I write a Dockerfile and docker-compose.yml to build a custom image which combines beakerx and cling, which contents are below. and Some logs of docker-compose build were But When I run docker-compose up -d, I got PermissionError: [Errno 13] Permission denied: '/home/beakerx/.local/share' error. So I drive into the docker image. Why the permission of ~/.local/share was a lot of question

Strange file permission in docker container (question marks on permission bit and user bit)

I write a Dockerfile and docker-compose.yml to build a custom image which combines beakerx and cling, which contents are below.

FROM beakerx/beakerx

MAINTAINER liudonghua123 <liudonghua123@gmail.com>

# not works
#RUN conda install xeus-cling notebook -c QuantStack -c conda-forge -y --quiet

USER root
# install gcc7
RUN add-apt-repository -y ppa:jonathonf/gcc-7.2
RUN apt-get update -y
RUN apt-get install -y gcc-7

# revert to beakerx user
USER beakerx
ARG CLING_FILENAME=cling_2018-09-04_ubuntu16
RUN echo "use ${CLING_FILENAME} for build"
# add the prebuild cling packages
ADD ${CLING_FILENAME}.tar.bz2 /home/beakerx
ENV PATH=/home/beakerx/${CLING_FILENAME}/bin:$PATH
USER root
RUN pip install --upgrade pip
# install steps, https://github.com/root-project/cling/tree/master/tools/Jupyter
RUN cd /home/beakerx/${CLING_FILENAME}/share/cling/Jupyter/kernel && pip install -e . && jupyter-kernelspec install --user cling-cpp17 && jupyter-kernelspec install --user cling-cpp1z && jupyter-kernelspec install --user cling-cpp14 && jupyter-kernelspec install --user cling-cpp11
RUN ln -s /usr/bin/gcc-7 /usr/bin/gcc

RUN echo "root:root" | chpasswd
RUN echo "beakerx:beakerx" | chpasswd

RUN chown -R beakerx:beakerx /home/beakerx/.local
RUN find /home/beakerx/.local -type d -exec chmod 755 {} ;
RUN find /home/beakerx/.local -type f -exec chmod 644 {} ;

RUN id
RUn ls -la /home/beakerx/.local
RUn ls -la /home/beakerx/.local/share

USER beakerx

JavaScript
​x
 
FROM beakerx/beakerx​MAINTAINER liudonghua123 <liudonghua123@gmail.com>​# not works#RUN conda install xeus-cling notebook -c QuantStack -c conda-forge -y --quiet​USER root# install gcc7RUN add-apt-repository -y ppa:jonathonf/gcc-7.2RUN apt-get update -yRUN apt-get install -y gcc-7​# revert to beakerx userUSER beakerxARG CLING_FILENAME=cling_2018-09-04_ubuntu16RUN echo "use ${CLING_FILENAME} for build"# add the prebuild cling packagesADD ${CLING_FILENAME}.tar.bz2 /home/beakerxENV PATH=/home/beakerx/${CLING_FILENAME}/bin:$PATHUSER rootRUN pip install --upgrade pip# install steps, https://github.com/root-project/cling/tree/master/tools/JupyterRUN cd /home/beakerx/${CLING_FILENAME}/share/cling/Jupyter/kernel && pip install -e . && jupyter-kernelspec install --user cling-cpp17 && jupyter-kernelspec install --user cling-cpp1z && jupyter-kernelspec install --user cling-cpp14 && jupyter-kernelspec install --user cling-cpp11RUN ln -s /usr/bin/gcc-7 /usr/bin/gcc​RUN echo "root:root" | chpasswdRUN echo "beakerx:beakerx" | chpasswd​RUN chown -R beakerx:beakerx /home/beakerx/.localRUN find /home/beakerx/.local -type d -exec chmod 755 {} ;RUN find /home/beakerx/.local -type f -exec chmod 644 {} ;​RUN idRUn ls -la /home/beakerx/.localRUn ls -la /home/beakerx/.local/share​USER beakerx​

and

version: '2'

services:
    beakerx-cling-prebuild:
        build: .
        image: liudonghua123/beakerx-cling-prebuild:latest
        ports:
            - "28888:8888"
        volumes:
            - ./work:/work
        restart: always

JavaScript
 
version: '2'​services:    beakerx-cling-prebuild:        build: .        image: liudonghua123/beakerx-cling-prebuild:latest        ports:            - "28888:8888"        volumes:            - ./work:/work        restart: always​

