fix for mpx sanitizer

matrix-profile-foundation · Mar 11, 2020 · c0b96ff · c0b96ff
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Showing 5 changed files with 17 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -42,7 +42,7 @@ URL: https://github.com/matrix-profile-foundation/tsmp
 BugReports: 
     https://github.com/matrix-profile-foundation/tsmp/issues
 Depends: 
-    R (>= 3.2)
+    R (>= 3.0)
 Imports:
     audio,
     checkmate,

diff --git a/README.Rmd b/README.Rmd
@@ -95,7 +95,7 @@ mbm_stamp_par <- round(median(microbenchmark::microbenchmark(tsmp(data, window_s
 ```{r bench_dataset, echo = FALSE, message=FALSE, warnings=FALSE}
 bench_data <- data.frame("Elapsed Time(s)" = c(mbm_stamp, mbm_stamp_par, mbm_stomp, mbm_stomp_par, mbm_scrimp, mbm_mpx, mbm_mpx_par), "Data Size" = data_size, "Window Size" = w, Threads = c(1, workers, 1, workers, 1, 1, workers), Lang = c("R", "R", "R", "R", "R", "Rcpp", "Rcpp"), row.names = c("`stamp`", "`stamp_par`", "`stomp`", "`stomp_par`", "`scrimp`", "`mpx`", "`mpx_par`"), check.names = FALSE)
 
-knitr::kable(bench_data[order(bench_data$`Elapsed Time(s)`),])
+knitr::kable(bench_data[order(bench_data$`Elapsed Time(s)`), ])
 ```
 
 ## Installation
@@ -165,6 +165,13 @@ Our next step unifying the Matrix Profile implementation in several programming
 
 Visit: [Matrix Profile Foundation](https://matrixprofile.org)
 
+## Package dependencies
+
+```{r dependency_plot, echo = FALSE, fig.width = 10, fig.height = 5, message = FALSE, warning = FALSE, fig.path = "man/figures/"}
+source("https://gist.githubusercontent.com/franzbischoff/3b83243dfdfa73e459935112f3f783e3/raw/239548243f984843b3a87d8cc82f99395a8ed26e/plot_dependencies.R")
+plot_dependencies()
+```
+
 ## Code of Conduct
 
 Please note that the 'tsmp' project is released with a

diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 README
 ================
 Francisco Bischoff
-\- 03 Mar 2020
+\- 06 Mar 2020
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
@@ -154,6 +154,10 @@ programming languages.
 
 Visit: [Matrix Profile Foundation](https://matrixprofile.org)
 
+## Package dependencies
+
+![](man/figures/dependency_plot-1.png)<!-- -->
+
 ## Code of Conduct
 
 Please note that the ‘tsmp’ project is released with a [Contributor Code

diff --git a/man/figures/dependency_plot-1.png b/man/figures/dependency_plot-1.png
diff --git a/src/mpx.cpp b/src/mpx.cpp
@@ -27,7 +27,7 @@ List mpx_rcpp(NumericVector a, uint16_t w, uint16_t minlag, bool idxs = false, b
     IntegerVector seq_diag = Range(minlag, profile_len - 1);
 
     NumericVector mmp(profile_len, -1.0);
-    IntegerVector mmpi(profile_len, R_NaN);
+    IntegerVector mmpi(profile_len, R_NaN); // TODO: SANITIZE?
 
     double *mp = &mmp[0];
     int *mpi = &mmpi[0];
@@ -152,7 +152,7 @@ List mpxab_rcpp(NumericVector a, NumericVector b, uint16_t w, bool idxs = false,
     ddg_a.push_front(0);
     NumericVector ddf_b = 0.5 * (b[Range(w, b_len - 1)] - b[Range(0, b_len - w - 1)]);
     ddf_b.push_front(0);
-    NumericVector ddg_b = (b[Range(w, a_len - 1)] - mmu_b[Range(1, profile_len_b - 1)]) + (b[Range(0, b_len - w - 1)] - mmu_b[Range(0, b_len - w - 1)]);
+    NumericVector ddg_b = (b[Range(w, b_len - 1)] - mmu_b[Range(1, profile_len_b - 1)]) + (b[Range(0, b_len - w - 1)] - mmu_b[Range(0, b_len - w - 1)]);
     ddg_b.push_front(0);
 
     double *df_a = &ddf_a[0];
@@ -523,7 +523,7 @@ List mpxab_rcpp_parallel(NumericVector a, NumericVector b, uint16_t w, bool idxs
     dg_a.push_front(0);
     NumericVector df_b = 0.5 * (b[Range(w, b_len - 1)] - b[Range(0, b_len - w - 1)]);
     df_b.push_front(0);
-    NumericVector dg_b = (b[Range(w, a_len - 1)] - mu_b[Range(1, profile_len_b - 1)]) + (b[Range(0, b_len - w - 1)] - mu_b[Range(0, b_len - w - 1)]);
+    NumericVector dg_b = (b[Range(w, b_len - 1)] - mu_b[Range(1, profile_len_b - 1)]) + (b[Range(0, b_len - w - 1)] - mu_b[Range(0, b_len - w - 1)]);
     dg_b.push_front(0);
 
     NumericVector ww_a = (a[Range(0, w - 1)] - mu_a[0]);