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Start RStudio if R is installed via conda

pull/838/head
Uwe L. Korn 2020-01-29 17:48:39 +01:00
rodzic db9f1ff9ce
commit e89378aea0
3 zmienionych plików z 160 dodań i 64 usunięć
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76
repo2docker/buildpacks/_r_base.py 100644
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@ -0,0 +1,76 @@
"""
Base information for using R in BuildPacks.
Keeping this in r.py would lead to cyclic imports.
"""
# Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/
RSTUDIO_URL = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb"
# This is MD5, because that is what RStudio download page provides!
RSTUDIO_CHECKSUM = "d33881b9ab786c09556c410e7dc477de"
# Via https://www.rstudio.com/products/shiny/download-server/
SHINY_URL = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb"
SHINY_CHECKSUM = "9aeef6613e7f58f21c97a4600921340e"
# Version of MRAN to pull devtools from.
DEVTOOLS_VERSION = "2018-02-01"
# IRKernel version - specified as a tag in the IRKernel repository
IRKERNEL_VERSION = "1.0.2"
def rstudio_base_scripts():
"""Base steps to install RStudio and shiny-server."""
return [
(
"root",
# Install RStudio!
r"""
curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \
echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \
apt-get update && \
apt install -y /tmp/rstudio.deb && \
rm /tmp/rstudio.deb && \
apt-get -qq purge && \
apt-get -qq clean && \
rm -rf /var/lib/apt/lists/*
""".format(
rstudio_url=RSTUDIO_URL, rstudio_checksum=RSTUDIO_CHECKSUM
),
),
(
"root",
# Install Shiny Server!
r"""
curl --silent --location --fail {url} > {deb} && \
echo '{checksum} {deb}' | md5sum -c - && \
dpkg -i {deb} && \
rm {deb}
""".format(
url=SHINY_URL, checksum=SHINY_CHECKSUM, deb="/tmp/shiny.deb"
),
),
(
"${NB_USER}",
# Install nbrsessionproxy
r"""
pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/7ac0125.zip && \
pip install --no-cache-dir jupyter-rsession-proxy==1.0b6 && \
jupyter serverextension enable jupyter_server_proxy --sys-prefix && \
jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \
jupyter nbextension enable --py jupyter_server_proxy --sys-prefix
""",
),
(
# Not all of these locations are configurable; so we make sure
# they exist and have the correct permissions
"root",
r"""
install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid
""",
),
]

77
repo2docker/buildpacks/conda/__init__.py
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@ -6,10 +6,12 @@ from collections import Mapping
from ruamel.yaml import YAML
from ..base import BaseImage
from .._r_base import rstudio_base_scripts, IRKERNEL_VERSION
from ...utils import is_local_pip_requirement
# pattern for parsing conda dependency line
PYTHON_REGEX = re.compile(r"python\s*=+\s*([\d\.]*)")
R_REGEX = re.compile(r"r-base\s*=+\s*([\d\.]*)")
# current directory
HERE = os.path.dirname(os.path.abspath(__file__))
@ -179,6 +181,7 @@ class CondaBuildPack(BaseImage):
Will return 'x.y' if version is found (e.g '3.6'),
or a Falsy empty string '' if not found.
Version information below the minor level is dropped.
"""
if not hasattr(self, "_python_version"):
py_version = None
@ -204,6 +207,40 @@ class CondaBuildPack(BaseImage):
return self._python_version
@property
def r_version(self):
"""Detect the Python version for a given `environment.yml`
Will return 'x.y' if version is found (e.g '3.6'),
or a Falsy empty string '' if not found.
"""
if not hasattr(self, "_r_version"):
self._r_version = ""
env = self.environment_yaml
for dep in env.get("dependencies", []):
if not isinstance(dep, str):
continue
match = R_REGEX.match(dep)
if not match:
continue
self._r_version = match.group(1)
break
return self._r_version
@property
def uses_r(self):
"""Detect whether the user also installs R packages.
Will return True when a package prefixed with 'r-' is being installed.
"""
if not hasattr(self, "_uses_r"):
deps = self.environment_yaml.get("dependencies", [])
self._uses_r = any(dep.startswith("r-") for dep in deps)
return self._uses_r
@property
def py2(self):
"""Am I building a Python 2 kernel environment?"""
@ -241,6 +278,46 @@ class CondaBuildPack(BaseImage):
),
)
)
if self.uses_r:
if self.r_version:
r_pin = "=" + self.r_version
else:
r_pin = ""
scripts.append(
(
"${NB_USER}",
r"""
conda install -p {0} r-base{1} r-irkernel={2} r-devtools && \
conda clean --all -f -y && \
conda list -p {0}
""".format(
env_prefix, r_pin, IRKERNEL_VERSION
),
)
)
scripts += rstudio_base_scripts()
scripts += [
(
"root",
r"""
echo auth-none=1 >> /etc/rstudio/rserver.conf && \
echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \
echo "rsession-which-r={0}/bin/R" >> /etc/rstudio/rserver.conf
""".format(
env_prefix
),
),
(
"${NB_USER}",
# Install a pinned version of IRKernel and set it up for use!
r"""
R --quiet -e "IRkernel::installspec(prefix='{0}')"
""".format(
env_prefix
),
),
]
return scripts
def get_preassemble_scripts(self):

