gh-38777: Check the system R in SPKG rpy2
    
<!-- ^ Please provide a concise and informative title. -->
<!-- ^ Don't put issue numbers in the title, do this in the PR
description below. -->
<!-- ^ For example, instead of "Fixes #12345" use "Introduce new method
to calculate 1 + 2". -->
<!-- v Describe your changes below in detail. -->
<!-- v Why is this change required? What problem does it solve? -->
<!-- v If this PR resolves an open issue, please link to it here. For
example, "Fixes #12345". -->

It is problematic to put a dummy package into the dependencies list. For
instance, see #38774.

We move the check for the system R to `spkg-configure.m4` of SPKG rpy2.
Then we can replace R in the dependencies list with rpy2.

### 📝 Checklist

<!-- Put an `x` in all the boxes that apply. -->

- [x] The title is concise and informative.
- [x] The description explains in detail what this PR is about.
- [x] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation and checked the documentation
preview.

### ⌛ Dependencies

<!-- List all open PRs that this PR logically depends on. For example,
-->
<!-- - #12345: short description why this is a dependency -->
<!-- - #34567: ... -->

#38774 (merged here)
    
URL: #38777
Reported by: Kwankyu Lee
Reviewer(s):

Author: Release Manager

build/pkgs/r/spkg-configure.m4

@@ -1 +1,5 @@
-notebook r
+notebook rpy2
+
+----------
+R is the real dependency. But SPKG r is a dummy package, and does not install R.
+Since SPKG rpy2 checks for the system R, we put rpy2 as a dependency instead.

build/pkgs/r_jupyter/dependencies

@@ -1,4 +1,4 @@
- cffi tzlocal pytz jinja2 | $(PYTHON_TOOLCHAIN) pycparser $(PYTHON)
+cffi tzlocal pytz jinja2 | $(PYTHON_TOOLCHAIN) pycparser $(PYTHON)
 
 ----------
 All lines of this file are ignored except the first.

build/pkgs/rpy2/dependencies

@@ -1,14 +1,36 @@
 SAGE_SPKG_CONFIGURE([rpy2], [
-    SAGE_PYTHON_PACKAGE_CHECK([rpy2])
+  SAGE_PYTHON_PACKAGE_CHECK([rpy2])
 ], [dnl REQUIRED-CHECK
-    AC_REQUIRE([SAGE_SPKG_CONFIGURE_R])
-    dnl rpy2 is only needed when there is a usable system R
-    AS_VAR_IF([sage_spkg_install_r], [yes], [dnl
-        AS_VAR_IF([sage_use_system_r], [installed], [dnl
-            dnl Legacy SPKG installation of r
-            AS_VAR_SET([SPKG_REQUIRE], [yes])
-        ], [dnl No system package, no legacy SPKG installation
-            AS_VAR_SET([SPKG_REQUIRE], [no])
-        ])
+  dnl rpy2 is only needed when there is a usable system R
+  dnl Check for the R installation and version
+  dnl https://rpy2.github.io/doc/v3.4.x/html/overview.html#requirements
+  m4_pushdef([SAGE_R_MINVER], ["3.5"])
+  PKG_CHECK_MODULES([R], [libR >= SAGE_R_MINVER], [dnl
+    AC_PATH_PROG([R_EXECUTABLE], [R])
+    AS_IF([test "x$R_EXECUTABLE" = x], [dnl
+      AC_MSG_NOTICE([R is not found])
+      dnl No R found, so do not require rpy2 package
+      AS_VAR_SET([SPKG_REQUIRE], [no])
+    ], [dnl Extract R version
+      AC_MSG_CHECKING([for version of R executable])
+      R_VERSION=$($R_EXECUTABLE --version | sed -n 's/^R version \([[0-9.]]*\).*/\1/p')
+      AC_MSG_RESULT([$R_VERSION])
+      dnl Extract libR version
+      AC_MSG_CHECKING([for version of libR])
+      LIBR_VERSION=$(pkg-config --modversion libR)
+      AC_MSG_RESULT([$LIBR_VERSION])
+      dnl Compare R and libR versions
+      AS_IF([test "x$R_VERSION" = "x$LIBR_VERSION"], [dnl
+        AC_MSG_NOTICE([R and libR versions match ($R_VERSION)])
+        dnl Good system R is found, require rpy2 package
+        AS_VAR_SET([SPKG_REQUIRE], [yes])
+      ], [dnl R and libR versions do not match
+        AC_MSG_NOTICE([R version ($R_VERSION) does not match libR version ($LIBR_VERSION)])
+        AS_VAR_SET([SPKG_REQUIRE], [no])
+      ])
     ])
+  ], [dnl libR not found or outdated
+    AS_VAR_SET([SPKG_REQUIRE], [no])
+  ])
+  m4_popdef([SAGE_R_MINVER])
 ])