Merge pull request #1117 from minrk/r-base-core

Only get R itself (r-base-core) from apt, not CRAN packages

repo2docker/buildpacks/_r_base.py

@@ -31,13 +31,16 @@ def rstudio_base_scripts(r_version):
     return [
         (
             "root",
+            # we should have --no-install-recommends on all our apt-get install commands,
+            # but here it's important because these recommend r-base,
+            # which will upgrade the installed version of R, undoing our pinned version
             r"""
             curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \
             curl --silent --location --fail {shiny_server_url} > /tmp/shiny.deb && \
             echo '{rstudio_sha256sum} /tmp/rstudio.deb' | sha256sum -c - && \
             echo '{shiny_sha256sum} /tmp/shiny.deb' | sha256sum -c - && \
             apt-get update > /dev/null && \
-            apt install -y /tmp/rstudio.deb /tmp/shiny.deb > /dev/null && \
+            apt install -y --no-install-recommends /tmp/rstudio.deb /tmp/shiny.deb && \
             rm /tmp/rstudio.deb && \
             apt-get -qq purge && \
             apt-get -qq clean && \

repo2docker/buildpacks/r.py

@@ -38,8 +38,9 @@ class RBuildPack(PythonBuildPack):
 
     - are needed by a specific tool
 
-    The `r-base` package from Ubuntu apt repositories is used to install
-    R itself, rather than any of the methods from https://cran.r-project.org/.
+    The `r-base-core` package from Ubuntu or "Ubuntu packages for R"
+    apt repositories is used to install R itself,
+    rather than any of the methods from https://cran.r-project.org/.
 
     The `r-base-dev` package is installed as advised in RStudio instructions.
     """
@@ -291,11 +292,14 @@ class RBuildPack(PythonBuildPack):
             ),
             (
                 "root",
+                # we should have --no-install-recommends on all our apt-get install commands,
+                # but here it's important because it will pull in CRAN packages
+                # via r-recommends, which is only guaranteed to be compatible with the latest r-base-core
                 r"""
                 apt-get update > /dev/null && \
-                apt-get install --yes r-base={R_version} r-base-core={R_version} \
+                apt-get install --yes --no-install-recommends \
+                        r-base-core={R_version} \
                         r-base-dev={R_version} \
-                        r-recommended={R_version} \
                         libclang-dev \
                         libzmq3-dev > /dev/null && \
                 apt-get -qq purge && \

tests/unit/test_r.py

@@ -147,7 +147,7 @@ def test_custom_cran_apt_repo(tmpdir):
 
     # check that we install the right package
     for user, script in scripts:
-        if "r-base=3.5" in script:
+        if "r-base-core=3.5" in script:
             break
     else:
         assert False, "Should have installed base R"