71
repo2docker/buildpacks/r.py
Wyświetl plik

@ -5,6 +5,7 @@ import datetime
from distutils.version import LooseVersion as V
from .python import PythonBuildPack
from ._r_base import rstudio_base_scripts, DEVTOOLS_VERSION, IRKERNEL_VERSION
class RBuildPack(PythonBuildPack):
@ -206,21 +207,6 @@ class RBuildPack(PythonBuildPack):
contents of runtime.txt.
"""
# Via https://rstudio.com/products/rstudio/download-server/debian-ubuntu/
rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5001-amd64.deb"
# This is MD5, because that is what RStudio download page provides!
rstudio_checksum = "d33881b9ab786c09556c410e7dc477de"
# Via https://www.rstudio.com/products/shiny/download-server/
shiny_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.12.933-amd64.deb"
shiny_checksum = "9aeef6613e7f58f21c97a4600921340e"
# Version of MRAN to pull devtools from.
devtools_version = "2018-02-01"
# IRKernel version - specified as a tag in the IRKernel repository
irkernel_version = "1.0.2"
mran_url = "https://mran.microsoft.com/snapshot/{}".format(
self.checkpoint_date.isoformat()
)
@ -261,38 +247,17 @@ class RBuildPack(PythonBuildPack):
),
]
scripts += [
scripts.append(
(
"root",
r"""
mkdir -p ${R_LIBS_USER} && \
chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}
""",
),
(
"root",
# Install RStudio!
r"""
curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \
echo '{rstudio_checksum} /tmp/rstudio.deb' | md5sum -c - && \
dpkg -i /tmp/rstudio.deb && \
rm /tmp/rstudio.deb
""".format(
rstudio_url=rstudio_url, rstudio_checksum=rstudio_checksum
),
),
(
"root",
# Install Shiny Server!
r"""
curl --silent --location --fail {url} > {deb} && \
echo '{checksum} {deb}' | md5sum -c - && \
dpkg -i {deb} && \
rm {deb}
""".format(
url=shiny_url, checksum=shiny_checksum, deb="/tmp/shiny.deb"
),
),
)
)
scripts += rstudio_base_scripts()
scripts += [
(
"root",
# Set paths so that RStudio shares libraries with base R
@ -303,17 +268,6 @@ class RBuildPack(PythonBuildPack):
echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
""",
),
(
"${NB_USER}",
# Install nbrsessionproxy
r"""
pip install --no-cache-dir https://github.com/jupyterhub/jupyter-server-proxy/archive/7ac0125.zip && \
pip install --no-cache-dir jupyter-rsession-proxy==1.0b6 && \
jupyter serverextension enable jupyter_server_proxy --sys-prefix && \
jupyter nbextension install --py jupyter_server_proxy --sys-prefix && \
jupyter nbextension enable --py jupyter_server_proxy --sys-prefix
""",
),
(
"${NB_USER}",
# Install a pinned version of IRKernel and set it up for use!
@ -322,7 +276,7 @@ class RBuildPack(PythonBuildPack):
R --quiet -e "devtools::install_github('IRkernel/IRkernel', ref='{irkernel_version}')" && \
R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
""".format(
devtools_version=devtools_version, irkernel_version=irkernel_version
devtools_version=DEVTOOLS_VERSION, irkernel_version=IRKERNEL_VERSION
),
),
(
@ -344,17 +298,6 @@ class RBuildPack(PythonBuildPack):
mran_url=mran_url
),
),
(
# Not all of these locations are configurable; so we make sure
# they exist and have the correct permissions
"root",
r"""
install -o ${NB_USER} -g ${NB_USER} -d /var/log/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} -d /var/lib/shiny-server && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/log/shiny-server.log && \
install -o ${NB_USER} -g ${NB_USER} /dev/null /var/run/shiny-server.pid
""",
),
]
if "r" in self.stencila_contexts: