CRAN fix

Author: markvanderloo

compile.sh

@@ -2,7 +2,7 @@
 
 cd pkg/src
 rm --verbose *.o *.so
-gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -fopenmp -O2 -Wall -pipe -g -c -Wstrict-prototypes *.c 
+gcc-10 -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -fopenmp -O4 -Wall -pipe -g -c -Wstrict-prototypes -Wformat *.c 
 #gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O2 -Wall -pipe -g -c *.c 
 gcc -std=gnu99 -shared -o stringdist.so *.o -L/usr/lib/R/lib -lR
 cd ../../

pkg/DESCRIPTION

@@ -23,7 +23,7 @@ Description: Implements an approximate string matching version of R's native
  vectors representing generic sequences. This package is built for speed and
  runs in parallel by using 'openMP'. An API for C or C++ is exposed as well.
  Reference: MPJ van der Loo (2014) <doi:10.32614/RJ-2014-011>.
-Version: 0.9.10
+Version: 0.9.12
 Depends:
  R (>= 2.15.3)
 URL: https://github.com/markvanderloo/stringdist
@@ -32,4 +32,4 @@ Suggests:
  tinytest
 Imports: parallel
 Encoding: UTF-8
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3

pkg/NEWS

@@ -1,3 +1,10 @@
+version 0.9.12
+- apparently R_xlen_t is long long int on CLANG/Windows and long int on gcc-13/debian
+
+version 0.9.11
+- Fixed a warning in gcc-13: changed specifier from %d to %ld.
+ (Thanks to Kurt Hornik for the head's up)
+
 version 0.9.10
 - Fixed another warning generated by new C compiler that I overlooked.
  (Thanks to the CRAN team for the head's up)

pkg/README.md

@@ -54,5 +54,5 @@ Examples of packages that link to `stringdist` can be found
 #### Resources
 
 * A [paper](https://journal.r-project.org/archive/2014-1/loo.pdf) on stringdist has been published in the R-journal
-* [Slides](https://www.markvanderloo.eu/files/statistics/stringdist_useR2014.pdf) of a talk given at te _useR!2014_ conference.
+* [Slides](https://www.markvanderloo.eu/files/share/loo2014approximate.pdf) of a talk given at te _useR!2014_ conference.
 

pkg/src/Rstringdist.c

@@ -64,7 +64,7 @@ SEXP R_stringdist(SEXP a, SEXP b, SEXP method
 
  // output vector
  SEXP yy;
- PROTECT(yy = allocVector(REALSXP, nt));
+ yy = PROTECT(allocVector(REALSXP, nt));
  double *y = REAL(yy);
 
  #ifdef _OPENMP 
@@ -149,7 +149,7 @@ SEXP R_amatch(SEXP x, SEXP table, SEXP method
 
  // output vector
  SEXP yy;
- PROTECT(yy = allocVector(INTSXP, nx));
+ yy = PROTECT(allocVector(INTSXP, nx));
  int *y = INTEGER(yy);
 
  #ifdef _OPENMP
@@ -244,13 +244,13 @@ SEXP R_lower_tri(SEXP a, SEXP method
  , N = n*(n-1)/2;
 
  if ( n > MAXN ){
- error("Length of input vector (%d) exceeds maximum allowed for this platform (%d)",n,MAXN);
+ error("Length of input vector (%1.0f) exceeds maximum allowed for this platform (%1.0f)",(double) n,(double) MAXN);
  } 
 
 
  // output vector
  SEXP yy;
- PROTECT(yy = allocVector(REALSXP, N));
+ yy = PROTECT(allocVector(REALSXP, N));
  // nothing to do if n=1 
  if (n == 1L) goto end ;
  double *y = REAL(yy);
@@ -346,7 +346,7 @@ SEXP R_afind(SEXP a, SEXP pattern, SEXP width
 
  // output list
  SEXP out_list;
- PROTECT(out_list = allocVector(VECSXP, 2));
+ out_list = PROTECT(allocVector(VECSXP, 2));
 
  // output location
  SEXP out_loc = PROTECT(allocMatrix(INTSXP, na, npat));
@@ -441,7 +441,7 @@ SEXP R_afind(SEXP a, SEXP pattern, SEXP width
 // helper function to determine whether all is INTSXP
 
 SEXP R_all_int(SEXP X){
- PROTECT(X);
+ 
  SEXP all_int;
  all_int = PROTECT(allocVector(LGLSXP,1L));
 
@@ -454,7 +454,7 @@ SEXP R_all_int(SEXP X){
  }
  }
 
- UNPROTECT(2);
+ UNPROTECT(1);
  return all_int;
 
 }

pkg/src/qgram.c

@@ -568,8 +568,8 @@ SEXP R_get_qgrams(SEXP a, SEXP qq){
  count_qtree(Q,nqgram); 
 
  SEXP qgrams, qcount;
- PROTECT(qgrams = allocVector(INTSXP, q*nqgram[0]));
- PROTECT(qcount = allocVector(REALSXP, nLoc*nqgram[0]));
+ qgrams = PROTECT(allocVector(INTSXP, q*nqgram[0]));
+ qcount = PROTECT(allocVector(REALSXP, nLoc*nqgram[0]));
 
  get_counts(Q, q, INTEGER(qgrams), nLoc, index, REAL(qcount));