kopia lustrzana https://github.com/jupyterhub/repo2docker
[MRG] Add support for installing different versions of R (#772)
[MRG] Add support for installing different versions of Rpull/797/head
Tim Head
GitHub
commit
bfbec349c2
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@ -212,7 +212,7 @@ If you only need to run things once during the build phase use :ref:`postBuild`.
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Sometimes you want to specify the version of the runtime
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(e.g. the version of Python or R),
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but the environment specification format don't let you specify this information
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but the environment specification format will not let you specify this information
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(e.g. requirements.txt or install.R).
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For these cases, we have a special file, ``runtime.txt``.
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@ -220,7 +220,7 @@ For these cases, we have a special file, ``runtime.txt``.
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``runtime.txt`` is only supported when used with environment specifications
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that do not already support specifying the runtime
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(e.g. when using ``environment.yml`` for conda or ``Project.toml`` for Julia,
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(when using ``environment.yml`` for conda or ``Project.toml`` for Julia,
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``runtime.txt`` will be ignored).
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To use python-2.7: add ``python-2.7`` in runtime.txt file.
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@ -231,8 +231,11 @@ Python 2 installed. To see a full example repository, visit our
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repo2docker uses R libraries pinned to a specific snapshot on
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`MRAN <https://mran.microsoft.com/documents/rro/reproducibility>`_.
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You need to have a ``runtime.txt`` file that is formatted as
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``r-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot at MRAN that will be
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used for installing libraries.
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``r-<RVERSION>-<YYYY>-<MM>-<DD>``, where YYYY-MM-DD is a snapshot at MRAN that will be
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used for installing libraries. You can set RVERSION to 3.4, 3.5 or 3.6 to select
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the version of R you want to use. If you do not specify a R version the latest
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released version will be used (currently R 3.6). You can also specify the exact
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patch release you want to use for the 3.5 and 3.6 series.
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To see an example R repository, visit our `R
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example in binder-examples <https://github.com/binder-examples/r/blob/master/runtime.txt>`_.
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@ -49,10 +49,11 @@ Julia versions 0.6.x and earlier are supported via a :ref:`REQUIRE <REQUIRE>` fi
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R
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~
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Only R 3.4.4 is currently supported, which is installed via ``apt`` from the
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`ubuntu bionic repository <https://packages.ubuntu.com/bionic/r-base>`_.
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The default version of R is currently R 3.6.1. You can select the version of
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R you want to use by specifying it in the :ref:`runtime.txt <runtime.txt>`
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file.
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We support R versions 3.4, 3.5 and 3.6.
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Why is my repository is failing to build with ``ResolvePackageNotFound`` ?
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@ -149,17 +150,17 @@ notebooks (among others).
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the container, use the ``--volumes`` option instead. Similarly,
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for a fully customized user Dockerfile, this option is not
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guaranteed to work.
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Why is my R shiny app not launching?
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----------------------------------------------------------------------------------
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If you are trying to run an R shiny app using the ``/shiny/folder_containing_shiny``
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url option, but the launch returns "The application exited during initialization.",
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there might be something wrong with the specification of the app. One way of debugging
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the app in the container is by running the ``rstudio`` url, open either the ui or
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server file for the app, and run the app in the container rstudio. This way you can
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see the rstudio logs as it tries to initialise the shiny app. If you a missing a
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the app in the container is by running the ``rstudio`` url, open either the ui or
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server file for the app, and run the app in the container rstudio. This way you can
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see the rstudio logs as it tries to initialise the shiny app. If you a missing a
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package or other dependency for the container, this will be obvious at this stage.
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@ -2,6 +2,8 @@ import re
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import os
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import datetime
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from distutils.version import LooseVersion as V
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from .python import PythonBuildPack
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@ -55,6 +57,41 @@ class RBuildPack(PythonBuildPack):
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return self._runtime
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@property
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def r_version(self):
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"""Detect the R version for a given `runtime.txt`
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Will return the version specified by the user or the current default
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version.
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"""
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version_map = {
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"3.4": "3.4",
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"3.5": "3.5.3-1bionic",
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"3.5.0": "3.5.0-1bionic",
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"3.5.1": "3.5.1-2bionic",
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"3.5.2": "3.5.2-1bionic",
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"3.5.3": "3.5.3-1bionic",
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"3.6": "3.6.1-3bionic",
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"3.6.0": "3.6.0-2bionic",
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"3.6.1": "3.6.1-3bionic",
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}
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# the default if nothing is specified
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r_version = "3.6"
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if not hasattr(self, "_r_version"):
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parts = self.runtime.split("-")
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if len(parts) == 5:
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r_version = parts[1]
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if r_version not in version_map:
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raise ValueError(
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"Version '{}' of R is not supported.".format(r_version)
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)
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# translate to the full version string
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self._r_version = version_map.get(r_version)
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return self._r_version
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@property
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def checkpoint_date(self):
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"""
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@ -63,11 +100,14 @@ class RBuildPack(PythonBuildPack):
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Returns '' if no date is specified
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"""
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if not hasattr(self, "_checkpoint_date"):
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match = re.match(r"r-(\d\d\d\d)-(\d\d)-(\d\d)", self.runtime)
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match = re.match(r"r-(\d.\d(.\d)?-)?(\d\d\d\d)-(\d\d)-(\d\d)", self.runtime)
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if not match:
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self._checkpoint_date = False
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else:
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self._checkpoint_date = datetime.date(*[int(s) for s in match.groups()])
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# turn the last three groups of the match into a date
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self._checkpoint_date = datetime.date(
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*[int(s) for s in match.groups()[-3:]]
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)
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return self._checkpoint_date
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@ -127,20 +167,19 @@ class RBuildPack(PythonBuildPack):
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We install a base version of R, and packages required for RStudio to
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be installed.
