-8")
+suppressWarnings(RNGversion("3.5.0"))
 @
 \section{Introduction}
 In classical frequentist statistics, the significance of a relationship or model is determined by reference to a null distribution for the test statistic. This distribution is derived mathematically and the probability of achieving a test statistic as large or larger if the null hypothesis were true is looked-up from this null distribution. In deriving this probability, some assumptions about the data or the errors are made. If these assumptions are violated, then the validity of the derived $p$-value may be questioned.