Merge pull request #1285 from minrk/rmmran

Microsoft killed MRAN, stop relying on it

docs/source/config_files.rst

@@ -118,7 +118,7 @@ with ``REQUIRE`` and ``environment.yml``, visit
 ================================================
 
 This is used to install R libraries pinned to a specific snapshot on
-`MRAN <https://mran.microsoft.com/documents/rro/reproducibility>`_.
+`Posit Package Manager <https://packagemanager.posit.co/>`_.
 To set the date of the snapshot add a runtime.txt_.
 For an example ``install.R`` file, visit our `example install.R file <https://github.com/binder-examples/r/blob/HEAD/install.R>`_.
 
@@ -207,7 +207,7 @@ For these cases, we have a special file, ``runtime.txt``.
 Have ``python-x.y`` in ``runtime.txt`` to run the repository with Python version x.y.
 See our `Python2 example repository <https://github.com/binder-examples/python2_runtime/blob/HEAD/runtime.txt>`_.
 
-Have ``r-<RVERSION>-<YYYY>-<MM>-<DD>`` in ``runtime.txt`` to run the repository with R version RVERSION and libraries from a YYYY-MM-DD snapshot of `MRAN <https://mran.microsoft.com/documents/rro/reproducibility>`_.
+Have ``r-<RVERSION>-<YYYY>-<MM>-<DD>`` in ``runtime.txt`` to run the repository with R version RVERSION and libraries from a YYYY-MM-DD snapshot of `Posit Package Manager <https://packagemanager.posit.co/client/#/repos/2/overview>`__.
 RVERSION can be set to 3.4, 3.5, 3.6, or to patch releases for the 3.5 and 3.6 series.
 If you do not specify a version, the latest release will be used (currently R 3.6).
 See our `R example repository <https://github.com/binder-examples/r/blob/HEAD/runtime.txt>`_.

docs/source/howto/languages.rst

@@ -65,17 +65,14 @@ to install libraries from on the given date. You can install more R packages fro
 by adding a :ref:`install.R<install.R>` file to your repo. RStudio and IRKernel are
 installed by default for all R versions.
 
-If you request R 4.1 or later, or specify a snapshot date newer than
-``2022-01-01``, `packagemanager.posit.co <https://packagemanager.posit.co/client/#/>`_
+`packagemanager.posit.co <https://packagemanager.posit.co/client/#/>`_
 will be used to provide much faster installations via `binary packages <https://www.rstudio.com/blog/package-manager-v1-1-no-interruptions/>`_.
 For *some* packages, this might require you install underlying system libraries
 using :ref:`apt.txt` - look at the page for the CRAN package you are interested in at
 `packagemanager.posit.co <https://packagemanager.posit.co/client/#/>`_ to find
 a list.
 
-For older R versions with an older snapshot date, `MRAN <https://mran.microsoft.com/>`_
-is used as source of packages. This purely provides source packages, and you should
-migrate away from this if possible.
+repo2docker stopped using the Microsoft mirror MRAN for older R versions after its shutdown in July, 2023.
 
 
 Julia

repo2docker/buildpacks/r.py

@@ -9,6 +9,10 @@ from ..semver import parse_version as V
 from ._r_base import rstudio_base_scripts
 from .python import PythonBuildPack
 
+# Aproximately the first snapshot on RSPM (Posit package manager)
+# that seems to have a working IRKernel.
+RSPM_CUTOFF_DATE = datetime.date(2018, 12, 7)
+
 
 class RBuildPack(PythonBuildPack):
     """
@@ -22,8 +26,7 @@ class RBuildPack(PythonBuildPack):
 
        Where 'year', 'month' and 'date' refer to a specific
        date whose CRAN snapshot we will use to fetch packages.
-       Uses https://packagemanager.posit.co, or MRAN if no snapshot
-       is found on packagemanager.posit.co
+       Uses https://packagemanager.posit.co.
 
     2. A `DESCRIPTION` file signaling an R package
 
@@ -229,31 +232,6 @@ class RBuildPack(PythonBuildPack):
             )
         )
 
-    @lru_cache()
-    def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7):
-        for i in range(max_days_prior):
-            try_date = snapshot_date - datetime.timedelta(days=i)
-            # Fall back to MRAN if packagemanager.posit.co doesn't have it
-            url = f"https://mran.microsoft.com/snapshot/{try_date.isoformat()}"
-            r = requests.head(url)
-            if r.ok:
-                return url
-        raise ValueError(
-            "No snapshot found for {} or {} days prior in mran.microsoft.com".format(
-                snapshot_date.strftime("%Y-%m-%d"), max_days_prior
-            )
-        )
-
-    @lru_cache()
-    def get_cran_mirror_url(self, snapshot_date):
-        # Date after which we will use rspm + binary packages instead of MRAN + source packages
-        rspm_cutoff_date = datetime.date(2022, 1, 1)
-
-        if snapshot_date >= rspm_cutoff_date or self.r_version >= V("4.1"):
-            return self.get_rspm_snapshot_url(snapshot_date)
-        else:
-            return self.get_mran_snapshot_url(snapshot_date)
-
     @lru_cache()
     def get_devtools_snapshot_url(self):
         """
@@ -291,8 +269,14 @@ class RBuildPack(PythonBuildPack):
         We set the snapshot date used to install R libraries from based on the
         contents of runtime.txt.
         """
+        if self.checkpoint_date < RSPM_CUTOFF_DATE:
+            raise RuntimeError(
+                f'Microsoft killed MRAN, the source of R package snapshots before {RSPM_CUTOFF_DATE.strftime("%Y-%m-%d")}. '
+                f'This repo has a snapshot date of {self.checkpoint_date.strftime("%Y-%m-%d")} specified in runtime.txt. '
+                "Please use a newer snapshot date"
+            )
 
-        cran_mirror_url = self.get_cran_mirror_url(self.checkpoint_date)
+        cran_mirror_url = self.get_rspm_snapshot_url(self.checkpoint_date)
 
         if self.platform != "linux/amd64":
             raise RuntimeError(

tests/r/README.md

@@ -24,18 +24,6 @@
   `runtime.txt` is omitted and a recent enough snapshot date is assumed a RSPM
   snapshot of CRAN to be used.
 
-### r3.6-mran
-
-- Test setup of a R 3.6 environment by specifying `r-3.6-...` in `runtime.txt`,
-  where the date provided in `runtime.txt` is old enough for a MRAN snapshot of
-  CRAN to be used.
-
-### r4.0-mran
-
-- Test setup of a R 4.0 environment by specifying `r-4.0-...` in `runtime.txt`,
-  where the date provided in `runtime.txt` is old enough for a MRAN snapshot of
-  CRAN to be used.
-
 ### r4.0-rspm
 
 - Test setup of a R 4.0 environment by specifying `r-4.0-...` in `runtime.txt`,

tests/r/r3.6-mran/runtime.txt

@@ -1 +0,0 @@
-r-3.6-2016-01-03

tests/r/r3.6-rspm/runtime.txt

@@ -0,0 +1 @@
+r-3.6-2018-12-07

tests/r/r3.6-rspm/verify

@@ -7,7 +7,7 @@ if (!(version$major == "3" && as.double(version$minor) >= 6 && as.double(version
   quit("yes", 1)
 }
 
-# Fail if MRAN isn't the configured CRAN mirror
-if (!(startsWith(options()$repos["CRAN"], "https://mran.microsoft.com"))) {
+# Fail if RSPM isn't the configured CRAN mirror
+if (!(startsWith(options()$repos["CRAN"], "https://packagemanager.posit.co"))) {
   quit("yes", 1)
 }

tests/r/r4.0-mran/install.R

@@ -1 +0,0 @@
-install.packages("digest")

tests/r/r4.0-mran/runtime.txt

@@ -1 +0,0 @@
-r-4.0-2021-07-07

tests/r/r4.0-mran/verify

@@ -1,13 +0,0 @@
-#!/usr/bin/env Rscript
-library('digest')
-
-# Fail if version is not 4.0
-print(version)
-if (!(version$major == "4" && as.double(version$minor) >= 0 && as.double(version$minor) < 1)) {
-  quit("yes", 1)
-}
-
-# The date we have chosen should give us an MRAN mirror
-if (!(startsWith(options()$repos["CRAN"], "https://mran.microsoft.com"))) {
-  quit("yes", 1)
-}

tests/unit/test_r.py

@@ -40,7 +40,7 @@ def test_version_completion(tmpdir, base_image):
         ("r-3.5-2019-01-01", (2019, 1, 1)),
     ],
 )
-def test_mran_date(tmpdir, runtime, expected, base_image):
+def test_cran_date(tmpdir, runtime, expected, base_image):
     tmpdir.chdir()
 
     with open("runtime.txt", "w") as f:
@@ -74,21 +74,15 @@ def test_snapshot_rspm_date(base_image):
         r.get_rspm_snapshot_url(date(1691, 9, 5))
 
 
-@pytest.mark.parametrize("expected", [date(2019, 12, 29), date(2019, 12, 26)])
-@pytest.mark.parametrize("requested", [date(2019, 12, 31)])
-def test_snapshot_mran_date(requested, expected, base_image):
-    def mock_request_head(url):
-        r = Response()
-        if url == "https://mran.microsoft.com/snapshot/" + expected.isoformat():
-            r.status_code = 200
-        else:
-            r.status_code = 404
-            r.reason = "Mock MRAN no snapshot"
-        return r
+def test_mran_dead(tmpdir, base_image):
+    tmpdir.chdir()
 
-    with patch("requests.head", side_effect=mock_request_head):
-        r = buildpacks.RBuildPack(base_image)
-        assert (
-            r.get_mran_snapshot_url(requested)
-            == f"https://mran.microsoft.com/snapshot/{expected.isoformat()}"
-        )
+    with open("runtime.txt", "w") as f:
+        f.write("r-3.6-2017-06-04")
+
+    r = buildpacks.RBuildPack(base_image)
+    with pytest.raises(
+        RuntimeError,
+        match=r"^Microsoft killed MRAN, the source of R package snapshots before 2018-12-07.*",
+    ):
+        r.get_build_scripts()