Fix build and R CMD check warnings; bump to 4.0.4

.Rbuildignore

@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.claude$
+^bcp_.*\.tar\.gz$
+^bcp\.Rcheck$

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: bcp
 Type: Package
 Title: Bayesian Analysis of Change Point Problems
-Version: 4.0.3
-Date: 2018-08-13
+Version: 4.0.4
+Date: 2026-05-01
 Author: Xiaofei Wang, Chandra Erdman, and John W. Emerson
 Maintainer: Xiaofei Wang <xiaofei.wang@yale.edu>
 Depends:

src/Cbcpgraph.cpp

@@ -55,7 +55,7 @@ void recomputeVals(Graph &graph, Partition &components, GraphParams &params)
     }
 
     W[i] -= B[i];
-    Rprintf("Recomputed: i:%d, W: %0.2f, B: %0.2f, size: %d, %0.2f\n", i, W[i], B[i],
+    Rprintf("Recomputed: i:%d, W: %0.2f, B: %0.2f, size: %d\n", i, W[i], B[i],
             components[i].size);
   }
 }

src/Graph.h

@@ -183,8 +183,8 @@ class Graph
   // other functions
   void print(bool all = false)
   {
-    Rprintf("overall mean:%0.2f, overall ysq:%0.2f, num pixels: %d\n", 
-            mean, sumysq, nodes.size());
+    Rprintf("overall mean:%0.2f, overall ysq:%0.2f, num pixels: %d\n",
+            mean, sumysq, (int)nodes.size());
 
     if (all) {
       for (int i = 0; i < nodes.size(); i++) {

src/Makevars

@@ -1,2 +1,2 @@
 ## Use the R_HOME indirection to support installations of multiple R version
-PKG_LIBS = `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,4 +1,4 @@
 
 ## Use the R_HOME indirection to support installations of multiple R version
-PKG_LIBS = $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 

src/Params.h

@@ -119,7 +119,7 @@ class GraphParams: public Params {
       Rprintf("multivariate: alpha=%0.2f, d=%0.2f w:%0.2f kk:%d\n", p0, d, w[0], kk);
     } else {
       // regression since multiple predictors
-      Rprintf("regression: alpha=%0.2f, d=%0.2f w.size:%d kk:%d\n", p0, d, w.size(), kk);
+      Rprintf("regression: alpha=%0.2f, d=%0.2f w.size:%d kk:%d\n", p0, d, (int)w.size(), kk);
     }
   }