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apt.txt is installed after R, but user is NB_USER not root #1114

Closed
manics opened this issue Jan 19, 2022 · 1 comment · Fixed by #1115
Closed

apt.txt is installed after R, but user is NB_USER not root #1114

manics opened this issue Jan 19, 2022 · 1 comment · Fixed by #1115
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@manics
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manics commented Jan 19, 2022 •
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Bug description

Reported in
https://discourse.jupyter.org/t/binder-failing-to-build-when-using-apt-txt-for-r-package-dependencies/12659

It sounds like R dependencies are installed before apt.txt. The last R installation script currently runs as NB_USER (changed in #1104):

repo2docker/repo2docker/buildpacks/r.py

Lines 347 to 357 in a37a205

(
"${NB_USER}",
# Install a pinned version of devtools, IRKernel and shiny
r"""
R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='{devtools_cran_mirror_url}')" && \
R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
""".format(
devtools_cran_mirror_url=self.get_devtools_snapshot_url()
),
),
]

whereas previously it ran as root

repo2docker/repo2docker/buildpacks/r.py

Lines 317 to 327 in d688997

(
"root",
# We set the default CRAN repo to the MRAN one at given date
# We set download method to be curl so we get HTTPS support
r"""
echo "options(repos = c(CRAN='{mran_url}'), download.file.method = 'libcurl')" > /etc/R/Rprofile.site
""".format(
mran_url=mran_url
),
),
]

repo2docker/repo2docker/buildpacks/base.py

Lines 473 to 477 in a37a205

last_user = "root"
for user, script in self.get_preassemble_scripts():
if last_user != user:
preassemble_script_directives.append("USER {}".format(user))
last_user = user

only checks whether the requested user is root, it doesn't check what the actual user is, so NB_USER remains in the Dockerfile and therefore apt.txt fails.

How to reproduce

https://mybinder.org/v2/gh/admivsn/r_with_python/f74afef0105dfae48bf5b4a552a44a392092e7d7

Example log below:

