Patch 1.0.1 (#48)

* Code clean-up and safety (#46) * code safety * remove dependence on qrng * some cleanup * avoid lower > upper by reversing the grid at the right places * ensure non-NaN bandwidth * unused variable * add randtoolbox to Imports * Prepare patch (#47) * code safety * remove dependence on qrng * some cleanup * avoid lower > upper by reversing the grid at the right places * ensure non-NaN bandwidth * unused variable * add randtoolbox to Imports * update NEWS and DESCRIPTION * update API docs * update CRAN comments
tnagler · Nov 15, 2019 · 3a56938 · 3a56938
1 parent 5eaf81f
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@
 docs
 ^cran-comments\.md$
 ^revdep$
+^.vscode$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: kde1d
 Type: Package
 Title: Univariate Kernel Density Estimation
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
         person("Thomas", "Nagler",, "mail@tnagler.com", role = c("aut", "cre")),
         person("Thibault", "Vatter",, "thibault.vatter@gmail.com", role = c("aut"))
@@ -22,7 +22,7 @@ LinkingTo:
 Imports:
     graphics,
     Rcpp, 
-    qrng,
+    randtoolbox,
     stats,
     utils
 RoxygenNote: 7.0.0

diff --git a/NAMESPACE b/NAMESPACE
@@ -14,7 +14,7 @@ export(rkde1d)
 importFrom(Rcpp,sourceCpp)
 importFrom(graphics,lines)
 importFrom(graphics,plot)
-importFrom(qrng,ghalton)
+importFrom(randtoolbox,sobol)
 importFrom(stats,logLik)
 importFrom(stats,na.omit)
 importFrom(stats,qnorm)

diff --git a/NEWS.md b/NEWS.md
@@ -1,13 +1,30 @@
+# kde1d 1.0.1
+
+DEPENDENCIES
+
+  * Removed dependence on `qrng` (#46).
+
+BUG FIXES
+
+  * Fixed undefined behavior with potential to cause memory issues (#46).
+
+  * Prevent rare `bw_ == NaN` cases (#46).
+
+  * Fixed compiler warnings due to unused or uninitialized variables (#46).
+
+
 # kde1d 1.0.0
 
+DEPENDENCIES
+
+  * removed dependency on `cctools`.
+
 NEW FEATURES
 
   * optimal plug-in bandwidth selection for all polynomial degrees (#38).
 
   * avoid randomness through simplified, deterministic jittering, see 
-  `equi_jitter()` (#40).
-
-  * removed dependency `cctools`.
+    `equi_jitter()` (#40).
 
   * headers in `inst/include` can be used as standalone C++ library with 
     convenience wrappers for R (#41).

diff --git a/R/kde1d-methods.R b/R/kde1d-methods.R
@@ -88,18 +88,18 @@ qkde1d <- function(p, obj) {
 #' @param n integer; number of observations.
 #' @param quasi logical; the default (`FALSE`) returns pseudo-random
 #' numbers, use `TRUE` for quasi-random numbers (generalized Halton, see
-#' [`qrng::ghalton()`]).
+#' [`randtoolbox::sobol()`]).
 #'
 #' @rdname dkde1d
-#' @importFrom qrng ghalton
+#' @importFrom randtoolbox sobol
 #' @importFrom stats runif
 #' @export
 rkde1d <- function(n, obj, quasi = FALSE) {
   # simulate (psuedo/quasi) uniform random variables
   if (!quasi) {
     U <- runif(n)
   } else {
-    U <- ghalton(n, d = 1)
+    U <- randtoolbox::sobol(n, scrambling = 1, seed = sample.int(1e10, 1))
   }
   # simulated data from KDE is the quantile transform of U
   qkde1d(U, obj)

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,4 +1,9 @@
+Patch to fix undefined behavior/heap overflow failures detected by the 
+sanitizers: https://cran.r-project.org/web/checks/check_results_kde1d.html
+
 ## Test environments
+* ubuntu 18.04 with valgrind (release)
+* ubuntu 18.04 with clang ASAN/UBSAN on rocker (devel)
 * ubuntu 14.04 on travis-ci (release, devel, oldrel)
 * win-builder (devel, release)
 

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