Install devtools, shiny & irkernel from a pin

We were doing this from an old MRAN snapshot. I moved the pin
a little ahead, so IRKernel can also be installed from CRAN
instead of from GitHub. R <= 4.0 gets the old version, and anything
newer gets a more recent version of devtools. This gives us
fast installs for IRkernel with binary packages.

Also add a R 4.0 and R 4.1 test

repo2docker/buildpacks/_r_base.py

@@ -13,13 +13,6 @@ RSTUDIO_CHECKSUM = "d33881b9ab786c09556c410e7dc477de"
 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 = "1.1"
-
-
 def rstudio_base_scripts():
     """Base steps to install RStudio and shiny-server."""
     return [

repo2docker/buildpacks/conda/__init__.py

@@ -6,7 +6,7 @@ from collections.abc import Mapping
 from ruamel.yaml import YAML
 
 from ..base import BaseImage
-from .._r_base import rstudio_base_scripts, IRKERNEL_VERSION
+from .._r_base import rstudio_base_scripts
 from ...utils import is_local_pip_requirement
 
 # pattern for parsing conda dependency line
@@ -356,11 +356,11 @@ class CondaBuildPack(BaseImage):
                 (
                     "${NB_USER}",
                     r"""
-                mamba install -p {0} r-base{1} r-irkernel={2} r-devtools -y && \
+                mamba install -p {0} r-base{1} r-irkernel=1.2 r-devtools -y && \
                 mamba clean --all -f -y && \
                 mamba list -p {0}
                 """.format(
-                        env_prefix, r_pin, IRKERNEL_VERSION
+                        env_prefix, r_pin
                     ),
                 )
             )

repo2docker/buildpacks/r.py

@@ -6,7 +6,7 @@ import requests
 from distutils.version import LooseVersion as V
 
 from .python import PythonBuildPack
-from ._r_base import rstudio_base_scripts, DEVTOOLS_VERSION, IRKERNEL_VERSION
+from ._r_base import rstudio_base_scripts
 
 
 class RBuildPack(PythonBuildPack):
@@ -186,7 +186,6 @@ class RBuildPack(PythonBuildPack):
         return super().get_packages().union(packages)
 
     def get_cran_mirror_url(self, snapshot_date):
-
         # Call the API to find out if we have a snapshot available for the given date.
         # If so, use the URL for that snapshot. If not, fall back to MRAN.
         snapshots = requests.post(
@@ -209,6 +208,19 @@ class RBuildPack(PythonBuildPack):
             snapshot_date.isoformat()
         )
 
+    def get_devtools_snapshot_date(self):
+        """
+        Return date of snapshot to use for getting devtools install
+
+        devtools is part of our 'core' base install, so we should have some
+        control over what version we install here.
+        """
+        if V(self.r_version) <= V('4.0'):
+            # IRKernel gets into CRAN on Nov 16 2018 (https://packagemanager.rstudio.com/client/#/repos/1/packages/IRkernel),
+            # so we try snapshot to just after that.
+            return datetime.date(2018, 12, 1)
+        return datetime.date(2021, 12, 16)
+
     def get_build_scripts(self):
         """
         Return series of build-steps common to all R repositories
@@ -312,26 +324,17 @@ class RBuildPack(PythonBuildPack):
             ),
             (
                 "${NB_USER}",
-                # Install a pinned version of IRKernel and set it up for use!
+                # Install a pinner version of devtools, IRKernel and shiny
                 r"""
-                R --quiet -e "install.packages('devtools')" && \
+                R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='{devtools_cran_mirror_url}')" && \
-                R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='{irkernel_version}')" && \
                 R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
                 """.format(
-                    cran_mirror_url=cran_mirror_url,
+                    devtools_cran_mirror_url=self.get_cran_mirror_url(self.get_devtools_snapshot_date()),
-                    devtools_version=DEVTOOLS_VERSION,
-                    irkernel_version=IRKERNEL_VERSION,
                 ),
-            ),
+            )
-            (
-                "${NB_USER}",
-                # Install shiny library
-                r"""
-                R --quiet -e "install.packages('shiny')"
-                """,
-            ),
         ]
 
+
         return super().get_build_scripts() + scripts
 
     def get_preassemble_script_files(self):

tests/r/r4.0/runtime.txt

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

tests/r/r4.0/verify

@@ -0,0 +1,8 @@
+#!/usr/bin/env Rscript
+library('ggplot2')
+
+print(version)
+# Fail if version is not 4.0
+if (!(version$major == "4" && as.double(version$minor) >= 0 && as.double(version$minor) < 1)) {
+  quit("yes", 1)
+}

tests/r/r4.1/install.R

@@ -0,0 +1 @@
+install.packages("ggplot2")