Binder-examples/r fails "apt-get update"

Building


failed “apt-get update” like

Please give me your advice if you have any ideas.

 && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker1jp4xo_i'...
HEAD is now at 20210ae Update install.R
Building conda environment for python=3.7Using RBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step1/69 : FROM buildpack-deps:bionic
 ---> da7bebef4e62
Step 2/69 : ENV DEBIAN_FRONTEND=noninteractive
 ---> Using cache
 ---> c1253d68468e
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
 ---> e36b12947298
Step 4/69 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
 ---> 406775215bb9
Step 5/69 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
 ---> c5b5be33fb8f
Step 6/69 : ENV LANG en_US.UTF-8
 ---> Using cache
 ---> c950fc6aa0be
Step 7/69 : ENV LANGUAGE en_US.UTF-8
 ---> Using cache
 ---> fcabb2252cea
Step 8/69 : ENV SHELL /bin/bash
 ---> Using cache
 ---> d580abd20183
Step 9/69 : ARG NB_USER
 ---> Using cache
 ---> 9a033668cfe0
Step 10/69 : ARG NB_UID
 ---> Using cache
 ---> 9b328c6c9787
Step 11/69 : ENV USER ${NB_USER}
 ---> Using cache
 ---> e9ff61876d4b
Step 12/69 : ENV HOME /home/${NB_USER}
 ---> Using cache
 ---> 3e53b32ff7ea
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
 ---> e31b3283d398
Step 14/69 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
 ---> 6b9a3dca655f
Step 15/69 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
 ---> f684b7e3a88f
Step 16/69 : 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
 ---> 442c09325f13
Step 17/69 : EXPOSE 8888
 ---> Using cache
 ---> cdb55be07d22
Step 18/69 : ENV APP_BASE /srv
 ---> Using cache
 ---> 0f97ca7553db
Step 19/69 : ENV NPM_DIR ${APP_BASE}/npm
 ---> Using cache
 ---> 0fec69309651
Step 20/69 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
 ---> Using cache
 ---> 4d574a5009d5
Step 21/69 : ENV CONDA_DIR ${APP_BASE}/conda
 ---> Using cache
 ---> 9ef40825cec6
Step 22/69 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
 ---> Using cache
 ---> 8a9ada30b406
Step 23/69 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
 ---> Using cache
 ---> c6a038c9bf0a
Step 24/69 : ENV R_LIBS_USER ${APP_BASE}/rlibs
 ---> Using cache
 ---> 9b56a77b5517
Step 25/69 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:/usr/lib/rstudio-server/bin/:${PATH}
 ---> Using cache
 ---> 3bfe8ff6d06a
Step 26/69 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-2747be /etc/profile.d/activate-conda.sh
 ---> Using cache
 ---> 7894abc99ea4
Step 27/69 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2efrozen-2eyml-b3d5bc /tmp/environment.yml
 ---> Using cache
 ---> f9ff457b7455
Step 28/69 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiconda-2ebash-12d101 /tmp/install-miniconda.bash
 ---> Using cache
 ---> d6429fe73286
Step 29/69 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
 ---> Using cache
 ---> b7d6ffff9b74
Step 30/69 : USER ${NB_USER}
 ---> Using cache
 ---> 8e2273b1910b
Step 31/69 : RUN npm config --global set prefix ${NPM_DIR}
 ---> Using cache
 ---> 5bc3355077a4
Step 32/69 : USER root
 ---> Using cache
 ---> 45fd85d89ee3
Step 33/69 : RUN bash /tmp/install-miniconda.bash && rm /tmp/install-miniconda.bash /tmp/environment.yml
 ---> Using cache
 ---> 99e12021b005
Step 34/69 : RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" > /etc/apt/sources.list.d/r3.6-ubuntu.list
 ---> Using cache
 ---> d0d5d7dbb64a
Step 35/69 : RUN apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
 ---> Using cache
 ---> afd864847834
Step 36/69 : RUN apt-get update && apt-get install --yes r-base=3.6.1-3bionic      r-base-dev=3.6.1-3bionic      libclang-dev && apt-get -qq purge && apt-get -qq clean && rm-rf /var/lib/apt/lists/*
 ---> Running in 69b0c14c018c
Get:1 https://deb.nodesource.com/node_10.x bionic InRelease [4,584 B]
Get:2 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
Get:3 http://archive.ubuntu.com/ubuntu bionic InRelease [242 kB]
Get:4 https://deb.nodesource.com/node_10.x bionic/main amd64 Packages [768 B]
Get:5 http://archive.ubuntu.com/ubuntu bionic-updates InRelease [88.7 kB]
Get:6 http://security.ubuntu.com/ubuntu bionic-security/main amd64 Packages [761 kB]
Get:7 http://archive.ubuntu.com/ubuntu bionic-backports InRelease [74.6 kB]
Get:8 http://archive.ubuntu.com/ubuntu bionic/main amd64 Packages [1,344 kB]
Get:9 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 Packages [795 kB]
Get:10 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 Packages [6,781 B]
Get:11 http://security.ubuntu.com/ubuntu bionic-security/restricted amd64 Packages [19.2 kB]
Get:12 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease [3,626 B]
Get:13 http://archive.ubuntu.com/ubuntu bionic/multiverse amd64 Packages [186 kB]
Get:14 http://archive.ubuntu.com/ubuntu bionic/restricted amd64 Packages [13.5 kB]
Get:15 http://archive.ubuntu.com/ubuntu bionic/universe amd64 Packages [11.3 MB]
Get:16 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 Packages [1,057 kB]
Get:17 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ Packages [81.6 kB]
Get:18 http://archive.ubuntu.com/ubuntu bionic-updates/multiverse amd64 Packages [10.5kB]
Get:19 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 Packages [1,322 kB]
Get:20 http://archive.ubuntu.com/ubuntu bionic-updates/restricted amd64 Packages [32.7kB]
Get:21 http://archive.ubuntu.com/ubuntu bionic-backports/main amd64 Packages [2,496 B]
Get:22 http://archive.ubuntu.com/ubuntu bionic-backports/universe amd64 Packages [4,244 B]
Fetched 17.5 MB in 3s (5,219 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 r-base : Depends: r-recommended (= 3.6.1-3bionic) but 3.6.2-1bionic is to be installed
          Recommends: r-base-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
Removing intermediate container 69b0c14c018c
The command '/bin/sh -c apt-get update && apt-get install --yes r-base=3.6.1-3bionic   r-base-dev=3.6.1-3bionic      libclang-dev && apt-get -qq purge && apt-get -qq clean && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100

Yes, this is a known issue discussed here. As I described in the thread we have one work-around that was still working as of the other day. I’ll verify it works on yours and provide you the details.

3 Likes

Thank you for information.
I understood.
I will check Cannot get R project working