[MRG] Add support for installing different versions of R (#772)

[MRG] Add support for installing different versions of R

docs/source/config_files.rst

@@ -212,7 +212,7 @@ If you only need to run things once during the build phase use :ref:`postBuild`.
 
 Sometimes you want to specify the version of the runtime
 (e.g. the version of Python or R),
-but the environment specification format don't let you specify this information
+but the environment specification format will not let you specify this information
 (e.g. requirements.txt or install.R).
 For these cases, we have a special file, ``runtime.txt``.
 
@@ -220,7 +220,7 @@ For these cases, we have a special file, ``runtime.txt``.
 
    ``runtime.txt`` is only supported when used with environment specifications
    that do not already support specifying the runtime
-   (e.g. when using ``environment.yml`` for conda or ``Project.toml`` for Julia,
+   (when using ``environment.yml`` for conda or ``Project.toml`` for Julia,
    ``runtime.txt`` will be ignored).
 
 To use python-2.7: add ``python-2.7`` in runtime.txt file.
@@ -231,8 +231,11 @@ Python 2 installed. To see a full example repository, visit our
 repo2docker uses R libraries pinned to a specific snapshot on
 `MRAN <https://mran.microsoft.com/documents/rro/reproducibility>`_.
 You need to have a ``runtime.txt`` file that is formatted as
-``r-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot at MRAN that will be
+``r-<RVERSION>-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot at MRAN that will be
-used for installing libraries.
+used for installing libraries. You can set RVERSION to 3.4, 3.5 or 3.6 to select
+the version of R you want to use. If you do not specify a R version the latest
+released version will be used (currently R 3.6). You can also specify the exact
+patch release you want to use for the 3.5 and 3.6 series.
 
 To see an example R repository, visit our `R
 example in binder-examples <https://github.com/binder-examples/r/blob/master/runtime.txt>`_.

docs/source/faq.rst

@@ -49,10 +49,11 @@ Julia versions 0.6.x and earlier are supported via a :ref:`REQUIRE <REQUIRE>` fi
 R
 ~
 
-Only R 3.4.4 is currently supported, which is installed via ``apt`` from the
+The default version of R is currently R 3.6.1. You can select the version of
-`ubuntu bionic repository <https://packages.ubuntu.com/bionic/r-base>`_.
+R you want to use by specifying it in the :ref:`runtime.txt <runtime.txt>`
-
+file.
 
+We support R versions 3.4, 3.5 and 3.6.
 
 
 Why is my repository is failing to build with ``ResolvePackageNotFound`` ?
@@ -149,17 +150,17 @@ notebooks (among others).
     the container, use the ``--volumes`` option instead. Similarly,
     for a fully customized user Dockerfile, this option is not
     guaranteed to work.
-    
+
-    
+
 Why is my R shiny app not launching?
 ----------------------------------------------------------------------------------
 
 If you are trying to run an R shiny app using the ``/shiny/folder_containing_shiny``
 url option, but the launch returns "The application exited during initialization.",
 there might be something wrong with the specification of the app. One way of debugging
-the app in the container is by running the ``rstudio`` url, open either the ui or 
+the app in the container is by running the ``rstudio`` url, open either the ui or
-server file for the app, and run the app in the container rstudio. This way you can 
+server file for the app, and run the app in the container rstudio. This way you can
-see the rstudio logs as it tries to initialise the shiny app. If you a missing a 
+see the rstudio logs as it tries to initialise the shiny app. If you a missing a
 package or other dependency for the container, this will be obvious at this stage.
 