Some logs of docker-compose build were

Step 22/24 : RUN ls -la /home/beakerx/.local
 ---> Running in 95457585aed0
total 12
drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 .
drwxr-xr-x 25 beakerx beakerx 4096 Sep  6 00:51 ..
drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 share
 ---> affcb9f1ca94
Removing intermediate container 95457585aed0
Step 23/24 : RUN ls -la /home/beakerx/.local/share
 ---> Running in 15ea51bcc3bf
total 12
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 .
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ..
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyter
 ---> 6f2ca28d4d21
Removing intermediate container 15ea51bcc3bf
Step 24/24 : USER beakerx
 ---> Running in 0ab6574079d7
 ---> 9561902b99ef
Removing intermediate container 0ab6574079d7
Successfully built 9561902b99ef

JavaScript
 
Step 22/24 : RUN ls -la /home/beakerx/.local ---> Running in 95457585aed0total 12drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 .drwxr-xr-x 25 beakerx beakerx 4096 Sep  6 00:51 ..drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 share ---> affcb9f1ca94Removing intermediate container 95457585aed0Step 23/24 : RUN ls -la /home/beakerx/.local/share ---> Running in 15ea51bcc3bftotal 12drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 .drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ..drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyter ---> 6f2ca28d4d21Removing intermediate container 15ea51bcc3bfStep 24/24 : USER beakerx ---> Running in 0ab6574079d7 ---> 9561902b99efRemoving intermediate container 0ab6574079d7Successfully built 9561902b99ef​

But When I run docker-compose up -d, I got PermissionError: [Errno 13] Permission denied: '/home/beakerx/.local/share' error. So I drive into the docker image.

ldh@ldh55:~/docker/cling/jupinger/beakerx-cling-prebuild$ docker run -it --entrypoint='' --rm liudonghua123/beakerx-cling-prebuild bash
beakerx@716d9a8334ca:~$ ls -la ~
total 108
drwxr-xr-x 25 beakerx beakerx  4096 Sep  6 00:51 .
drwxr-xr-x 11 root    root     4096 Sep  6 00:51 ..
-rw-r--r--  1 beakerx beakerx   220 Aug 31  2015 .bash_logout
-rw-r--r--  1 beakerx beakerx  3771 Aug 31  2015 .bashrc
drwxr-xr-x  3 root    root     4096 Mar 13 13:32 .config
-rw-r--r--  1 beakerx beakerx   938 Mar  8 14:03 .gitignore
-rw-r--r--  1 beakerx beakerx    53 Feb 27  2018 .jscsrc
drwxr-xr-x  6 beakerx beakerx  4096 Sep  6 00:51 .local
drwxr-xr-x  3 root    root     4096 Mar 13 13:32 .npm
-rw-r--r--  1 beakerx beakerx   655 May 16  2017 .profile
-rw-r--r--  1 beakerx beakerx  2285 Feb 27  2018 CONTRIBUTING.md
-rw-r--r--  1 beakerx beakerx 11325 Feb 27  2018 LICENSE
-rw-r--r--  1 beakerx beakerx   193 Feb 27  2018 NOTICE
-rw-r--r--  1 beakerx beakerx  8682 Mar 12 14:27 README.md
-rw-r--r--  1 beakerx beakerx  5821 Mar 12 20:04 StartHere.ipynb
-rw-r--r--  1 beakerx beakerx     6 Mar 13 13:32 VERSION
drwxr-xr-x 16 beakerx beakerx  4096 Mar 12 20:11 beakerx
drwxr-xr-x  8   14806    2735  4096 Sep  5 07:44 cling_2018-09-04_ubuntu16
drwxr-xr-x 22 beakerx beakerx  4096 Feb 27  2018 doc
-rw-r--r--  1 beakerx beakerx    81 Feb 27  2018 environment.yml
