resoved issue #47

markvanderloo · Aug 12, 2016 · b904e31 · b904e31
1 parent 22a953a
commit b904e31
Show file tree

Hide file tree

Showing 9 changed files with 20 additions and 9 deletions.
diff --git a/build.bash b/build.bash
diff --git a/compile.sh b/compile.sh
diff --git a/document.bash b/document.bash
diff --git a/drat.sh b/drat.sh
diff --git a/pkg/R/stringdist.R b/pkg/R/stringdist.R
@@ -254,6 +254,8 @@ stringdistmatrix <- function(a, b
         , method=method
         , useBytes=useBytes
         , weight=weight
+        , q=q
+        , p=p
         , useNames=useNames
         , nthread=nthread)
     )
@@ -341,11 +343,13 @@ do_dist <- function(a, b, method, weight, maxDist=Inf, q, p, useBytes=FALSE, nth
 
 # more efficient function that returns a square distance matrix as a 'stats::dist' object.
 lower_tri <- function(a
-   , method=c("osa","lv","dl","hamming","lcs","qgram","cosine","jaccard","jw","soundex")
-   , useBytes = FALSE
-   , weight=c(d=1,i=1,s=1,t=1), q=1, p=0
-   , useNames=FALSE
-   , nthread = getOption("sd_num_thread")
+  , method=c("osa","lv","dl","hamming","lcs","qgram","cosine","jaccard","jw","soundex")
+  , useBytes = FALSE
+  , weight=c(d=1,i=1,s=1,t=1)
+  , q=1
+  , p=0
+  , useNames=FALSE
+  , nthread = getOption("sd_num_thread")
 ){
   methnr <- METHODS[method]
   if (is.na(method)){

diff --git a/pkg/src/Rstringdist.c b/pkg/src/Rstringdist.c
@@ -308,7 +308,7 @@ SEXP R_lower_tri(SEXP a, SEXP method
       , n_threads = 1
       , col_max = n-1;
 
-    R_xlen_t p = 0
+    R_xlen_t pp = 0
       , k_start = 0
       , k_end = N;
 
@@ -317,9 +317,9 @@ SEXP R_lower_tri(SEXP a, SEXP method
       n_threads = omp_get_num_threads();
     #endif
       // some administration to parallelize the loop.
-      p = N / n_threads;
-      k_start = thread_id * p;
-      k_end   = (thread_id < n_threads - 1 ) ? k_start + p : N;
+      pp = N / n_threads;
+      k_start = thread_id * pp;
+      k_end   = (thread_id < n_threads - 1 ) ? k_start + pp : N;
       j = get_j(k_start,n);
       i = k_start + j * (j - 2*n + 3)/2;
     for ( R_xlen_t k=k_start; k < k_end; k++ ){

diff --git a/pkg/src/qgram.c b/pkg/src/qgram.c
@@ -149,6 +149,7 @@ typedef enum { uInt, Double, Qtree } type;
 static void *alloc(type t){
   Shelf *shelf = &wall[get_shelf_num()];
 
+
   if ( 
     shelf->nboxes == 0L &&
     !add_box(MIN_BOX_SIZE)

diff --git a/pkg/tests/testthat/testStringdist.R b/pkg/tests/testthat/testStringdist.R
@@ -486,6 +486,12 @@ test_that("stringdistmatrix with single argument",{
     , c("k1","k2")
   )
 
+  # bug reported by Max Fritsche; issue #47
+  x <- c("aap","apen")
+  expect_equivalent(
+    as.matrix(stringdistmatrix(x,method="jw",p=0.1))
+    , stringdistmatrix(x,x,method="jw",p=0.1)
+  )
 
 })
 

diff --git a/ubsan.sh b/ubsan.sh