 

repo2docker/buildpacks/r.py

@@ -2,6 +2,8 @@ import re
 import os
 import datetime
 
+from distutils.version import LooseVersion as V
+
 from .python import PythonBuildPack
 
 
@@ -55,6 +57,41 @@ class RBuildPack(PythonBuildPack):
 
         return self._runtime
 
+    @property
+    def r_version(self):
+        """Detect the R version for a given `runtime.txt`
+
+        Will return the version specified by the user or the current default
+        version.
+        """
+        version_map = {
+            "3.4": "3.4",
+            "3.5": "3.5.3-1bionic",
+            "3.5.0": "3.5.0-1bionic",
+            "3.5.1": "3.5.1-2bionic",
+            "3.5.2": "3.5.2-1bionic",
+            "3.5.3": "3.5.3-1bionic",
+            "3.6": "3.6.1-3bionic",
+            "3.6.0": "3.6.0-2bionic",
+            "3.6.1": "3.6.1-3bionic",
+        }
+        # the default if nothing is specified
+        r_version = "3.6"
+
+        if not hasattr(self, "_r_version"):
+            parts = self.runtime.split("-")
+            if len(parts) == 5:
+                r_version = parts[1]
+                if r_version not in version_map:
+                    raise ValueError(
+                        "Version '{}' of R is not supported.".format(r_version)
+                    )
+
+            # translate to the full version string
+            self._r_version = version_map.get(r_version)
+
+        return self._r_version
+
     @property
     def checkpoint_date(self):
         """
@@ -63,11 +100,14 @@ class RBuildPack(PythonBuildPack):
         Returns '' if no date is specified
         """
         if not hasattr(self, "_checkpoint_date"):
-            match = re.match(r"r-(\d\d\d\d)-(\d\d)-(\d\d)", self.runtime)
+            match = re.match(r"r-(\d.\d(.\d)?-)?(\d\d\d\d)-(\d\d)-(\d\d)", self.runtime)
             if not match:
                 self._checkpoint_date = False
             else:
-                self._checkpoint_date = datetime.date(*[int(s) for s in match.groups()])
+                # turn the last three groups of the match into a date
+                self._checkpoint_date = datetime.date(
+                    *[int(s) for s in match.groups()[-3:]]
+                )
 
         return self._checkpoint_date
 
@@ -127,20 +167,19 @@ class RBuildPack(PythonBuildPack):
         We install a base version of R, and packages required for RStudio to
         be installed.
         """
-        return (
+        packages = [
-            super()
+            # For rstudio
-            .get_packages()
+            "psmisc",
-            .union(
+            "libapparmor1",
-                [
+            "sudo",
-                    "r-base",
+            "lsb-release",
-                    # For rstudio
+        ]
-                    "psmisc",
+        # For R 3.4 we use the default Ubuntu package, for other versions we
-                    "libapparmor1",
+        # install from a different PPA
-                    "sudo",
+        if V(self.r_version) < V("3.5"):
-                    "lsb-release",
+            packages.append("r-base")
-                ]
+
-            )
+        return super().get_packages().union(packages)
-        )
 
     def get_build_scripts(self):
         """
@@ -180,7 +219,38 @@ class RBuildPack(PythonBuildPack):
             self.checkpoint_date.isoformat()
         )
 
-        scripts = [
+        scripts = []
+        # For R 3.4 we want to use the default Ubuntu package but otherwise
+        # we use the packages from a PPA
+        if V(self.r_version) >= V("3.5"):
+            scripts += [
+                (
+                    "root",
+                    r"""
+                    echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" > /etc/apt/sources.list.d/r3.6-ubuntu.list
+                    """,
+                ),
+                (
+                    "root",
+                    r"""
+                    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+                    """,
+                ),
+                (
+                    "root",
+                    r"""
+                    apt-get update && \
+                    apt-get install --yes r-base={} && \
+                    apt-get -qq purge && \
+                    apt-get -qq clean && \
+                    rm -rf /var/lib/apt/lists/*
+                    """.format(
+                        self.r_version
+                    ),
+                ),
+            ]
+
+        scripts += [
             (
                 "root",
                 r"""
@@ -277,17 +347,32 @@ class RBuildPack(PythonBuildPack):
         ]
 