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2dockercni2iasz'...
HEAD is now at f74afef Create apt.txt
Building conda environment for python=3.7Using RBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/69 : FROM buildpack-deps:bionic
 ---> 872a6bfe806a
Step 2/69 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 5429cf904159
Step 3/69 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 3a6d744f8fc2
Step 4/69 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 3e5043c5a3b9
Step 5/69 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> f6d7dfc1fd91
Step 6/69 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> 6f250ad18d9c
Step 7/69 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> 46a25e22e1b9
Step 8/69 : ENV SHELL /bin/bash
 ---> Using cache
 ---> 22aaa3abc963
Step 9/69 : ARG NB_USER
 ---> Using cache
 ---> 06858f8ceec7
Step 10/69 : ARG NB_UID
 ---> Using cache
 ---> 824b8ce23dcf
Step 11/69 : ENV USER ${NB_USER}
 ---> Using cache
 ---> 0f86c6990172
Step 12/69 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 7fb25afd19b7
Step 13/69 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
 ---> 8c496325764b
Step 14/69 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> c17414a3f0a6
Step 15/69 : RUN apt-get -qq update &&     apt-get -qq install --yes        libapparmor1        lsb-release        psmisc        sudo        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 1a5c890fbaa5
Step 16/69 : EXPOSE 8888
 ---> Using cache
 ---> 9217a48f49e1
Step 17/69 : ENV APP_BASE /srv
 ---> Using cache
 ---> 37e89778e15e
Step 18/69 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> a9b7e7f7317a
Step 19/69 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 71d38a4aa907
Step 20/69 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 03e8b60712bc
Step 21/69 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 60dba4756e63
Step 22/69 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock
 ---> Using cache
 ---> 5671ec76c193
Step 23/69 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> 075b7f3bf2ea
Step 24/69 : ENV R_LIBS_USER ${APP_BASE}/rlibs
 ---> Using cache
 ---> 61b748230d31
Step 25/69 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:/usr/lib/rstudio-server/bin/:${PATH}
 ---> Using cache
 ---> aad718415127
Step 26/69 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> b42df1bd8a3e
Step 27/69 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock
 ---> Using cache
 ---> a8baeac06b9b
Step 28/69 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash
 ---> Using cache
 ---> cfa934b5e1a8
Step 29/69 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env
 ---> Using cache
 ---> a196f765486c
Step 30/69 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 9abe1b6c1107
Step 31/69 : RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/" > /etc/apt/sources.list.d/r-ubuntu.list
 ---> Using cache
 ---> 8a347850c1f1
Step 32/69 : RUN wget --quiet -O - 'https://keyserver.ubuntu.com/pks/lookup?op=get&search=0xe298a3a825c0d65dfd57cbb651716619e084dab9' | apt-key add -
 ---> Using cache
 ---> efc03030785e
Step 33/69 : RUN apt-get update > /dev/null && apt-get install --yes r-base=4.1.2-1.1804.0 r-base-core=4.1.2-1.1804.0         r-base-dev=4.1.2-1.1804.0         r-recommended=4.1.2-1.1804.0         libclang-dev         libzmq3-dev > /dev/null && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 882e79479d57
Step 34/69 : RUN curl --silent --location --fail https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2021.09.1-372-amd64.deb > /tmp/rstudio.deb && curl --silent --location --fail https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.17.973-amd64.deb > /tmp/shiny.deb && echo 'c58df09468870b89f1796445853dce2dacaa0fc5b7bb1f92b036fa8da1d1f8a3 /tmp/rstudio.deb' | sha256sum -c - && echo '80f1e48f6c824be7ef9c843bb7911d4981ac7e8a963e0eff823936a8b28476ee /tmp/shiny.deb' | sha256sum -c - && apt-get update > /dev/null && apt install -y /tmp/rstudio.deb /tmp/shiny.deb > /dev/null && rm /tmp/rstudio.deb && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 410758d8fdc1
Step 35/69 : USER ${NB_USER}
 ---> Using cache
 ---> 1d0ee5a2a9cd
Step 36/69 : RUN pip install --no-cache     jupyter-rsession-proxy==2.0.1     jupyter-shiny-proxy==1.1
 ---> Using cache
 ---> 40f2aa8f79eb
Step 37/69 : USER root
 ---> Using cache
 ---> 2099c9ca9b44
Step 38/69 : RUN 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
 ---> Using cache
 ---> b78484028fe4
Step 39/69 : RUN mkdir -p ${R_LIBS_USER} && chown -R ${NB_USER}:${NB_USER} ${R_LIBS_USER}
 ---> Using cache
 ---> a2dbf86c0c7a
Step 40/69 : RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
 ---> Using cache
 ---> 22253891a0a5
Step 41/69 : RUN R RHOME && mkdir -p /usr/lib/R/etc /etc/rstudio && echo 'options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/bionic/2018-11-01+Y3Jhbjs0MDNGMDM0MA"))' > /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 && echo 'r-cran-repos=https://packagemanager.rstudio.com/all/__linux__/bionic/2018-11-01+Y3Jhbjs0MDNGMDM0MA' > /etc/rstudio/rsession.conf
 ---> Running in cb2a4a77f18b
/usr/lib/R
Removing intermediate container cb2a4a77f18b
 ---> 194460591662
Step 42/69 : USER ${NB_USER}
 ---> Running in 0523d57a95d5
Removing intermediate container 0523d57a95d5
 ---> 02dac382cbb7
Step 43/69 : RUN R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg')" && R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')"
 ---> Running in 3b49ef71e28c
> install.packages(c('devtools', 'IRkernel', 'shiny'), repos='https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg')
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�[0m�[91mtrying URL 'https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg/src/contrib/cachem_1.0.6.tar.gz'
�[0m�[91mContent type 'binary/octet-stream' length 68513 bytes (66 KB)
===========�[0m�[91m============�[0m�[91m============�[0m�[91m===============
downloaded 66 KB

�[0m�[91mtrying URL 'https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg/src/contrib/devtools_2.4.3.tar.gz'
�[0m�[91mContent type 'binary/octet-stream' length 421402 bytes (411 KB)
�[0m�[91m=�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m=�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m==�[0m�[91m====�[0m�[91m==�[0m�[91m==�[0m�[91m==
downloaded 411 KB

�[0m�[91mtrying URL 'https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg/src/contrib/IRkernel_1.3.tar.gz'
�[0m�[91mContent type 'binary/octet-stream' length 221354 bytes (216 KB)
===�[0m�[91m====�[0m�[91m===�[0m�[91m====�[0m�[91m====�[0m�[91m====�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m==�[0m�[91m====�[0m�[91m===�[0m�[91m====�[0m�[91m====�[0m�[91m===�[0m�[91m===
downloaded 216 KB

