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R examples fail to build on myBinder #41

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gjhltn opened this issue Jan 18, 2024 · 3 comments · May be fixed by #42
Open

R examples fail to build on myBinder #41

gjhltn opened this issue Jan 18, 2024 · 3 comments · May be fixed by #42

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@gjhltn
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gjhltn commented Jan 18, 2024

The examples at https://github.com/binder-examples/r all fail for me with the error

debconf:%20delaying%20package%20configuration,%0Asince%20apt-utils%20is%20not%20installed

Step to reproduce:
@ShimantoBhowmik
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Following. I get something like this:

---> Removed intermediate container 05d758ecd611
The command '/bin/sh -c apt-get update > /dev/null && apt-get install --yes --no-install-recommends libclang-dev libzmq3-dev > /dev/null && wget --quiet -O /tmp/r-4.3.deb https://cdn.rstudio.com/r/ubuntu-$(. /etc/os-release && echo $VERSION_ID | sed 's/.//')/pkgs/r-4.3_1_amd64.deb && apt install --yes --no-install-recommends /tmp/r-4.3.deb > /dev/null && rm /tmp/r-4.3.deb && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/* && ln -s /opt/R/4.3/bin/R /usr/local/bin/R && ln -s /opt/R/4.3/bin/Rscript /usr/local/bin/Rscript && R --version' returned a non-zero code: 8

@lbianchi-lbl
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lbianchi-lbl commented Feb 21, 2024 •
edited

I can confirm I also get the same error.

FWIW, changing the contents of runtime.txt to R-4.3 (i.e. removing the rest of the version specifier after the X.Y component) seems to resolve this specific error. However, I'm still getting a 404 when trying to access the ...?urlpath=shiny/bus-dashboard or ...?urlpath=shiny URLs.

EDIT the possible workaround mentioned above doesn't seem to be working after all. The Binder/repo2docker build doesn't fail at that command; however, once the default JupyterLab interface starts up, none of the R launchers are shown:

image

I believe this would also explain why, using my supposed "workaround", the ?urlpath=shiny, etc endpoints don't work.

(For reference, this is how the same page for a different Binder repo containing R files looks like)

image

EDIT 2 Adding the micro version (i.e. 4.3.2-2024-01-10 instead of 4.3-2024-01-10) seems to work. I've opened #42 with this minimal possible fix.

@lbianchi-lbl lbianchi-lbl linked a pull request Feb 21, 2024 that will close this issue
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@arnim
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arnim commented Apr 8, 2024

Failing with

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker7bhm2z88'...
HEAD is now at 02cff45 Merge pull request #40 from binder-examples/yuvipanda-patch-1
Python version unspecified, using current default Python version 3.10. This will change in the future.Building conda environment for python=3.10
Using RBuildPack builder
Step 1/69 : FROM docker.io/library/buildpack-deps:jammy
 ---> f899440a738f
Step 2/69 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> 3edf75f3731d
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
 ---> 5e0ee3043e5d
Step 4/69 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> e71a44dc37f4
Step 5/69 : ENV LC_ALL=en_US.UTF-8     LANG=en_US.UTF-8     LANGUAGE=en_US.UTF-8
 ---> Using cache
 ---> df89788c286b
Step 6/69 : ENV SHELL=/bin/bash
 ---> Using cache
 ---> cf9d6de478b4
Step 7/69 : ARG NB_USER
 ---> Using cache
 ---> 1affa0d0d8f1
Step 8/69 : ARG NB_UID
 ---> Using cache
 ---> 8e3ee4a169c4
Step 9/69 : ENV USER=${NB_USER}     HOME=/home/${NB_USER}
 ---> Using cache
 ---> 617e2287167f
Step 10/69 : 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}         ${NB_USER}
 ---> Using cache
 ---> 925f55ead1b0
Step 11/69 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        gettext-base        less        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> a5567b4b2f83
Step 12/69 : RUN apt-get -qq update &&     apt-get -qq install --yes        libapparmor1        libssl-dev        lsb-release        psmisc        sudo        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> 82705c056e98
Step 13/69 : EXPOSE 8888
 ---> Using cache
 ---> 55eedfef98eb
Step 14/69 : ENV APP_BASE=/srv
 ---> Using cache
 ---> 2d8ae2954187
Step 15/69 : ENV CONDA_DIR=${APP_BASE}/conda
 ---> Using cache
 ---> bc8ca1b39481
Step 16/69 : ENV NB_PYTHON_PREFIX=${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 21a707d075a1
Step 17/69 : ENV NPM_DIR=${APP_BASE}/npm
 ---> Using cache
 ---> d1f231c8949a
Step 18/69 : ENV NPM_CONFIG_GLOBALCONFIG=${NPM_DIR}/npmrc
 ---> Using cache
 ---> 04e6b82f7db6
Step 19/69 : ENV NB_ENVIRONMENT_FILE=/tmp/env/environment.lock
 ---> Using cache
 ---> eb70d87a1106
Step 20/69 : ENV MAMBA_ROOT_PREFIX=${CONDA_DIR}
 ---> Using cache
 ---> 0abdb9141802
Step 21/69 : ENV MAMBA_EXE=${CONDA_DIR}/bin/mamba
 ---> Using cache
 ---> 557d24cb3b01
Step 22/69 : ENV CONDA_PLATFORM=linux-64
 ---> Using cache
 ---> 37b895059e52
Step 23/69 : ENV KERNEL_PYTHON_PREFIX=${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> a9cde8cb6764
Step 24/69 : ENV R_LIBS_USER=${APP_BASE}/rlibs
 ---> Using cache
 ---> ab9687433695
Step 25/69 : ENV PATH=${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:/usr/lib/rstudio-server/bin/:${PATH}
 ---> Using cache
 ---> d20cc793cb45
Step 26/69 : COPY --chown=1000:1000 build_script_files/-2fopt-2fvenv-2flib-2fpython3-2e11-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-e70a7b /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> c4f0bafbe951
Step 27/69 : COPY --chown=1000:1000 build_script_files/-2fopt-2fvenv-2flib-2fpython3-2e11-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e10-2dlinux-2d64-2elock-8fa955 /tmp/env/environment.lock
 ---> Using cache
 ---> 44deb7eb6b7d
Step 28/69 : COPY --chown=1000:1000 build_script_files/-2fopt-2fvenv-2flib-2fpython3-2e11-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dbase-2denv-2ebash-6a6072 /tmp/install-base-env.bash
 ---> Using cache
 ---> c0b2c4e0024f
Step 29/69 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-base-env.bash' && rm -rf /tmp/install-base-env.bash /tmp/env
 ---> Using cache
 ---> 381cfae2ea99
Step 30/69 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> 863a96d72d0f
Step 31/69 : RUN apt-get update > /dev/null && apt-get install --yes --no-install-recommends         libclang-dev         libzmq3-dev > /dev/null && wget --quiet -O /tmp/r-4.3.deb     https://cdn.rstudio.com/r/ubuntu-$(. /etc/os-release && echo $VERSION_ID | sed 's/\.//')/pkgs/r-4.3_1_amd64.deb && apt install --yes --no-install-recommends /tmp/r-4.3.deb > /dev/null && rm /tmp/r-4.3.deb && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/* && ln -s /opt/R/4.3/bin/R /usr/local/bin/R && ln -s /opt/R/4.3/bin/Rscript /usr/local/bin/Rscript && R --version
 ---> Running in 417d1ece263f
�[91mdebconf: delaying package configuration, since apt-utils is not installed
�[0m ---> Removed intermediate container 417d1ece263f
The command '/bin/sh -c apt-get update > /dev/null && apt-get install --yes --no-install-recommends         libclang-dev         libzmq3-dev > /dev/null && wget --quiet -O /tmp/r-4.3.deb     https://cdn.rstudio.com/r/ubuntu-$(. /etc/os-release && echo $VERSION_ID | sed 's/\.//')/pkgs/r-4.3_1_amd64.deb && apt install --yes --no-install-recommends /tmp/r-4.3.deb > /dev/null && rm /tmp/r-4.3.deb && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/* && ln -s /opt/R/4.3/bin/R /usr/local/bin/R && ln -s /opt/R/4.3/bin/Rscript /usr/local/bin/Rscript && R --version' returned a non-zero code: 8

Last commit 02cff45 3 months ago by @yuvipanda

cc @rgaiacs

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Include R version micro component in runtime.txt lbianchi-lbl/binder-examples-r
4 participants
@arnim @gjhltn @lbianchi-lbl @ShimantoBhowmik