Start RStudio if R is installed via conda

repo2docker/buildpacks/_r_base.py

@@ -0,0 +1,76 @@
+"""
+Base information for using R in BuildPacks.
+
+Keeping this in r.py would lead to cyclic imports.
+"""
+
+# Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/
+RSTUDIO_URL = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb"
+# This is MD5, because that is what RStudio download page provides!
+RSTUDIO_CHECKSUM = "d33881b9ab786c09556c410e7dc477de"
+
+# Via https://www.rstudio.com/products/shiny/download-server/
+SHINY_URL = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb"
+SHINY_CHECKSUM = "9aeef6613e7f58f21c97a4600921340e"
+
+# Version of MRAN to pull devtools from.
+DEVTOOLS_VERSION = "2018-02-01"
+
+# IRKernel version - specified as a tag in the IRKernel repository
+IRKERNEL_VERSION = "1.0.2"
+
+
+def rstudio_base_scripts():
+    """Base steps to install RStudio and shiny-server."""
+    return [
+        (
+            "root",
+            # Install RStudio!
+            r"""
+                curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \
+                echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \
+                apt-get update && \
+                apt install -y /tmp/rstudio.deb && \
+                rm /tmp/rstudio.deb && \
+                apt-get -qq purge && \
+                apt-get -qq clean && \
+                rm -rf /var/lib/apt/lists/*
+                """.format(
+                rstudio_url=RSTUDIO_URL, rstudio_checksum=RSTUDIO_CHECKSUM
+            ),
+        ),
+        (
+            "root",
+            # Install Shiny Server!
+            r"""
+                curl --silent --location --fail {url} > {deb} && \
+                echo '{checksum} {deb}' | md5sum -c - && \
+                dpkg -i {deb} && \
+                rm {deb}
+                """.format(
+                url=SHINY_URL, checksum=SHINY_CHECKSUM, deb="/tmp/shiny.deb"
+            ),
+        ),
+        (
+            "${NB_USER}",
+            # Install nbrsessionproxy
+            r"""
+                pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/7ac0125.zip && \
+                pip install --no-cache-dir jupyter-rsession-proxy==1.0b6 && \
+                jupyter serverextension enable jupyter_server_proxy --sys-prefix && \
+                jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \
+                jupyter nbextension enable --py jupyter_server_proxy --sys-prefix
+                """,
+        ),
+        (
+            # Not all of these locations are configurable; so we make sure
+            # they exist and have the correct permissions
+            "root",
+            r"""
+                install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \
+                install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \
+                install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \
+                install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid
+                """,
+        ),
+    ]

repo2docker/buildpacks/conda/__init__.py

@@ -6,10 +6,12 @@ from collections import Mapping
 from ruamel.yaml import YAML
 
 from ..base import BaseImage
+from .._r_base import rstudio_base_scripts, IRKERNEL_VERSION
 from ...utils import is_local_pip_requirement
 
 # pattern for parsing conda dependency line
 PYTHON_REGEX = re.compile(r"python\s*=+\s*([\d\.]*)")
+R_REGEX = re.compile(r"r-base\s*=+\s*([\d\.]*)")
 # current directory
 HERE = os.path.dirname(os.path.abspath(__file__))
 
@@ -179,6 +181,7 @@ class CondaBuildPack(BaseImage):
         Will return 'x.y' if version is found (e.g '3.6'),
         or a Falsy empty string '' if not found.
 
+        Version information below the minor level is dropped.
         """
         if not hasattr(self, "_python_version"):
             py_version = None
@@ -204,6 +207,40 @@ class CondaBuildPack(BaseImage):
 
         return self._python_version
 
+    @property
+    def r_version(self):
+        """Detect the Python version for a given `environment.yml`
+
+        Will return 'x.y' if version is found (e.g '3.6'),
+        or a Falsy empty string '' if not found.
+
+        """
+        if not hasattr(self, "_r_version"):
+            self._r_version = ""
+            env = self.environment_yaml
+            for dep in env.get("dependencies", []):
+                if not isinstance(dep, str):
+                    continue
+                match = R_REGEX.match(dep)
+                if not match:
+                    continue
+                self._r_version = match.group(1)
+                break
+
+        return self._r_version
+
+    @property
+    def uses_r(self):
+        """Detect whether the user also installs R packages.
+
+        Will return True when a package prefixed with 'r-' is being installed.
+        """
+        if not hasattr(self, "_uses_r"):
+            deps = self.environment_yaml.get("dependencies", [])
+            self._uses_r = any(dep.startswith("r-") for dep in deps)
+
+        return self._uses_r
+
     @property
     def py2(self):
         """Am I building a Python 2 kernel environment?"""
@@ -241,6 +278,46 @@ class CondaBuildPack(BaseImage):
                     ),
                 )
             )
+
+        if self.uses_r:
+            if self.r_version:
+                r_pin = "=" + self.r_version
+            else:
+                r_pin = ""
+            scripts.append(
+                (
+                    "${NB_USER}",
+                    r"""
+                conda install -p {0} r-base{1} r-irkernel={2} r-devtools && \
+                conda clean --all -f -y && \
+                conda list -p {0}
+                """.format(
+                        env_prefix, r_pin, IRKERNEL_VERSION
+                    ),
+                )
+            )
+            scripts += rstudio_base_scripts()
+            scripts += [
+                (
+                    "root",
+                    r"""
+                    echo auth-none=1 >> /etc/rstudio/rserver.conf && \
+                    echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \
+                    echo "rsession-which-r={0}/bin/R" >> /etc/rstudio/rserver.conf
+                    """.format(
+                        env_prefix
+                    ),
+                ),
+                (
+                    "${NB_USER}",
+                    # Install a pinned version of IRKernel and set it up for use!
+                    r"""
+                 R --quiet -e "IRkernel::installspec(prefix='{0}')"
+                 """.format(
+                        env_prefix
+                    ),
+                ),
+            ]
         return scripts
 
