diff --git a/build/pkgs/r/spkg-configure.m4 b/build/pkgs/r/spkg-configure.m4
index d42e9cd5c54..e88f3393a91 100644
--- a/build/pkgs/r/spkg-configure.m4
+++ b/build/pkgs/r/spkg-configure.m4
@@ -1,16 +1,22 @@
 SAGE_SPKG_CONFIGURE([r], [
     m4_pushdef([SAGE_R_MINVER],["3.4.4"])
     SAGE_SPKG_DEPCHECK([atlas openblas iconv readline bzip2 xz pcre curl], [
-      PKG_CHECK_MODULES([R], [libR >= $SAGE_R_MINVER], [
-        AC_PATH_PROG([R], [R])
-          AS_IF([test "x$R" = x], [
-            AC_MSG_NOTICE([R is not found])
-            sage_spkg_install_r=yes
-            ], [
-            dnl TODO: check that versions of R and libR match
-            sage_spkg_install_r=no
-            ])
-     ], [sage_spkg_install_r=yes])
+      AS_CASE([$host],
+        [*-*-cygwin*], [
+          dnl #29486: rpy2 2.8.x does not build against system R on cygwin.
+          sage_spkg_install_r=yes
+        ], [
+          PKG_CHECK_MODULES([R], [libR >= $SAGE_R_MINVER], [
+            AC_PATH_PROG([R], [R])
+              AS_IF([test "x$R" = x], [
+                AC_MSG_NOTICE([R is not found])
+                sage_spkg_install_r=yes
+                ], [
+                dnl TODO: check that versions of R and libR match
+                sage_spkg_install_r=no
+                ])
+         ], [sage_spkg_install_r=yes])
+        ])
     ])
     m4_popdef([SAGE_R_MINVER])
 ])