From cc8f5485da933d3e417688d3987af85b21cfbcba Mon Sep 17 00:00:00 2001 From: Thomas Nagler Date: Mon, 26 Oct 2020 14:11:42 +0100 Subject: [PATCH] Patch valgrind (#51) * prevent false positive on valgrind * update CRAN comments * update docs --- DESCRIPTION | 2 +- NEWS.md | 7 +++++++ cran-comments.md | 6 +++--- docs/404.html | 4 ++-- docs/LICENSE-text.html | 4 ++-- docs/authors.html | 4 ++-- docs/index.html | 22 +++++++++++----------- docs/news/index.html | 28 +++++++++++++++++++--------- docs/pkgdown.yml | 4 ++-- docs/reference/dkde1d.html | 8 ++++---- docs/reference/equi_jitter.html | 4 ++-- docs/reference/index.html | 4 ++-- docs/reference/kde1d-package.html | 4 ++-- docs/reference/kde1d.html | 16 ++++++++-------- docs/reference/plot.kde1d.html | 12 ++++++------ inst/include/kde1d/kdefft.hpp | 2 +- inst/include/kde1d/stats.hpp | 8 +++++--- inst/include/kde1d/tools.hpp | 8 ++------ 18 files changed, 81 insertions(+), 66 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b2a06a3..8fd20d2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: kde1d Type: Package Title: Univariate Kernel Density Estimation -Version: 1.0.1 +Version: 1.0.2 Authors@R: c( person("Thomas", "Nagler",, "mail@tnagler.com", role = c("aut", "cre")), person("Thibault", "Vatter",, "thibault.vatter@gmail.com", role = c("aut")) diff --git a/NEWS.md b/NEWS.md index 99a3eb1..c4fbd24 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# kde1d 1.0.2 + +BUG FIXES + + * Prevent false positive on valgrind. + + # kde1d 1.0.1 DEPENDENCIES diff --git a/cran-comments.md b/cran-comments.md index 99f62be..3ba6bae 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,8 +1,8 @@ -Patch to fix undefined behavior/heap overflow failures detected by the -sanitizers: https://cran.r-project.org/web/checks/check_results_kde1d.html +Patch to prevent possible false positive on valgrind (only on some platforms): https://cran.r-project.org/web/checks/check_results_kde1d.html ## Test environments -* ubuntu 18.04 with valgrind (release) +* ubuntu 18.04 with gcc7 and valgrind (release) +* ubuntu 18.04 clang 9 and 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) diff --git a/docs/404.html b/docs/404.html index ee5a16c..e1a60ba 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -123,7 +123,7 @@

Page not found (404)

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.4.1.9000.

diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index fecd3f4..4ec016a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -67,7 +67,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -125,7 +125,7 @@

License

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.4.1.9000.

diff --git a/docs/authors.html b/docs/authors.html index b076654..2d6d5ea 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -67,7 +67,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -132,7 +132,7 @@

Authors

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.4.1.9000.

diff --git a/docs/index.html b/docs/index.html index 7f4bde4..a7d54fb 100644 --- a/docs/index.html +++ b/docs/index.html @@ -36,7 +36,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -99,7 +99,7 @@

  • the latest development version:
    • +devtools::install_github("tnagler/kde1d@dev")

    @@ -108,8 +108,8 @@

    Unbounded data
    x <- rnorm(100)                    # simulate data
-fit <- kde1d(x)                    # estimate density
-dkde1d(0, fit)                     # evaluate density estimate
+fit <- kde1d(x)                    # estimate density
+dkde1d(0, fit)                     # evaluate density estimate
 summary(fit)                       # information about the estimate
 plot(fit)                          # plot the density estimate
 curve(dnorm(x), add = TRUE,        # add true density
@@ -119,8 +119,8 @@ 
    
 
    
 Bounded data, log-linear
    
 
    x <- rgamma(100, shape = 1)        # simulate data
-fit <- kde1d(x, xmin = 0, deg = 1) # estimate density
-dkde1d(seq(0, 5, by = 1), fit)     # evaluate density estimate
+fit <- kde1d(x, xmin = 0, deg = 1) # estimate density
+dkde1d(seq(0, 5, by = 1), fit)     # evaluate density estimate
 summary(fit)                       # information about the estimate
 plot(fit)                          # plot the density estimate
 curve(dgamma(x, shape = 1),        # add true density
@@ -132,8 +132,8 @@ 
    
