kopia lustrzana https://github.com/jupyterhub/repo2docker
Add more docstrings in R BuildPack
- Version-pin the devtools package installation independent of the current version - Make sure get_build_scripts is independent of contents of current repositorypull/210/head
yuvipanda
rodzic
25611f0230
commit
39d3e6a8f7
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@ -10,19 +10,19 @@ class RBuildPack(PythonBuildPack):
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This sets up R + RStudio + IRKernel for a repository that contains:
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1. A `runtime.txt` file with the text:
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1. A `runtime.txt` file with the text:
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r-<year>-<month>-<date>
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r-<year>-<month>-<date>
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Where 'year', 'month' and 'date' refer to a specific
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date snapshot of https://mran.microsoft.com/timemachine
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from which libraries are to be installed.
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Where 'year', 'month' and 'date' refer to a specific
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date snapshot of https://mran.microsoft.com/timemachine
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from which libraries are to be installed.
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2. An optional `install.R` file that will be executed at build time,
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and can be used for installing packages from both MRAN and GitHub.
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2. An optional `install.R` file that will be executed at build time,
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and can be used for installing packages from both MRAN and GitHub.
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It currently sets up R from the ubuntu repository being used. This
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is unideal, and we should investigate other solutions!
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The `r-base` package from Ubuntu apt repositories is used to install
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R itself, rather than any of the methods from https://cran.r-project.org/.
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"""
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@property
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def runtime(self):
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@ -59,23 +59,48 @@ class RBuildPack(PythonBuildPack):
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"""
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Check if current repo should be built with the R Build pack
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Note that we explicitly do *not* check if a requirements.txt
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is present here (by calling super().detect()).
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super().detect() is not called in this function - it would return false
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unless a `requirements.txt` is present and we do not want to require the
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presence of a `requirements.txt` to use R.
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Instead we just check if runtime.txt contains a string of the form
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`r-<YYYY>-<MM>-<DD>`
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"""
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# If no date is found, then self.checkpoint_date will be False
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# Otherwise, it'll be a date object, which will evaluate to True
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return bool(self.checkpoint_date)
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def get_path(self):
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"""
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Return paths to be added to the PATH environment variable.
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The RStudio package installs its binaries in a non-standard path,
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so we explicitly add that path to PATH.
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"""
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return super().get_path() + [
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'/usr/lib/rstudio-server/bin/'
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]
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def get_env(self):
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"""
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Return environment variables to be set.
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We want libraries to be installed in a path that users can write to
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without needing root. This is set via the `R_LIBS_USER` environment
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variable, so we set that here.
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"""
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return super().get_env() + [
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# This is the path where user libraries are installed
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('R_LIBS_USER', '${APP_BASE}/rlibs')
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]
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def get_packages(self):
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"""
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Return list of packages to be installed.
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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 super().get_packages().union([
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'r-base',
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# For rstudio
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@ -86,12 +111,29 @@ class RBuildPack(PythonBuildPack):
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])
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def get_build_scripts(self):
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mran_url = 'https://mran.microsoft.com/snapshot/{}'.format(
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self.checkpoint_date.isoformat()
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)
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"""
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Return series of build-steps common to all R repositories
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All scripts here should be independent of contents of the repository.
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This sets up:
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- A directory owned by non-root in ${R_LIBS_USER} for installing R packages into
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- RStudio
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- R's devtools package, at a particular frozen version (determined by MRAN)
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- IRKernel
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- nbrsessionproxy (to access RStudio via Jupyter Notebook)
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"""
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rstudio_url = 'https://download2.rstudio.org/rstudio-server-1.1.419-amd64.deb'
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# This is MD5, because that is what RStudio download page provides!
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rstudio_checksum = '24cd11f0405d8372b4168fc9956e0386'
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# Version of MRAN to pull devtools from.
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devtools_version = '2018-02-01'
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# IRKernel version - specified as a tag in the IRKernel repository
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irkernel_version = '0.8.11'
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return super().get_build_scripts() + [
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(
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"root",
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@ -100,19 +142,11 @@ class RBuildPack(PythonBuildPack):
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chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}
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"""
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),
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(
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"root",
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# We set the default CRAN repo to the MRAN one at given date
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# We set download method to be curl so we get HTTPS support
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r"""
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echo "options(repos = c(CRAN='{mran_url}'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site
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""".format(mran_url=mran_url)
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),
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(
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"root",
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# Install RStudio!
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r"""
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curl -L --fail {rstudio_url} > /tmp/rstudio.deb && \
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curl --quiet -L --fail {rstudio_url} > /tmp/rstudio.deb && \
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echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \
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dpkg -i /tmp/rstudio.deb && \
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rm /tmp/rstudio.deb
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@ -121,15 +155,6 @@ class RBuildPack(PythonBuildPack):
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rstudio_checksum=rstudio_checksum
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)
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),
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(
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"${NB_USER}",
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# Install a pinned version of IRKernel and set it up for use!
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r"""
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R --quiet -e "install.packages('devtools')" && \
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R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='0.8.11')" && \
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R --quiet -e "IRkernel::installspec(prefix='${NB_PYTHON_PREFIX}')"
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"""
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),
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(
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"${NB_USER}",
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# Install nbrsessionproxy
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@ -139,12 +164,42 @@ class RBuildPack(PythonBuildPack):
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jupyter nbextension install --py nbrsessionproxy --sys-prefix && \
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jupyter nbextension enable --py nbrsessionproxy --sys-prefix
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"""
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),
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(
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"${NB_USER}",
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# Install a pinned version of IRKernel and set it up for use!
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r"""
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R --quiet -e "install.packages('devtools', repos='https://mran.microsoft.com/snapshot/{devtools_version}', method='libcurl')" && \
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R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='{irkernel_version}')" && \
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R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
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""".format(
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devtools_version=devtools_version,
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irkernel_version=irkernel_version
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)
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)
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]
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def get_assemble_scripts(self):
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assemble_scripts = super().get_assemble_scripts()
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"""
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Return series of build-steps specific to this repository
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We set the snapshot date used to install R libraries from based on the
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contents of runtime.txt, and run the `install.R` script if it exists.
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"""
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mran_url = 'https://mran.microsoft.com/snapshot/{}'.format(
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self.checkpoint_date.isoformat()
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)
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assemble_scripts = super().get_assemble_scripts() + [
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(
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"root",
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# We set the default CRAN repo to the MRAN one at given date
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# We set download method to be curl so we get HTTPS support
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r"""
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echo "options(repos = c(CRAN='{mran_url}'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site
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""".format(mran_url=mran_url)
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),
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]
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if os.path.exists('install.R'):
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assemble_scripts += [
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(
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