fix calls to all.equal/expect_equal for R 4.1.x (#234) (#235)

* fix calls to all.equal/expect_equal * bump version + update NEWS * update docs * avoid CRAN note
vinecopulib · Jun 8, 2021 · c3bd17e · c3bd17e
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diff --git a/.gitignore b/.gitignore
@@ -38,3 +38,4 @@ vignettes/*.pdf
 config.log
 config.status
 revdep/
+.vscode/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rvinecopulib
 Type: Package
 Title: High Performance Algorithms for Vine Copula Modeling
-Version: 0.5.5.1.0
+Version: 0.5.5.1.1
 Authors@R: c(
         person("Thomas", "Nagler",, "[email protected]", role = c("aut", "cre")),
         person("Thibault", "Vatter",, "[email protected]", role = c("aut"))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# rvinecopulib 0.5.5.1.1 (December 15, 2020)
+
+Maintenance release following the changes to `all.equal()` in R 4.1.x.
+
+
 # rvinecopulib 0.5.5.1.0 (November 24, 2020)
 
 Release following the updates of vinecopulib to 0.5.5, see 

diff --git a/R/bicop_methods.R b/R/bicop_methods.R
@@ -215,7 +215,8 @@ ktau_to_par <- function(family, tau) {
 #' fit <- bicop(u, family = "par", keep_data = TRUE)
 #'
 #' # Predictions
-#' all.equal(predict(fit, u, "hfunc1"), fitted(fit, "hfunc1"))
+#' all.equal(predict(fit, u, "hfunc1"), fitted(fit, "hfunc1"),
+#'           check.environment = FALSE)
 #' @rdname predict_bicop
 #' @export
 predict.bicop_dist <- function(object, newdata, what = "pdf", ...) {

diff --git a/R/getters.R b/R/getters.R
@@ -55,12 +55,13 @@
 #'
 #' # get the structure
 #' get_structure(vc)
-#' all.equal(get_matrix(vc), mat, check.attributes = FALSE)
+#' all(get_matrix(vc) == mat)
 #'
 #' # get pair-copulas
 #' get_pair_copula(vc, 1, 1)
 #' get_all_pair_copulas(vc)
-#' all.equal(get_all_pair_copulas(vc), pcs, check.attributes = FALSE)
+#' all.equal(get_all_pair_copulas(vc), pcs,
+#'           check.attributes = FALSE, check.environment = FALSE)
 #' @return
 #' The structure matrix, or pair-copulas, their parameters, Kendall's taus,
 #' or families.

diff --git a/R/tools.R b/R/tools.R
@@ -385,3 +385,5 @@ print_fit_info <- function(x) {
 get_seeds <- function() {
   as.numeric(sprintf("%20.0f", runif(20, 1e6, 1e7)))
 }
+
+
diff --git a/R/vine_methods.R b/R/vine_methods.R
@@ -188,7 +188,7 @@ get_vine_dist_margin_summary <- function(vd) {
 #' @examples
 #' x <- sapply(1:5, function(i) rnorm(50))
 #' fit <- vine(x, copula_controls = list(family_set = "par"), keep_data = TRUE)
-#' all.equal(predict(fit, x), fitted(fit))
+#' all.equal(predict(fit, x), fitted(fit), check.environment = FALSE)
 predict.vine <- function(object, newdata, what = "pdf", n_mc = 10^4,
                          cores = 1, ...) {
   stopifnot(what %in% c("pdf", "cdf"))

diff --git a/R/vinecop_methods.R b/R/vinecop_methods.R
@@ -192,7 +192,7 @@ summary.vinecop_dist <- function(object, ...) {
 #' @examples
 #' u <- sapply(1:5, function(i) runif(50))
 #' fit <- vinecop(u, family = "par", keep_data = TRUE)
-#' all.equal(predict(fit, u), fitted(fit))
+#' all.equal(predict(fit, u), fitted(fit), check.environment = FALSE)
 predict.vinecop <- function(object, newdata, what = "pdf", n_mc = 10^4,
                             cores = 1, ...) {
   assert_that(

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,13 +1,12 @@
-Fixes "uninitialised value" detected by valgrind 
-(https://cran.r-project.org/web/checks/check_results_rvinecopulib.html).
+Maintenance release following the changes to `all.equal()` in R 4.1.x.
 
 ## Test environments
 
 * CRAN win builder (devel)
 * Windows Server 2019 (release)
 * macOS (release)
 * ubuntu 16.04 (release, oldrel, devel)
-* ubuntu 20.04 with valgrind (release)
+* ubuntu 20.04 (release)
 
 ## R CMD check results
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 2.7.3
 pkgdown: 1.5.1
 pkgdown_sha: ~
 articles: []
-last_built: 2020-11-23T18:30Z
+last_built: 2020-12-15T08:12Z
 
diff --git a/docs/reference/as_rvine_structure.html b/docs/reference/as_rvine_structure.html
diff --git a/docs/reference/bicop.html b/docs/reference/bicop.html
diff --git a/docs/reference/bicop_dist.html b/docs/reference/bicop_dist.html
diff --git a/docs/reference/bicop_methods.html b/docs/reference/bicop_methods.html
diff --git a/docs/reference/getters.html b/docs/reference/getters.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/mBICV.html b/docs/reference/mBICV.html
diff --git a/docs/reference/pairs_copula_data.html b/docs/reference/pairs_copula_data.html
diff --git a/docs/reference/par_to_ktau.html b/docs/reference/par_to_ktau.html
diff --git a/docs/reference/plot.bicop_dist.html b/docs/reference/plot.bicop_dist.html
diff --git a/docs/reference/plot.rvine_structure.html b/docs/reference/plot.rvine_structure.html
diff --git a/docs/reference/plot.vinecop_dist.html b/docs/reference/plot.vinecop_dist.html
diff --git a/docs/reference/predict_bicop.html b/docs/reference/predict_bicop.html
diff --git a/docs/reference/predict_vine.html b/docs/reference/predict_vine.html
Original file line number	Diff line number	Diff line change
Expand Up		@@ -385,3 +385,5 @@ print_fit_info <- function(x) {
		get_seeds <- function() {
		as.numeric(sprintf("%20.0f", runif(20, 1e6, 1e7)))
		}