 Discrete data
    
 
    x <- rbinom(100, size = 5, prob = 0.5)  # simulate data
 x <- ordered(x, levels = 0:5)           # declare as ordered
-fit <- kde1d(x)                         # estimate density
-dkde1d(sort(unique(x)), fit)            # evaluate density estimate
+fit <- kde1d(x)                         # estimate density
+dkde1d(sort(unique(x)), fit)            # evaluate density estimate
 summary(fit)                            # information about the estimate
 plot(fit)                               # plot the density estimate
 points(ordered(0:5, 0:5),               # add true density
@@ -144,9 +144,9 @@ 
    
 Weighted estimate
    
 
    x <- rnorm(100)                         # simulate data
 weights <- rexp(100)                    # weights as in Bayesian bootstrap
-fit <- kde1d(x, weights = weights)      # weighted fit
+fit <- kde1d(x, weights = weights)      # weighted fit
 plot(fit)                               # compare with unweighted fit
-lines(kde1d(x), col = 2)
    
+lines(kde1d(x), col = 2)
    @@ -207,7 +207,7 @@

    Dev status

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.4.1.9000.

    diff --git a/docs/news/index.html b/docs/news/index.html index f2969b6..d4bf3f6 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -67,7 +67,7 @@ kde1d - 1.0.1 + 1.0.2
    @@ -110,13 +110,22 @@

    Changelog

    Source: NEWS.md +
    +

    +kde1d 1.0.2 Unreleased +

    +

    BUG FIXES

    +
      +
    • Prevent false positive on valgrind.
      • +
    +

    -kde1d 1.0.1 Unreleased +kde1d 1.0.1 2019-11-15

    DEPENDENCIES

      -
    • Removed dependence on qrng package because it was to heavy (qrng <- copula <- gsl, #46).
      • +
    • Removed dependence on qrng (#46).

    BUG FIXES

      @@ -136,10 +145,10 @@

      NEW FEATURES

      • optimal plug-in bandwidth selection for all polynomial degrees (#38).

        • -

      • avoid randomness through simplified, deterministic jittering, see equi_jitter() (#40).

        • +

      • avoid randomness through simplified, deterministic jittering, see equi_jitter() (#40).

      • headers in inst/include can be used as standalone C++ library with convenience wrappers for R (#41).

        • -

      • (several times) faster pkde1d(), qkde1d(), and rkde1d() due to a more clever algorithm for numerical integration (#42).

        • -

      • faster kde1d() thanks to the Fast Fourier Transform (#43).

        • +

      • (several times) faster pkde1d(), qkde1d(), and rkde1d() due to a more clever algorithm for numerical integration (#42).

        • +

      • faster kde1d() thanks to the Fast Fourier Transform (#43).

      BUG FIXES

        @@ -152,7 +161,7 @@

        NEW FEATURE

        BUG FIX

          @@ -170,7 +179,7 @@

        BUG FIXES

          -

        • consistent behavior when dkde1d() and pkde1d() are called with non-ordered input although data are discrete (#19).

          • +

        • consistent behavior when dkde1d() and pkde1d() are called with non-ordered input although data are discrete (#19).

        • fixed bug in computation of kernel density estimates (#20).

        • adapt minimum bw allowed for discrete data to truncated Gaussian kernel (#20).

        @@ -203,6 +212,7 @@

        Contents

        -

        Site built with pkgdown 1.4.1.

        +

        Site built with pkgdown 1.4.1.9000.

        diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 8999c6f..2079fee 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.3.1 -pkgdown: 1.4.1 -pkgdown_sha: ~ +pkgdown: 1.4.1.9000 +pkgdown_sha: 61c3999702966dd75267b98ce905df22521ebd11 articles: [] diff --git a/docs/reference/dkde1d.html b/docs/reference/dkde1d.html index 9a347b3..b30442a 100644 --- a/docs/reference/dkde1d.html +++ b/docs/reference/dkde1d.html @@ -70,7 +70,7 @@ kde1d - 1.0.1 + 1.0.2

    @@ -172,12 +172,12 @@

    Details is the length of the numerical argument for the other functions.

