install R for Stencila from R buildpack

repo2docker/buildpacks/base.py

@@ -301,7 +301,7 @@ class BuildPack:
 
         for root, dirs, files in os.walk("."):
             for filename in files:
-                if filename.endswith(".test.jats.xml"):
+                if filename.endswith(".jats.xml"):
                     self.log.debug("Found a .jats.xml: %s", filename)
                     self._stencila_manifest_contexts = set()
 
@@ -558,22 +558,7 @@ class BaseImage(BuildPack):
             pass
         if self.stencila_manifest_contexts:
             for context in self.stencila_manifest_contexts:
-                if(context == 'r'):
-
-                    # TODO: can I trigger the RBuildPack from here?
-
-                    assemble_scripts.extend(
-                        [
-                            (
-                                "${NB_USER}",
-                                r"""
-                                R --quiet -e "library('devtools'); options(unzip = 'internal'); devtools::install_github('stencila/r', ref = 'f220361438432abca968d2e76a4efe7c5ddde7f1')" && \
-                                R --quiet -e "stencila::register()"
-                                """,
-                            )
-                        ]
-                    )
-                elif(context == 'py' or context == 'pyjp'):
+                if(context == 'py' or context == 'pyjp'):
                     assemble_scripts.extend(
                         [
                             (
@@ -585,6 +570,8 @@ class BaseImage(BuildPack):
                             )
                         ]
                     )
+                #elif(context == 'r'):
+                    # handled in RBuildPack
         if self.stencila_manifest_dir:
             assemble_scripts.extend(
                 [

repo2docker/buildpacks/r.py

@@ -19,7 +19,14 @@ class RBuildPack(PythonBuildPack):
        date snapshot of https://mran.microsoft.com/timemachine
        from which libraries are to be installed.
 
-    2. An optional `install.R` file that will be executed at build time,
+    2. A `DESCRIPTION` file signaling an R package, or
+       a Stencila document (*.jats.xml) with R code chunks (i.e. language="r")
+       is found:
+
+       MRAN snapshot is set to latest date that is guaranteed to exist
+       across timezones.
+
+    3. (Optional) An `install.R` file that will be executed at build time,
        and can be used for installing packages from both MRAN and GitHub.
 
     The `r-base` package from Ubuntu apt repositories is used to install
@@ -64,21 +71,22 @@ class RBuildPack(PythonBuildPack):
         unless a `requirements.txt` is present and we do not want to require the
         presence of a `requirements.txt` to use R.
 
-        Instead we just check if runtime.txt contains a string of the form
-        `r-<YYYY>-<MM>-<DD>`
+        Instead we check the options described in the class comment above.
         """
         # If no date is found, then self.checkpoint_date will be False
         # Otherwise, it'll be a date object, which will evaluate to True
         if self.checkpoint_date:
             return True
+
         description_R = 'DESCRIPTION'
-        if not os.path.exists('binder') and os.path.exists(description_R):
-            if not self.checkpoint_date:
-                # no R snapshot date set through runtime.txt
-                # set the R runtime to the latest date that is guaranteed to be on MRAN across timezones
-                self._checkpoint_date = datetime.date.today() - datetime.timedelta(days=2)
-                self._runtime = "r-{}".format(str(self._checkpoint_date))
-            return True
+        if not os.path.exists('binder'): 
+            if os.path.exists(description_R) or (self.stencila_manifest_contexts and "r" in self.stencila_manifest_contexts):
+                if not self.checkpoint_date:
+                    # no R snapshot date set through runtime.txt
+                    # set the R runtime to the latest date that is guaranteed to be on MRAN across timezones
+                    self._checkpoint_date = datetime.date.today() - datetime.timedelta(days=2)
+                    self._runtime = "r-{}".format(str(self._checkpoint_date))
+                return True
 
     def get_path(self):
         """
@@ -133,6 +141,7 @@ class RBuildPack(PythonBuildPack):
         - R's devtools package, at a particular frozen version (determined by MRAN)
         - IRKernel
         - nbrsessionproxy (to access RStudio via Jupyter Notebook)
+        - stencila R package (if Stencila document with R code chunks detected)
         """
         rstudio_url = 'https://download2.rstudio.org/rstudio-server-1.1.419-amd64.deb'
         # This is MD5, because that is what RStudio download page provides!
@@ -148,7 +157,7 @@ class RBuildPack(PythonBuildPack):
         # IRKernel version - specified as a tag in the IRKernel repository
         irkernel_version = '0.8.11'
 
-        return super().get_build_scripts() + [
+        scripts = [
             (
                 "root",
                 r"""
@@ -226,6 +235,21 @@ class RBuildPack(PythonBuildPack):
             ),
         ]
 
+        if self.stencila_manifest_contexts:
+            if "r" in self.stencila_manifest_contexts:
+                scripts += [
+                (
+                    "${NB_USER}",
+                    # Install and register stencila library
+                    r"""
+                    R --quiet -e "devtools::install_github('stencila/r', ref = 'f220361438432abca968d2e76a4efe7c5ddde7f1')" && \
+                    R --quiet -e "stencila::register()"
+                    """
+                ),
+            ]
+
+        return super().get_build_scripts() + scripts
+
     def get_assemble_scripts(self):
         """
         Return series of build-steps specific to this repository