�[0m�[91mtrying URL 'https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg/src/contrib/shiny_1.7.1.tar.gz'
�[0m�[91mContent type 'binary/octet-stream' length 4155823 bytes (4.0 MB)
�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m===�[0m�[91m==�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m==�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=�[0m�[91m=
downloaded 4.0 MB

�[0m�[91m* installing *binary* package ‘pkgconfig’ ...
�[0m�[91m* DONE (pkgconfig)
�[0m�[91m* installing *binary* package ‘sys’ ...
�[0m�[91m* DONE (sys)
�[0m�[91m* installing *binary* package ‘zip’ ...
�[0m�[91m* DONE (zip)
�[0m�[91m* installing *binary* package ‘gitcreds’ ...
�[0m�[91m* DONE (gitcreds)
�[0m�[91m* installing *binary* package ‘ini’ ...
�[0m�[91m* DONE (ini)
�[0m�[91m* installing *binary* package ‘xfun’ ...
�[0m�[91m* DONE (xfun)
�[0m�[91m* installing *binary* package ‘fansi’ ...
�[0m�[91m* DONE (fansi)
�[0m�[91m* installing *binary* package ‘utf8’ ...
�[0m�[91m* DONE (utf8)
�[0m�[91m* installing *binary* package ‘clipr’ ...
�[0m�[91m* DONE (clipr)
�[0m�[91m* installing *binary* package ‘curl’ ...
�[0m�[91m* DONE (curl)
�[0m�[91m* installing *binary* package ‘rappdirs’ ...
�[0m�[91m* DONE (rappdirs)
�[0m�[91m* installing *binary* package ‘rprojroot’ ...
�[0m�[91m* DONE (rprojroot)
�[0m�[91m* installing *binary* package ‘whisker’ ...
�[0m�[91m* DONE (whisker)
�[0m�[91m* installing *binary* package ‘yaml’ ...
�[0m�[91m* DONE (yaml)
�[0m�[91m* installing *binary* package ‘prettyunits’ ...
�[0m�[91m* DONE (prettyunits)
�[0m�[91m* installing *binary* package ‘brew’ ...
�[0m�[91m* DONE (brew)
�[0m�[91m* installing *binary* package ‘stringi’ ...
�[0m�[91m* DONE (stringi)
�[0m�[91m* installing *binary* package ‘xml2’ ...
�[0m�[91m* DONE (xml2)
�[0m�[91m* installing *binary* package ‘cpp11’ ...
�[0m�[91m* DONE (cpp11)
�[0m�[91m* installing *binary* package ‘brio’ ...
�[0m�[91m* DONE (brio)
�[0m�[91m* installing *binary* package ‘magrittr’ ...
�[0m�[91m* DONE (magrittr)
�[0m�[91m* installing *binary* package ‘praise’ ...
�[0m�[91m* DONE (praise)
�[0m�[91m* installing *binary* package ‘ps’ ...
�[0m�[91m* DONE (ps)
�[0m�[91m* installing *binary* package ‘base64enc’ ...
�[0m�[91m* DONE (base64enc)
�[0m�[91m* installing *binary* package ‘Rcpp’ ...
�[0m�[91m* DONE (Rcpp)
�[0m�[91m* installing *binary* package ‘fs’ ...
�[0m�[91m* DONE (fs)
�[0m�[91m* installing *binary* package ‘remotes’ ...
�[0m�[91m* DONE (remotes)
�[0m�[91m* installing *binary* package ‘rlang’ ...
�[0m�[91m* DONE (rlang)
�[0m�[91m* installing *binary* package ‘rstudioapi’ ...
�[0m�[91m* DONE (rstudioapi)
�[0m�[91m* installing *binary* package ‘withr’ ...
�[0m�[91m* DONE (withr)
�[0m�[91m* installing *binary* package ‘evaluate’ ...
�[0m�[91m* DONE (evaluate)
�[0m�[91m* installing *binary* package ‘pbdZMQ’ ...
�[0m�[91m* DONE (pbdZMQ)
�[0m�[91m* installing *binary* package ‘crayon’ ...
�[0m�[91m* DONE (crayon)
�[0m�[91m* installing *binary* package ‘jsonlite’ ...
�[0m�[91m* DONE (jsonlite)
�[0m�[91m* installing *binary* package ‘uuid’ ...
�[0m�[91m* DONE (uuid)
�[0m�[91m* installing *binary* package ‘digest’ ...
�[0m�[91m* DONE (digest)
�[0m�[91m* installing *binary* package ‘mime’ ...
�[0m�[91m* DONE (mime)
�[0m�[91m* installing *binary* package ‘xtable’ ...
�[0m�[91m* DONE (xtable)
