fix issue with vignettes that are not included

try to solve issue with Solaris on the CRAN checks results.

Author: boennecd

.Rbuildignore

@@ -1,3 +1,4 @@
+^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 \.log$
@@ -12,14 +13,11 @@ dynamichazard\.dll$
 ^\.travis\.yml$
 release_questions\.R$
 cran-comments\.md$
-
 src/pf/est_params_generic.cpp
-
 ^README
 ^README_cache
 ^examples
-
-^vignettes/[^/]*\.(?!(Rnw|bib|pdf\.asis|pdf|Rmd|csl)).*$
+^vignettes/[^\./]*\.(?!(Rnw|bib|pdf\.asis|pdf|Rmd|csl))
 vignettes/ddhazard\.pdf
 vignettes/fig
 vignettes/tex2pdf
@@ -28,7 +26,6 @@ vignettes/Diagnostics/data_prep\.R
 vignettes/Diagnostics/Rossi_ex\.html
 vignettes/Diagnostics/Rossi_source\.url
 vignettes/Diagnostics/Rossi\.txt
-
 ^\.sandbox
 ^speedtest
 tests/testthat/previous_results/local_tests

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynamichazard
 Type: Package
 Title: Dynamic Hazard Models using State Space Models
-Version: 0.6.2
+Version: 0.6.3
 Authors@R: c(person("Benjamin", "Christoffersen", 
                     email = "boennecd@gmail.com", 
                     role = c("cre", "aut")),

cran-comments.md

@@ -24,3 +24,10 @@ I still get this error with the UBSAN check: https://github.com/RcppCore/Rcpp/is
 
 Though, it does not seem to trigger on CRAN and Dirk Eddelbuettel and Kevin 
 Ushey indicate that it may not be a problem.
+
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Added vignettes which are currently not included due to an error in 
+  `.Rbuildignore`.
+* Tried to fix the error on Solaris in the CRAN check results.

src/BLAS_LAPACK/R_BLAS_LAPACK.cpp

@@ -63,7 +63,8 @@ namespace R_BLAS_LAPACK {
   void square_tri_inv(double *out, int n, int ldr){
     int info;
 
-    F77_CALL(dtrtri)("L", "N", &n, out, &ldr, &info);
+    char c1 = 'L', c2 = 'N';
+    F77_CALL(dtrtri)(&c1, &c2, &n, out, &ldr, &info);
 
     if(info != 0){
       std::stringstream str;
@@ -75,7 +76,8 @@ namespace R_BLAS_LAPACK {
   void symmetric_mat_chol(double *out, int n, int lda){
     int info;
 
-    F77_CALL(dpotrf)("L", &n, out, &lda, &info);
+    char c1 = 'L';
+    F77_CALL(dpotrf)(&c1, &n, out, &lda, &info);
 
     if(info != 0){
       std::stringstream str;
@@ -92,7 +94,9 @@ namespace R_BLAS_LAPACK {
     // ( 1 + ( n - 1 )*abs( INCX ) ).
 
     int incx = 1;
-    F77_CALL(dtrmv)("L", is_transpose ? "T" : "N", "N", &n, A, &lda, x, &incx);
+    char c1 = 'L', c2 = is_transpose ? 'T' : 'N', c3 = 'N';
+    F77_CALL(dtrmv)(
+        &c1, &c2, &c3, &n, A, &lda, x, &incx);
   }
 
   void sym_mat_rank_one_update(
@@ -104,13 +108,14 @@ namespace R_BLAS_LAPACK {
     // See http://www.netlib.org/lapack/explore-html/d7/d15/group__double__blas__level2_ga35ca25bb135cd7bfdd5d6190b1aa4d07.html#ga35ca25bb135cd7bfdd5d6190b1aa4d07
 
     int inx = 1;
+    char c1 = 'U';
 
     //F77_CALL(dger)(const int *m, const int *n, const double *alpha,
     // const double *x, const int *incx,
     // const double *y, const int *incy,
     // double *a, const int *lda);
     F77_CALL(dsyr)(
-        "U", n, alpha,
+        &c1, n, alpha,
         x, &inx,
         A, n);
   }
@@ -132,9 +137,10 @@ namespace R_BLAS_LAPACK {
 
     const double dum_d = 1.0;
     const int dum_i = 1L;
+    char c1 = 'U';
 
     F77_CALL(dsymv)(
-        "U", n,
+        &c1, n,
         &dum_d, A, n,
         x, &dum_i, &dum_d,
         y, &dum_i);
@@ -160,9 +166,10 @@ namespace R_BLAS_LAPACK {
     // Notice that we set UPLO to U so only the upper part is updated
 
     const double dum_d = 1.0;
+    char c1 = 'U', c2 = 'N';
 
     F77_CALL(dsyrk)(
-        "U", "N",
+        &c1, &c2,
         n, k, &dum_d,
         A, n,
         &dum_d, C, n);
@@ -181,12 +188,10 @@ namespace R_BLAS_LAPACK {
      */
 
     int info;
-    char uplo[2] = { is_upper ? 'U' : 'L' }, tra[2] = { trans ? 'T' : 'N' };
+    char c1 = is_upper ? 'U' : 'L', c2 = trans ? 'T' : 'N', c3 = 'N';
 
     F77_CALL(dtrtrs)(
-        uplo,
-        tra,
-        "N",
+        &c1, &c2, &c3,
         &n, &nrhs,
         A, &n,
         B, &n,

src/PF/dmvnrm.cpp

@@ -9,8 +9,9 @@ double dmvnrm_log(
 
   // z = sigma_chol_inv.t() * z;
   int incx = 1;
+  char uplo = 'U', trans = 'T', diag = 'N';
   R_BLAS_LAPACK::dtrmv(
-    "U" /* UPLO */, "T" /* TRANS */, "N" /* diag */,
+    &uplo, &trans, &diag,
     &xdim /* N */, sigma_chol_inv.memptr() /* A */,
     &xdim /* LDA */, z.memptr() /* X */, &incx /* INCX */);
 
@@ -36,8 +37,9 @@ double dmvtrm_log(
 
   /* z = sigma_chol_inv.t() * z; */
   int incx = 1;
+  char uplo = 'U', trans = 'T', diag = 'N';
   R_BLAS_LAPACK::dtrmv(
-    "U" /* UPLO */, "T" /* TRANS */, "N" /* diag */,
+    &uplo, &trans, &diag,
     &xdim /* N */, sigma_chol_inv.memptr() /* A */,
     &xdim /* LDA */, z.memptr() /* X */, &incx /* INCX */);
 

src/sample_funcs.cpp

@@ -59,8 +59,9 @@ arma::mat mvrnorm(const int m, const arma::mat &sigma_chol){
 
   // Y <-- Y * chol(Sigma)
   const double alpha = 1.;
+  char side = 'R', uplo = 'U', transa = 'N', diag = 'N';
   R_BLAS_LAPACK::dtrmm(
-    "R" /* side */, "U" /* UPLO */, "N" /* TRANSA */, "N" /* DIAG */,
+    &side, &uplo, &transa, &diag,
     &m /* M */, &n /* N */, &alpha /* ALPHA */,
     sigma_chol.memptr() /* A */, &n /* LDA */,
     Y.memptr() /* B */, &m /* LDB */);