Get R from RStudio provided apt packages (.deb files)

repo2docker/buildpacks/r.py

@@ -38,11 +38,7 @@ class RBuildPack(PythonBuildPack):
 
  - are needed by a specific tool
 
- 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.
+ R is installed from https://docs.rstudio.com/resources/install-r/
  """
 
  @property
@@ -68,33 +64,29 @@ def r_version(self):
  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": "3.6.3-1bionic",
- "3.6.0": "3.6.0-2bionic",
- "3.6.1": "3.6.1-3bionic",
- "4.0": "4.0.5-1.1804.0",
- "4.0.2": "4.0.2-1.1804.0",
- "4.1": "4.1.2-1.1804.0",
+ "4.2": "4.2.0",
+ "4.1": "4.1.3",
+ "4.0": "4.0.5",
+ "3.6": "3.6.3",
+ "3.5": "3.5.3",
+ "3.4": "3.4.0",
+ "3.3": "3.3.3",
  }
+
  # the default if nothing is specified
- r_version = "4.1"
+ r_version = "4.1.0"
 
  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)
- )
+ # For versions of form x.y, we want to explicitly provide x.y.z - latest patchlevel
+ # available. Users can however explicitly specify the full version to get something specific
+ if r_version in version_map:
+ r_version = version_map[r_version]
 
  # translate to the full version string
- self._r_version = version_map.get(r_version)
+ self._r_version = r_version
 
  return self._r_version
 
@@ -141,6 +133,20 @@ def detect(self):
  self._runtime = "r-{}".format(str(self._checkpoint_date))
  return True
 
+ def get_env(self):
+ """
+ Set custom env vars needed for RStudio to load
+ """
+ return super().get_env() + [
+ # rstudio (rsession) can't seem to find R unless we explicitly tell it where
+ # it is - just $PATH isn't enough. I discovered these are the env vars it
+ # looks for by digging through RStudio source and finding
+ # https://github.com/rstudio/rstudio/blob/v2022.02.3+492/src/cpp/r/session/RDiscovery.cpp
+ ("R_HOME", f"/opt/R/{self.r_version}/lib/R"),
+ ("R_DOC_DIR", "${R_HOME}/doc"),
+ ("LD_LIBRARY_PATH", "${R_HOME}/lib:${LD_LIBRARY_PATH}"),
+ ]
+
  def get_path(self):
  """
  Return paths to be added to the PATH environment variable.
@@ -177,12 +183,6 @@ def get_packages(self):
  "sudo",
  "lsb-release",
  ]
- # For R 3.4 we use the default Ubuntu package, for other versions we
- # install from a different apt repository
- if V(self.r_version) < V("3.5"):
- packages.append("r-base")
- packages.append("r-base-dev")
- packages.append("libclang-dev")
 
  return super().get_packages().union(packages)
 
@@ -268,46 +268,25 @@ def get_build_scripts(self):
 
  cran_mirror_url = self.get_cran_mirror_url(self.checkpoint_date)
 
- # Determine which R apt repository should be enabled
- if V(self.r_version) >= V("3.5"):
- if V(self.r_version) >= V("4"):
- vs = "40"
- else:
- vs = "35"
-
  scripts = [
  (
  "root",
  rf"""
- echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran{vs}/" > /etc/apt/sources.list.d/r-ubuntu.list
- """,
- ),
- # Dont use apt-key directly, as gpg does not always respect *_proxy vars. This increase the chances
- # of being able to reach it from behind a firewall
- (
- "root",
- r"""
- wget --quiet -O - 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xe298a3a825c0d65dfd57cbb651716619e084dab9' | apt-key add -
- """,
- ),
- (
- "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 --no-install-recommends \
- r-base-core={R_version} \
- r-base-dev={R_version} \
  libclang-dev \
  libzmq3-dev > /dev/null && \
+ wget --quiet -O /tmp/r-{self.r_version}.deb \
+ https://cdn.rstudio.com/r/ubuntu-$(. /etc/os-release && echo $VERSION_ID | sed 's/\.//')/pkgs/r-{self.r_version}_1_amd64.deb && \
+ apt install --yes --no-install-recommends /tmp/r-{self.r_version}.deb > /dev/null && \
+ rm /tmp/r-{self.r_version}.deb && \
  apt-get -qq purge && \
  apt-get -qq clean && \
- rm -rf /var/lib/apt/lists/*
- """.format(
- R_version=self.r_version
- ),
+ rm -rf /var/lib/apt/lists/* && \
+ ln -s /opt/R/{self.r_version}/bin/R /usr/local/bin/R && \
+ ln -s /opt/R/{self.r_version}/bin/Rscript /usr/local/bin/Rscript && \
+ R --version
+ """,
  ),
  ]
 
@@ -326,9 +305,9 @@ def get_build_scripts(self):
  # Set paths so that RStudio shares libraries with base R
  # install. This first comments out any R_LIBS_USER that
  # might be set in /etc/R/Renviron and then sets it.
- r"""
- sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \
- echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
+ rf"""
+ sed -i -e '/^R_LIBS_USER=/s/^/#/' /opt/R/{self.r_version}/lib/R/etc/Renviron && \
+ echo "R_LIBS_USER=${{R_LIBS_USER}}" >> /opt/R/{self.r_version}/lib/R/etc/Renviron
  """,
  ),
  (
@@ -338,15 +317,12 @@ def get_build_scripts(self):
  # Quite hilarious, IMO.
  # See https://docs.rstudio.com/rspm/1.0.12/admin/binaries.html
  # Set mirror for RStudio too, by modifying rsession.conf
- r"""
+ rf"""
  R RHOME && \
- mkdir -p /usr/lib/R/etc /etc/rstudio && \
- echo 'options(repos = c(CRAN = "{cran_mirror_url}"))' > /usr/lib/R/etc/Rprofile.site && \
- echo 'options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))' >> /usr/lib/R/etc/Rprofile.site && \
+ mkdir -p /etc/rstudio && \
+ echo 'options(repos = c(CRAN = "{cran_mirror_url}"))' > /opt/R/{self.r_version}/lib/R/etc/Rprofile.site && \
  echo 'r-cran-repos={cran_mirror_url}' > /etc/rstudio/rsession.conf
- """.format(
- cran_mirror_url=cran_mirror_url
- ),
+ """,
  ),
  (
  "${NB_USER}",

tests/unit/test_r.py

@@ -7,20 +7,6 @@
 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", [("", "4.1"), ("3.6", "3.6"), ("3.5.1", "3.5")]
 )
@@ -43,7 +29,7 @@ def test_version_completion(tmpdir):
  f.write(f"r-3.6-2019-01-01")
 
  r = buildpacks.RBuildPack()
- assert r.r_version == "3.6.3-1bionic"
+ assert r.r_version == "3.6.3"
 
 
 @pytest.mark.parametrize(
@@ -104,50 +90,3 @@ def mock_request_head(url):
  assert r.get_mran_snapshot_url(
  requested
  ) == "https://mran.microsoft.com/snapshot/{}".format(expected.isoformat())
-
-
-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_cran_apt_repo(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_cran_apt_repo(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 apt repository
- 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 apt repository"
-
- # check that we install the right package
- for user, script in scripts:
- if "r-base-core=3.5" in script:
- break
- else:
- assert False, "Should have installed base R"