    See also

    -

    kde1d()

    +

    kde1d()

    Examples

    set.seed(0) # for reproducibility
 x <- rnorm(100) # simulate some data
-fit <- kde1d(x) # estimate density
+fit <- kde1d(x) # estimate density
 dkde1d(0, fit) # evaluate density estimate (close to dnorm(0))
 pkde1d(0, fit) # evaluate corresponding cdf (close to pnorm(0))
    #> [1] 0.5008513
    qkde1d(0.5, fit) # quantile function (close to qnorm(0))
    #> [1] -0.001893213
    hist(rkde1d(100, fit)) # simulate
    @@ -201,7 +201,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.4.1.9000.

    diff --git a/docs/reference/equi_jitter.html b/docs/reference/equi_jitter.html index 908695d..f21382a 100644 --- a/docs/reference/equi_jitter.html +++ b/docs/reference/equi_jitter.html @@ -70,7 +70,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -177,7 +177,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.4.1.9000.

    diff --git a/docs/reference/index.html b/docs/reference/index.html index 066f71f..295dcaf 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -174,7 +174,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.4.1.9000.

    diff --git a/docs/reference/kde1d-package.html b/docs/reference/kde1d-package.html index 6f12b05..3df9029 100644 --- a/docs/reference/kde1d-package.html +++ b/docs/reference/kde1d-package.html @@ -72,7 +72,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -158,7 +158,7 @@

    Contents

    -

    Site built with pkgdown 1.4.1.

    +

    Site built with pkgdown 1.4.1.9000.

    diff --git a/docs/reference/kde1d.html b/docs/reference/kde1d.html index f0ec6d4..4a2ac90 100644 --- a/docs/reference/kde1d.html +++ b/docs/reference/kde1d.html @@ -70,7 +70,7 @@ kde1d - 1.0.1 + 1.0.2 @@ -179,7 +179,7 @@

    Details log-transform is used if there is only one boundary (see, Geenens and Wang, 2018); a probit transform is used if there are two (see, Geenens, 2014).

    Discrete variables are handled via jittering (see, Nagler, 2018a, 2018b). -A specific form of deterministic jittering is used, see equi_jitter().

    +A specific form of deterministic jittering is used, see equi_jitter().

    References

    Geenens, G. (2014). Probit transformation for kernel density @@ -201,15 +201,15 @@

    R Statistical Society, Series B, 53, 683–690.

    See also

    -

    dkde1d(), pkde1d(), qkde1d(), rkde1d(), -plot.kde1d(), lines.kde1d()

    +

    dkde1d(), pkde1d(), qkde1d(), rkde1d(), +plot.kde1d(), lines.kde1d()

    Examples

    
 ## unbounded data
 x <- rnorm(500) # simulate data
 fit <- kde1d(x) # estimate density
-dkde1d(0, fit) # evaluate density estimate
+dkde1d(0, fit) # evaluate density estimate
 summary(fit) # information about the estimate
    #> kernel density estimate ('kde1d'), log-quadratic
 #> -----------------------------------------------------------------
 #> nobs = 500, bw = 0.71, loglik = -712.05, d.f. = 4.65
    plot(fit) # plot the density estimate
    curve(dnorm(x),
@@ -219,7 +219,7 @@ 
    Examp
 ## bounded data, log-linear
 x <- rgamma(500, shape = 1) # simulate data
 fit <- kde1d(x, xmin = 0, deg = 1) # estimate density
-dkde1d(seq(0, 5, by = 1), fit) # evaluate density estimate
+dkde1d(seq(0, 5, by = 1), fit) # evaluate density estimate
 summary(fit) # information about the estimate
    #> kernel density estimate ('kde1d'), log-linear with bounded support (xmin = 0)
 #> -----------------------------------------------------------------
 #> nobs = 500, bw = 0.3, loglik = -450.93, d.f. = 12.89
    plot(fit) # plot the density estimate
    curve(dgamma(x, shape = 1), # add true density
@@ -230,7 +230,7 @@ 
    Examp
 x <- rbinom(500, size = 5, prob = 0.5) # simulate data
 x <- ordered(x, levels = 0:5) # declare as ordered
 fit <- kde1d(x) # estimate density
-dkde1d(sort(unique(x)), fit) # evaluate density estimate
+dkde1d(sort(unique(x)), fit) # evaluate density estimate
 summary(fit) # information about the estimate
    #> (jittered) kernel density estimate ('kde1d'), log-quadratic
 #> -----------------------------------------------------------------
 #> nobs = 500, bw = 1.12, loglik = -789.98, d.f. = 10.08
    plot(fit) # plot the density estimate
    points(ordered(0:5, 0:5), # add true density
@@ -264,7 +264,7 @@ 
    Contents
    
 
    
 
 
    
-  
    Site built with pkgdown 1.4.1.
    
+  
    Site built with pkgdown 1.4.1.9000.
    