�[0m�[91m* installing *binary* package ‘R6’ ...
�[0m�[91m* DONE (R6)
�[0m�[91m* installing *binary* package ‘sourcetools’ ...
�[0m�[91m* DONE (sourcetools)
�[0m�[91m* installing *binary* package ‘fastmap’ ...
�[0m�[91m* DONE (fastmap)
�[0m�[91m* installing *binary* package ‘commonmark’ ...
�[0m�[91m* DONE (commonmark)
�[0m�[91m* installing *binary* package ‘glue’ ...
�[0m�[91m* DONE (glue)
�[0m�[91m* installing *binary* package ‘askpass’ ...
�[0m�[91m* DONE (askpass)
�[0m�[91m* installing *binary* package ‘highr’ ...
�[0m�[91m* DONE (highr)
�[0m�[91m* installing *binary* package ‘diffobj’ ...
�[0m�[91m* DONE (diffobj)
�[0m�[91m* installing *binary* package ‘purrr’ ...
�[0m�[91m* DONE (purrr)
�[0m�[91m* installing *binary* package ‘processx’ ...
�[0m�[91m* DONE (processx)
�[0m�[91m* installing *binary* package ‘stringr’ ...
�[0m�[91m* DONE (stringr)
�[0m�[91m* installing *binary* package ‘cli’ ...
�[0m�[91m* DONE (cli)
�[0m�[91m* installing *binary* package ‘desc’ ...
�[0m�[91m* DONE (desc)
�[0m�[91m* installing *binary* package ‘ellipsis’ ...
�[0m�[91m* DONE (ellipsis)
�[0m�[91m* installing *binary* package ‘lifecycle’ ...
�[0m�[91m* DONE (lifecycle)
�[0m�[91m* installing *binary* package ‘rversions’ ...
�[0m�[91m* DONE (rversions)
�[0m�[91m* installing *binary* package ‘htmltools’ ...
�[0m�[91m* DONE (htmltools)
�[0m�[91m* installing *binary* package ‘later’ ...
�[0m�[91m* DONE (later)
�[0m�[91m* installing *binary* package ‘cachem’ ...
�[0m�[91m* DONE (cachem)
�[0m�[91m* installing *binary* package ‘vctrs’ ...
�[0m�[91m* DONE (vctrs)
�[0m�[91m* installing *binary* package ‘openssl’ ...
�[0m�[91m* DONE (openssl)
�[0m�[91m* installing *binary* package ‘xopen’ ...
�[0m�[91m* DONE (xopen)
�[0m�[91m* installing *binary* package ‘knitr’ ...
�[0m�[91m* DONE (knitr)
�[0m�[91m* installing *binary* package ‘sass’ ...
�[0m�[91m* DONE (sass)
�[0m�[91m* installing *binary* package ‘jquerylib’ ...
�[0m�[91m* DONE (jquerylib)
�[0m�[91m* installing *binary* package ‘callr’ ...
�[0m�[91m* DONE (callr)
�[0m�[91m* installing *binary* package ‘memoise’ ...
�[0m�[91m* DONE (memoise)
�[0m�[91m* installing *binary* package ‘pkgload’ ...
�[0m�[91m* DONE (pkgload)
�[0m�[91m* installing *binary* package ‘sessioninfo’ ...
�[0m�[91m* DONE (sessioninfo)
�[0m�[91m* installing *binary* package ‘fontawesome’ ...
�[0m�[91m* DONE (fontawesome)
�[0m�[91m* installing *binary* package ‘promises’ ...
�[0m�[91m* DONE (promises)
�[0m�[91m* installing *binary* package ‘credentials’ ...
�[0m�[91m* DONE (credentials)
�[0m�[91m* installing *binary* package ‘pillar’ ...
�[0m�[91m* DONE (pillar)
�[0m�[91m* installing *binary* package ‘httr’ ...
�[0m�[91m* DONE (httr)
�[0m�[91m* installing *binary* package ‘pkgbuild’ ...
�[0m�[91m* DONE (pkgbuild)
�[0m�[91m* installing *binary* package ‘roxygen2’ ...
�[0m�[91m* DONE (roxygen2)
�[0m�[91m* installing *binary* package ‘httpuv’ ...
�[0m�[91m* DONE (httpuv)
�[0m�[91m* installing *binary* package ‘bslib’ ...
�[0m�[91m* DONE (bslib)
�[0m�[91m* installing *binary* package ‘tibble’ ...
�[0m�[91m* DONE (tibble)
�[0m�[91m* installing *binary* package ‘gert’ ...
�[0m�[91m* DONE (gert)
�[0m�[91m* installing *binary* package ‘gh’ ...
�[0m�[91m* DONE (gh)
�[0m�[91m* installing *binary* package ‘rcmdcheck’ ...
�[0m�[91m* DONE (rcmdcheck)
�[0m�[91m* installing *binary* package ‘repr’ ...
�[0m�[91m* DONE (repr)
�[0m�[91m* installing *binary* package ‘shiny’ ...
�[0m�[91m* DONE (shiny)
�[0m�[91m* installing *binary* package ‘rematch2’ ...
�[0m�[91m* DONE (rematch2)
�[0m�[91m* installing *binary* package ‘usethis’ ...
�[0m�[91m* DONE (usethis)
�[0m�[91m* installing *binary* package ‘IRdisplay’ ...
�[0m�[91m* DONE (IRdisplay)
�[0m�[91m* installing *binary* package ‘waldo’ ...
�[0m�[91m* DONE (waldo)
�[0m�[91m* installing *binary* package ‘IRkernel’ ...
�[0m�[91m* DONE (IRkernel)
�[0m�[91m* installing *binary* package ‘testthat’ ...
�[0m�[91m* DONE (testthat)
�[0m�[91m* installing *binary* package ‘devtools’ ...
�[0m�[91m* DONE (devtools)
�[0m�[91m
The downloaded source packages are in
	‘/tmp/RtmpvjMsJo/downloaded_packages’
�[0m> 
> 
> IRkernel::installspec(prefix='/srv/conda/envs/notebook')
> 
> 
Removing intermediate container 3b49ef71e28c
 ---> e4322d701856
Step 44/69 : ARG REPO_DIR=${HOME}
 ---> Running in 919bfcaea19d
Removing intermediate container 919bfcaea19d
 ---> 49ba285e83e0
Step 45/69 : ENV REPO_DIR ${REPO_DIR}
 ---> Running in 9254e469c03d
Removing intermediate container 9254e469c03d
 ---> b339c6b98cfa
Step 46/69 : WORKDIR ${REPO_DIR}
 ---> Running in d0b6cde8e228
Removing intermediate container d0b6cde8e228
 ---> 9c5558ffe24e
Step 47/69 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}
 ---> Running in 9a0dac360b18
Removing intermediate container 9a0dac360b18
 ---> e4655825fd47
Step 48/69 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
 ---> Running in 4e5bdca3f1ad
Removing intermediate container 4e5bdca3f1ad
 ---> a2c71e2f4fcf
Step 49/69 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
 ---> Running in 9dcdf1b15a76
Removing intermediate container 9dcdf1b15a76
 ---> 4966e5ea7f1e
Step 50/69 : COPY --chown=1000:1000 src/binder/environment.yml ${REPO_DIR}/binder/environment.yml
 ---> cc280823ef74
Step 51/69 : COPY --chown=1000:1000 src/binder/install.R ${REPO_DIR}/binder/install.R
 ---> a1fec6be4362
Step 52/69 : RUN apt-get -qq update && apt-get install --yes --no-install-recommends libcurl4-openssl-dev libglpk-dev libgmp3-dev libicu-dev libssl-dev libxml2-dev zlib1g-dev && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*
 ---> Running in 106d8de34cae
�[91mE: List directory /var/lib/apt/lists/partial is missing. - Acquire (13: Permission denied)
�[0mRemoving intermediate container 106d8de34cae
The command '/bin/sh -c apt-get -qq update && apt-get install --yes --no-install-recommends libcurl4-openssl-dev libglpk-dev libgmp3-dev libicu-dev libssl-dev libxml2-dev zlib1g-dev && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100Built image, launching...
Failed to connect to event stream
@meeseeksmachine
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This issue has been mentioned on Jupyter Community Forum. There might be relevant details there:

https://discourse.jupyter.org/t/binder-failing-to-build-when-using-apt-txt-for-r-package-dependencies/12659/3

@manics manics added the bug label Jan 19, 2022
@admivsn admivsn mentioned this issue Jan 19, 2022
Closed
@minrk minrk mentioned this issue Jan 20, 2022
Merged
This was referenced Jan 25, 2022
Closed
Closed
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set USER root after each directive block minrk/repo2docker
2 participants
@manics @meeseeksmachine