         if "r" in self.stencila_contexts:
-            scripts += [
+            # new versions of R require a different way of installing bioconductor
-                (
+            if V(self.r_version) <= V("3.5"):
-                    "${NB_USER}",
+                scripts += [
-                    # Install and register stencila library
+                    (
-                    r"""
+                        "${NB_USER}",
-                R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \
+                        # Install and register stencila library
-                R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
+                        r"""
-                R --quiet -e "stencila::register()"
+                    R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \
-                """,
+                    R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
-                )
+                    R --quiet -e "stencila::register()"
-            ]
+                    """,
+                    )
+                ]
+
+            else:
+                scripts += [
+                    (
+                        "${NB_USER}",
+                        # Install and register stencila library
+                        r"""
+                    R --quiet -e "install.packages('BiocManager'); BiocManager::install(); BiocManager::install(c('graph'))" && \
+                    R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
+                    R --quiet -e "stencila::register()"
+                    """,
+                    )
+                ]
 
         return super().get_build_scripts() + scripts
 

tests/unit/test_r.py

@@ -0,0 +1,109 @@
+from datetime import date
+
+import pytest
+
+from repo2docker import buildpacks
+
+
+def test_unsupported_version(tmpdir):
+    tmpdir.chdir()
+
+    with open("runtime.txt", "w") as f:
+        f.write("r-3.8-2019-01-01")
+
+    r = buildpacks.RBuildPack()
+    with pytest.raises(ValueError) as excinfo:
+        # access the property to trigger the exception
+        _ = r.r_version
+        # check the version is mentioned in the exception
+        assert "'3.8'" in str(excinfo.value)
+
+
+@pytest.mark.parametrize(
+    "runtime_version, expected", [("", "3.6"), ("3.6", "3.6"), ("3.5.1", "3.5")]
+)
+def test_version_specification(tmpdir, runtime_version, expected):
+    tmpdir.chdir()
+
+    with open("runtime.txt", "w") as f:
+        if runtime_version:
+            runtime_version += "-"
+        f.write(f"r-{runtime_version}2019-01-01")
+
+    r = buildpacks.RBuildPack()
+    assert r.r_version.startswith(expected)
+
+
+def test_version_completion(tmpdir):
+    tmpdir.chdir()
+
+    with open("runtime.txt", "w") as f:
+        f.write(f"r-3.6-2019-01-01")
+
+    r = buildpacks.RBuildPack()
+    assert r.r_version == "3.6.1-3bionic"
+
+
+@pytest.mark.parametrize(
+    "runtime, expected",
+    [
+        ("r-2019-01-01", (2019, 1, 1)),
+        ("r-3.6.1-2019-01-01", (2019, 1, 1)),
+        ("r-3.5-2019-01-01", (2019, 1, 1)),
+    ],
+)
+def test_mran_date(tmpdir, runtime, expected):
+    tmpdir.chdir()
+
+    with open("runtime.txt", "w") as f:
+        f.write(runtime)
+
+    r = buildpacks.RBuildPack()
+    assert r.checkpoint_date == date(*expected)
+
+
+def test_install_from_base(tmpdir):
+    # check that for R==3.4 we install from ubuntu
+    tmpdir.chdir()
+
+    with open("runtime.txt", "w") as f:
+        f.write("r-3.4-2019-01-02")
+
+    r = buildpacks.RBuildPack()
+    assert "r-base" in r.get_packages()
+
+
+def test_install_from_ppa(tmpdir):
+    # check that for R>3.4 we don't install r-base from Ubuntu
+    tmpdir.chdir()
+
+    with open("runtime.txt", "w") as f:
+        f.write("r-3.5-2019-01-02")
+
+    r = buildpacks.RBuildPack()
+    assert "r-base" not in r.get_packages()
+
+
+def test_custom_ppa(tmpdir):
+    tmpdir.chdir()
+
+    with open("runtime.txt", "w") as f:
+        f.write("r-3.5-2019-01-02")
+
+    r = buildpacks.RBuildPack()
+
+    scripts = r.get_build_scripts()
+
+    # check that at least one of the build scripts adds this new PPA
+    for user, script in scripts:
+        if "https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" in script:
+            break
+    else:
+        assert False, "Should have added a new PPA"
+
+    # check that we install the right package
+    for user, script in scripts:
+        if "r-base=3.5" in script:
+            break
+    else:
+        assert False, "Should have installed base R"