drwxr-xr-x  6 beakerx beakerx  4096 Feb 27  2018 js
-rwxr-xr-x  1 beakerx beakerx   927 Mar 13 12:42 setup.sh
beakerx@716d9a8334ca:~$ ls -la ~/.local/
ls: cannot access '/home/beakerx/.local/share': Permission denied
total 8
drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 .
drwxr-xr-x 25 beakerx beakerx 4096 Sep  6 00:51 ..
d?????????  ? ?       ?          ?            ? share
beakerx@716d9a8334ca:~$ ls -la ~/.local/share
ls: cannot access '/home/beakerx/.local/share': Permission denied
beakerx@716d9a8334ca:~$ 
beakerx@716d9a8334ca:~$ su
Password: 
root@716d9a8334ca:/home/beakerx# ls -la ~
total 28
drwx------  4 root root 4096 Mar 13 13:27 .
drwxr-xr-x 77 root root 4096 Sep  6 01:06 ..
-rw-r--r--  1 root root 3106 Oct 22  2015 .bashrc
drwxr-xr-x  3 root root 4096 Mar 13 13:20 .conda
-rw-r--r--  1 root root   38 Mar 13 13:20 .condarc
drwxr-xr-x  5 root root 4096 Mar 13 13:28 .gradle
-rw-r--r--  1 root root  148 Aug 17  2015 .profile
root@716d9a8334ca:/home/beakerx# ls -la /home/beakerx/
total 108
drwxr-xr-x 25 beakerx beakerx  4096 Sep  6 00:51 .
drwxr-xr-x 11 root    root     4096 Sep  6 00:51 ..
-rw-r--r--  1 beakerx beakerx   220 Aug 31  2015 .bash_logout
-rw-r--r--  1 beakerx beakerx  3771 Aug 31  2015 .bashrc
drwxr-xr-x  3 root    root     4096 Mar 13 13:32 .config
-rw-r--r--  1 beakerx beakerx   938 Mar  8 14:03 .gitignore
-rw-r--r--  1 beakerx beakerx    53 Feb 27  2018 .jscsrc
drwxr-xr-x  6 beakerx beakerx  4096 Sep  6 00:51 .local
drwxr-xr-x  3 root    root     4096 Mar 13 13:32 .npm
-rw-r--r--  1 beakerx beakerx   655 May 16  2017 .profile
-rw-r--r--  1 beakerx beakerx  2285 Feb 27  2018 CONTRIBUTING.md
-rw-r--r--  1 beakerx beakerx 11325 Feb 27  2018 LICENSE
-rw-r--r--  1 beakerx beakerx   193 Feb 27  2018 NOTICE
-rw-r--r--  1 beakerx beakerx  8682 Mar 12 14:27 README.md
-rw-r--r--  1 beakerx beakerx  5821 Mar 12 20:04 StartHere.ipynb
-rw-r--r--  1 beakerx beakerx     6 Mar 13 13:32 VERSION
drwxr-xr-x 16 beakerx beakerx  4096 Mar 12 20:11 beakerx
drwxr-xr-x  8   14806    2735  4096 Sep  5 07:44 cling_2018-09-04_ubuntu16
drwxr-xr-x 22 beakerx beakerx  4096 Feb 27  2018 doc
-rw-r--r--  1 beakerx beakerx    81 Feb 27  2018 environment.yml
drwxr-xr-x  6 beakerx beakerx  4096 Feb 27  2018 js
-rwxr-xr-x  1 beakerx beakerx   927 Mar 13 12:42 setup.sh
root@716d9a8334ca:/home/beakerx# ls -la /home/beakerx/.local/
total 12
drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 .
drwxr-xr-x 25 beakerx beakerx 4096 Sep  6 00:51 ..
drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 share
root@716d9a8334ca:/home/beakerx# ls -la /home/beakerx/.local/share/
total 12
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 .
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ..
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyter
root@716d9a8334ca:/home/beakerx# exit
exit
beakerx@716d9a8334ca:~$ ls -la ~/.local/share
total 12
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 .
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ..
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyter
beakerx@716d9a8334ca:~$