     def get_preassemble_scripts(self):

repo2docker/buildpacks/r.py

@@ -5,6 +5,7 @@ import datetime
 from distutils.version import LooseVersion as V
 
 from .python import PythonBuildPack
+from ._r_base import rstudio_base_scripts, DEVTOOLS_VERSION, IRKERNEL_VERSION
 
 
 class RBuildPack(PythonBuildPack):
@@ -206,21 +207,6 @@ class RBuildPack(PythonBuildPack):
         contents of runtime.txt.
         """
 
-        # Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/
-        rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb"
-        # This is MD5, because that is what RStudio download page provides!
-        rstudio_checksum = "d33881b9ab786c09556c410e7dc477de"
-
-        # Via https://www.rstudio.com/products/shiny/download-server/
-        shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb"
-        shiny_checksum = "9aeef6613e7f58f21c97a4600921340e"
-
-        # Version of MRAN to pull devtools from.
-        devtools_version = "2018-02-01"
-
-        # IRKernel version - specified as a tag in the IRKernel repository
-        irkernel_version = "1.0.2"
-
         mran_url = "https://mran.microsoft.com/snapshot/{}".format(
             self.checkpoint_date.isoformat()
         )
@@ -261,38 +247,17 @@ class RBuildPack(PythonBuildPack):
                 ),
             ]
 
-        scripts += [
+        scripts.append(
             (
                 "root",
                 r"""
                 mkdir -p ${R_LIBS_USER} && \
                 chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}
                 """,
-            ),
+            )
-            (
+        )
-                "root",
+        scripts += rstudio_base_scripts()
-                # Install RStudio!
+        scripts += [
-                r"""
-                curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \
-                echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \
-                dpkg -i /tmp/rstudio.deb && \
-                rm /tmp/rstudio.deb
-                """.format(
-                    rstudio_url=rstudio_url, rstudio_checksum=rstudio_checksum
-                ),
-            ),
-            (
-                "root",
-                # Install Shiny Server!
-                r"""
-                curl --silent --location --fail {url} > {deb} && \
-                echo '{checksum} {deb}' | md5sum -c - && \
-                dpkg -i {deb} && \
-                rm {deb}
-                """.format(
-                    url=shiny_url, checksum=shiny_checksum, deb="/tmp/shiny.deb"
-                ),
-            ),
             (
                 "root",
                 # Set paths so that RStudio shares libraries with base R
@@ -303,17 +268,6 @@ class RBuildPack(PythonBuildPack):
                 echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
                 """,
             ),
-            (
-                "${NB_USER}",
-                # Install nbrsessionproxy
-                r"""
-                pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/7ac0125.zip && \
-                pip install --no-cache-dir jupyter-rsession-proxy==1.0b6 && \
-                jupyter serverextension enable jupyter_server_proxy --sys-prefix && \
-                jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \
-                jupyter nbextension enable --py jupyter_server_proxy --sys-prefix
-                """,
-            ),
             (
                 "${NB_USER}",
                 # Install a pinned version of IRKernel and set it up for use!
@@ -322,7 +276,7 @@ class RBuildPack(PythonBuildPack):
                 R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='{irkernel_version}')" && \
                 R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
                 """.format(
-                    devtools_version=devtools_version, irkernel_version=irkernel_version
+                    devtools_version=DEVTOOLS_VERSION, irkernel_version=IRKERNEL_VERSION
                 ),
             ),
             (
@@ -344,17 +298,6 @@ class RBuildPack(PythonBuildPack):
                     mran_url=mran_url
                 ),
             ),
-            (
-                # Not all of these locations are configurable; so we make sure
-                # they exist and have the correct permissions
-                "root",
-                r"""
-                install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \
-                install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \
-                install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \
-                install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid
-                """,
-            ),
         ]
 
         if "r" in self.stencila_contexts: