Fix macOS deployment target mismatch by detecting R actual target

The Rust cc crate defaults to the SDK version (xcrun --show-sdk-version)
when MACOSX_DEPLOYMENT_TARGET is unset, which can exceed the deployment
target used by R compiler and linked libraries (e.g., libgfortran),
causing an ld warning. Instead of re-exporting an env var that may not
exist, configure now compiles a test object with R compiler and reads
the minos value via otool to determine the correct deployment target.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: bnaras

configure

@@ -8,4 +8,22 @@ fi
 
 CC_ALONE=`$R_HOME/bin/R CMD config CC | awk '{print $1}'`
 
-sed -e "s/@TARGET@/${TARGET}/" -e "s|@R_HOME@|${R_HOME}|" -e "s|@CC_ALONE@|${CC_ALONE}|" src/Makevars.in > src/Makevars
+# Detect macOS deployment target for Rust cc crate.
+# The cc crate defaults to the SDK version (via xcrun --show-sdk-version)
+# which can exceed the target used by R's compiler, causing an ld warning.
+# We compile a test object with R's compiler to determine the actual target.
+MACOSX_DT=""
+if [ "$(uname)" = "Darwin" ]; then
+  if [ -n "$MACOSX_DEPLOYMENT_TARGET" ]; then
+    MACOSX_DT="$MACOSX_DEPLOYMENT_TARGET"
+  else
+    R_CC=`"${R_HOME}/bin/R" CMD config CC`
+    R_CFLAGS=`"${R_HOME}/bin/R" CMD config CFLAGS`
+    echo "int x;" > conftest_dt.c
+    $R_CC $R_CFLAGS -c conftest_dt.c -o conftest_dt.o 2>/dev/null
+    MACOSX_DT=`otool -l conftest_dt.o 2>/dev/null | awk '/LC_BUILD_VERSION/{found=1} found && /minos/{print $2; exit}'`
+    rm -f conftest_dt.c conftest_dt.o
+  fi
+fi
+
+sed -e "s/@TARGET@/${TARGET}/" -e "s|@R_HOME@|${R_HOME}|" -e "s|@CC_ALONE@|${CC_ALONE}|" -e "s|@MACOSX_DT@|${MACOSX_DT}|" src/Makevars.in > src/Makevars

src/Makevars.in

@@ -1,6 +1,7 @@
 TARGET = @TARGET@
 R_HOME = @R_HOME@
 CC_ALONE = @CC_ALONE@
+MACOSX_DT = @MACOSX_DT@
 VENDORING = yes
 VENDOR_SRC = ./rust/vendor.tar.xz
 VENDOR_DIR = ./rust/vendor
@@ -17,6 +18,16 @@ CARGOTMP = $(CURDIR)/rust/.cargo
 CARGO_BUILD_ARGS = -j 2 --lib --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
 RUST_BACKTRACE=1
 
+# Ensure the Rust cc crate uses the correct macOS deployment target.
+# Without this, cc falls back to xcrun --show-sdk-version which may
+# return a newer version than the R link target, causing an ld warning.
+ifneq ($(MACOSX_DT),)
+  MACOSX_DEPLOYMENT_TARGET = $(MACOSX_DT)
+endif
+ifdef MACOSX_DEPLOYMENT_TARGET
+  export MACOSX_DEPLOYMENT_TARGET
+endif
+
 all: $(SHLIB) clean_intermediate
 
 $(SHLIB): $(STATLIB)
@@ -37,7 +48,6 @@ $(STATLIB):
 	      export R_HOME=$(R_HOME);  \
 	      export PATH="$(PATH):$(HOME)/.cargo/bin";  \
 	      export RUSTFLAGS="-C linker=${CC_ALONE}"; \
-	      export MACOSX_DEPLOYMENT_TARGET; \
 	      cargo build $(CARGO_BUILD_ARGS) --release --offline; \
 	    else \
 	      cargo build $(CARGO_BUILD_ARGS); \