 
    
 
       
diff --git a/docs/reference/plot.kde1d.html b/docs/reference/plot.kde1d.html
index e79632b..f665fbc 100644
--- a/docs/reference/plot.kde1d.html
+++ b/docs/reference/plot.kde1d.html
@@ -69,7 +69,7 @@
       
       
         kde1d
-        1.0.1
+        1.0.2
       
     
 
@@ -138,20 +138,20 @@ 
    Arg
 
     
    See also
    
 
-    
    kde1d()
    
+    
    kde1d()
    
 
     
    Examples
    
     
    ## continuous data
 x <- rbeta(100, shape1 = 0.3, shape2 = 0.4) # simulate data
-fit <- kde1d(x) # unbounded estimate
+fit <- kde1d(x) # unbounded estimate
 plot(fit, ylim = c(0, 4)) # plot estimate
    curve(dbeta(x, 0.3, 0.4), # add true density
   col = "red", add = TRUE
-)
    fit_bounded <- kde1d(x, xmin = 0, xmax = 1) # bounded estimate
+)
    fit_bounded <- kde1d(x, xmin = 0, xmax = 1) # bounded estimate
 lines(fit_bounded, col = "green")
    
 ## discrete data
 x <- rpois(100, 3) # simulate data
 x <- ordered(x, levels = 0:20) # declare variable as ordered
-fit <- kde1d(x) # estimate density
+fit <- kde1d(x) # estimate density
 plot(fit, ylim = c(0, 0.25)) # plot density estimate
    points(ordered(0:20, 0:20), # add true density values
   dpois(0:20, 3),
   col = "red"
@@ -175,7 +175,7 @@ 
    Contents
    
 
    
 
 
    
-  
    Site built with pkgdown 1.4.1.
    
+  
    Site built with pkgdown 1.4.1.9000.
    
 
    
 
       
diff --git a/inst/include/kde1d/kdefft.hpp b/inst/include/kde1d/kdefft.hpp
index 997d4ac..eca525c 100644
--- a/inst/include/kde1d/kdefft.hpp
+++ b/inst/include/kde1d/kdefft.hpp
@@ -27,10 +27,10 @@ class KdeFFT
 
 private:
   double bw_;
-  Eigen::VectorXd bin_counts_;
   double lower_;
   double upper_;
   static constexpr size_t num_bins_{ 400 };
+  Eigen::VectorXd bin_counts_;
 };
 
 //! @param x vector of observations.
diff --git a/inst/include/kde1d/stats.hpp b/inst/include/kde1d/stats.hpp
index 16dc113..c99dddd 100644
--- a/inst/include/kde1d/stats.hpp
+++ b/inst/include/kde1d/stats.hpp
@@ -161,7 +161,7 @@ equi_jitter(const Eigen::VectorXd& x)
     srt(i) = x(perm(i));
 
   // compute contingency table
-  Eigen::MatrixXd tab(n + 1, 2);
+  Eigen::MatrixXd tab(n, 2);
   size_t lev = 0;
   size_t cnt = 1;
   for (size_t k = 1; k < n; ++k) {
@@ -171,14 +171,16 @@ equi_jitter(const Eigen::VectorXd& x)
       cnt = 1;
     } else {
       cnt++;
-      if (k == n - 1)
+      if (k == n - 1) {
+        tab(lev, 0) = srt(k);
         tab(lev++, 1) = cnt;
+      }
     }
   }
   tab.conservativeResize(lev, 2);
 
   // add deterministic, conditionally uniorm noise
-  Eigen::VectorXd noise(n);
+  Eigen::VectorXd noise = Eigen::VectorXd::Zero(n);
   size_t i = 0;
   for (size_t k = 0; k < tab.rows(); ++k) {
     for (size_t cnt = 1; cnt <= tab(k, 1); ++cnt)
diff --git a/inst/include/kde1d/tools.hpp b/inst/include/kde1d/tools.hpp
index 00fd3a3..52bebd9 100644
--- a/inst/include/kde1d/tools.hpp
+++ b/inst/include/kde1d/tools.hpp
@@ -107,13 +107,9 @@ linbin(const Eigen::VectorXd& x,
        const Eigen::VectorXd& weights)
 {
   Eigen::VectorXd gcnts = Eigen::VectorXd::Zero(num_bins + 1);
-  double rem, lxi, delta;
+  double delta = (upper - lower) / num_bins;
+  double rem, lxi;
   size_t li;
-
-  if (upper <= lower)
-    throw std::runtime_error("upper != lower");
-
-  delta = (upper - lower) / num_bins;
   for (size_t i = 0; i < x.size(); ++i) {
     lxi = (x(i) - lower) / delta;
     li = static_cast(lxi);