From 1ab6aca64894ac6f68282f3b868737ff17508345 Mon Sep 17 00:00:00 2001
From: Michael Kane <kaneplusplus@gmail.com>
Date: Fri, 1 May 2026 11:56:16 -0400
Subject: [PATCH] Fix build and R CMD check warnings; bump to 4.0.4

- Drop deprecated Rcpp:::LdFlags() from src/Makevars and src/Makevars.win
  (no longer needed since 2013; Rcpp is linked automatically via LinkingTo).
- Cast .size() results to int in Rprintf calls in Params.h and Graph.h to
  match %d format specifier.
- Remove orphan %0.2f format specifier in Cbcpgraph.cpp Rprintf with no
  matching argument.
- Add .claude and build-artifact patterns to .Rbuildignore.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
---
 .Rbuildignore     | 3 +++
 DESCRIPTION       | 4 ++--
 src/Cbcpgraph.cpp | 2 +-
 src/Graph.h       | 4 ++--
 src/Makevars      | 2 +-
 src/Makevars.win  | 2 +-
 src/Params.h      | 2 +-
 7 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 91114bf..ab089e6 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -1,2 +1,5 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^\.claude$
+^bcp_.*\.tar\.gz$
+^bcp\.Rcheck$
diff --git a/DESCRIPTION b/DESCRIPTION
index 28be19d..263e7d1 100644
--- a/DESCRIPTION
+++ b/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:
diff --git a/src/Cbcpgraph.cpp b/src/Cbcpgraph.cpp
index 303e9ff..eb89f57 100755
--- a/src/Cbcpgraph.cpp
+++ b/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);
   }
 }
diff --git a/src/Graph.h b/src/Graph.h
index c39c5bc..fc19e5b 100644
--- a/src/Graph.h
+++ b/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++) {
diff --git a/src/Makevars b/src/Makevars
index 6961fc9..d711999 100755
--- a/src/Makevars
+++ b/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)
diff --git a/src/Makevars.win b/src/Makevars.win
index 23d51b8..40c8dcf 100755
--- a/src/Makevars.win
+++ b/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)
 
diff --git a/src/Params.h b/src/Params.h
index 12b98b8..cd35cb0 100644
--- a/src/Params.h
+++ b/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);
     }
   }