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"""
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return (
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super()
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.get_packages()
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.union(
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[
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"r-base",
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# For rstudio
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"psmisc",
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"libapparmor1",
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"sudo",
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"lsb-release",
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]
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)
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)
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packages = [
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# For rstudio
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"psmisc",
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"libapparmor1",
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"sudo",
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"lsb-release",
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]
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# For R 3.4 we use the default Ubuntu package, for other versions we
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# install from a different PPA
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if V(self.r_version) < V("3.5"):
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packages.append("r-base")
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return super().get_packages().union(packages)
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def get_build_scripts(self):
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"""
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@ -180,7 +219,38 @@ class RBuildPack(PythonBuildPack):
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self.checkpoint_date.isoformat()
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)
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scripts = [
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scripts = []
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# For R 3.4 we want to use the default Ubuntu package but otherwise
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# we use the packages from a PPA
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if V(self.r_version) >= V("3.5"):
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scripts += [
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(
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"root",
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r"""
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echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" > /etc/apt/sources.list.d/r3.6-ubuntu.list
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""",
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),
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(
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"root",
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r"""
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apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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""",
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),
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(
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"root",
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r"""
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apt-get update && \
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apt-get install --yes r-base={} && \
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apt-get -qq purge && \
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apt-get -qq clean && \
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rm -rf /var/lib/apt/lists/*
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""".format(
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self.r_version
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),
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),
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]
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scripts += [
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(
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"root",
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r"""
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@ -277,17 +347,32 @@ class RBuildPack(PythonBuildPack):
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]
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if "r" in self.stencila_contexts:
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scripts += [
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(
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"${NB_USER}",
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# Install and register stencila library
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r"""
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R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \
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R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
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R --quiet -e "stencila::register()"
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""",
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)
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]
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# new versions of R require a different way of installing bioconductor
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if V(self.r_version) <= V("3.5"):
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scripts += [
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(
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"${NB_USER}",
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# Install and register stencila library
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r"""
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R --quiet -e "source('https://bioconductor.org/biocLite.R'); biocLite('graph')" && \
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R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
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R --quiet -e "stencila::register()"
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""",
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)
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]
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else:
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scripts += [
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(
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"${NB_USER}",
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# Install and register stencila library
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r"""
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R --quiet -e "install.packages('BiocManager'); BiocManager::install(); BiocManager::install(c('graph'))" && \
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R --quiet -e "devtools::install_github('stencila/r', ref = '361bbf560f3f0561a8612349bca66cd8978f4f24')" && \
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R --quiet -e "stencila::register()"
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""",
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)
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]
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return super().get_build_scripts() + scripts
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@ -0,0 +1,109 @@
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from datetime import date
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import pytest
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from repo2docker import buildpacks
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def test_unsupported_version(tmpdir):
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tmpdir.chdir()
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with open("runtime.txt", "w") as f:
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f.write("r-3.8-2019-01-01")
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r = buildpacks.RBuildPack()
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with pytest.raises(ValueError) as excinfo:
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# access the property to trigger the exception
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_ = r.r_version
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# check the version is mentioned in the exception
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assert "'3.8'" in str(excinfo.value)
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@pytest.mark.parametrize(
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"runtime_version, expected", [("", "3.6"), ("3.6", "3.6"), ("3.5.1", "3.5")]
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)
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def test_version_specification(tmpdir, runtime_version, expected):
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tmpdir.chdir()
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with open("runtime.txt", "w") as f:
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if runtime_version:
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runtime_version += "-"
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f.write(f"r-{runtime_version}2019-01-01")
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r = buildpacks.RBuildPack()
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assert r.r_version.startswith(expected)
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def test_version_completion(tmpdir):
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tmpdir.chdir()
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with open("runtime.txt", "w") as f:
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f.write(f"r-3.6-2019-01-01")
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r = buildpacks.RBuildPack()
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assert r.r_version == "3.6.1-3bionic"
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@pytest.mark.parametrize(
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"runtime, expected",
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[
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("r-2019-01-01", (2019, 1, 1)),
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("r-3.6.1-2019-01-01", (2019, 1, 1)),
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("r-3.5-2019-01-01", (2019, 1, 1)),
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],
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)
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def test_mran_date(tmpdir, runtime, expected):
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tmpdir.chdir()
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with open("runtime.txt", "w") as f:
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f.write(runtime)
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r = buildpacks.RBuildPack()
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assert r.checkpoint_date == date(*expected)
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def test_install_from_base(tmpdir):
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# check that for R==3.4 we install from ubuntu
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tmpdir.chdir()
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with open("runtime.txt", "w") as f:
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f.write("r-3.4-2019-01-02")
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r = buildpacks.RBuildPack()
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assert "r-base" in r.get_packages()
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def test_install_from_ppa(tmpdir):
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# check that for R>3.4 we don't install r-base from Ubuntu
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tmpdir.chdir()
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with open("runtime.txt", "w") as f:
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f.write("r-3.5-2019-01-02")
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r = buildpacks.RBuildPack()
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assert "r-base" not in r.get_packages()
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def test_custom_ppa(tmpdir):
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tmpdir.chdir()
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with open("runtime.txt", "w") as f:
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f.write("r-3.5-2019-01-02")
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r = buildpacks.RBuildPack()
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scripts = r.get_build_scripts()
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# check that at least one of the build scripts adds this new PPA
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for user, script in scripts:
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if "https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" in script:
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break
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else:
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assert False, "Should have added a new PPA"
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# check that we install the right package
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for user, script in scripts:
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if "r-base=3.5" in script:
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break
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else:
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assert False, "Should have installed base R"
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