JavaScript
 
ldh@ldh55:~/docker/cling/jupinger/beakerx-cling-prebuild$ docker run -it --entrypoint='' --rm liudonghua123/beakerx-cling-prebuild bashbeakerx@716d9a8334ca:~$ ls -la ~total 108drwxr-xr-x 25 beakerx beakerx  4096 Sep  6 00:51 .drwxr-xr-x 11 root    root     4096 Sep  6 00:51 ..-rw-r--r--  1 beakerx beakerx   220 Aug 31  2015 .bash_logout-rw-r--r--  1 beakerx beakerx  3771 Aug 31  2015 .bashrcdrwxr-xr-x  3 root    root     4096 Mar 13 13:32 .config-rw-r--r--  1 beakerx beakerx   938 Mar  8 14:03 .gitignore-rw-r--r--  1 beakerx beakerx    53 Feb 27  2018 .jscsrcdrwxr-xr-x  6 beakerx beakerx  4096 Sep  6 00:51 .localdrwxr-xr-x  3 root    root     4096 Mar 13 13:32 .npm-rw-r--r--  1 beakerx beakerx   655 May 16  2017 .profile-rw-r--r--  1 beakerx beakerx  2285 Feb 27  2018 CONTRIBUTING.md-rw-r--r--  1 beakerx beakerx 11325 Feb 27  2018 LICENSE-rw-r--r--  1 beakerx beakerx   193 Feb 27  2018 NOTICE-rw-r--r--  1 beakerx beakerx  8682 Mar 12 14:27 README.md-rw-r--r--  1 beakerx beakerx  5821 Mar 12 20:04 StartHere.ipynb-rw-r--r--  1 beakerx beakerx     6 Mar 13 13:32 VERSIONdrwxr-xr-x 16 beakerx beakerx  4096 Mar 12 20:11 beakerxdrwxr-xr-x  8   14806    2735  4096 Sep  5 07:44 cling_2018-09-04_ubuntu16drwxr-xr-x 22 beakerx beakerx  4096 Feb 27  2018 doc-rw-r--r--  1 beakerx beakerx    81 Feb 27  2018 environment.ymldrwxr-xr-x  6 beakerx beakerx  4096 Feb 27  2018 js-rwxr-xr-x  1 beakerx beakerx   927 Mar 13 12:42 setup.shbeakerx@716d9a8334ca:~$ ls -la ~/.local/ls: cannot access '/home/beakerx/.local/share': Permission deniedtotal 8drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 .drwxr-xr-x 25 beakerx beakerx 4096 Sep  6 00:51 ..d?????????  ? ?       ?          ?            ? sharebeakerx@716d9a8334ca:~$ ls -la ~/.local/sharels: cannot access '/home/beakerx/.local/share': Permission deniedbeakerx@716d9a8334ca:~$ beakerx@716d9a8334ca:~$ suPassword: root@716d9a8334ca:/home/beakerx# ls -la ~total 28drwx------  4 root root 4096 Mar 13 13:27 .drwxr-xr-x 77 root root 4096 Sep  6 01:06 ..-rw-r--r--  1 root root 3106 Oct 22  2015 .bashrcdrwxr-xr-x  3 root root 4096 Mar 13 13:20 .conda-rw-r--r--  1 root root   38 Mar 13 13:20 .condarcdrwxr-xr-x  5 root root 4096 Mar 13 13:28 .gradle-rw-r--r--  1 root root  148 Aug 17  2015 .profileroot@716d9a8334ca:/home/beakerx# ls -la /home/beakerx/total 108drwxr-xr-x 25 beakerx beakerx  4096 Sep  6 00:51 .drwxr-xr-x 11 root    root     4096 Sep  6 00:51 ..-rw-r--r--  1 beakerx beakerx   220 Aug 31  2015 .bash_logout-rw-r--r--  1 beakerx beakerx  3771 Aug 31  2015 .bashrcdrwxr-xr-x  3 root    root     4096 Mar 13 13:32 .config-rw-r--r--  1 beakerx beakerx   938 Mar  8 14:03 .gitignore-rw-r--r--  1 beakerx beakerx    53 Feb 27  2018 .jscsrcdrwxr-xr-x  6 beakerx beakerx  4096 Sep  6 00:51 .localdrwxr-xr-x  3 root    root     4096 Mar 13 13:32 .npm-rw-r--r--  1 beakerx beakerx   655 May 16  2017 .profile-rw-r--r--  1 beakerx beakerx  2285 Feb 27  2018 CONTRIBUTING.md-rw-r--r--  1 beakerx beakerx 11325 Feb 27  2018 LICENSE-rw-r--r--  1 beakerx beakerx   193 Feb 27  2018 NOTICE-rw-r--r--  1 beakerx beakerx  8682 Mar 12 14:27 README.md-rw-r--r--  1 beakerx beakerx  5821 Mar 12 20:04 StartHere.ipynb-rw-r--r--  1 beakerx beakerx     6 Mar 13 13:32 VERSIONdrwxr-xr-x 16 beakerx beakerx  4096 Mar 12 20:11 beakerxdrwxr-xr-x  8   14806    2735  4096 Sep  5 07:44 cling_2018-09-04_ubuntu16drwxr-xr-x 22 beakerx beakerx  4096 Feb 27  2018 doc-rw-r--r--  1 beakerx beakerx    81 Feb 27  2018 environment.ymldrwxr-xr-x  6 beakerx beakerx  4096 Feb 27  2018 js-rwxr-xr-x  1 beakerx beakerx   927 Mar 13 12:42 setup.shroot@716d9a8334ca:/home/beakerx# ls -la /home/beakerx/.local/total 12drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 .drwxr-xr-x 25 beakerx beakerx 4096 Sep  6 00:51 ..drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 00:51 shareroot@716d9a8334ca:/home/beakerx# ls -la /home/beakerx/.local/share/total 12drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 .drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ..drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyterroot@716d9a8334ca:/home/beakerx# exitexitbeakerx@716d9a8334ca:~$ ls -la ~/.local/sharetotal 12drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 .drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ..drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyterbeakerx@716d9a8334ca:~$​

Why the permission of ~/.local/share was a lot of question marks at the first sight, and when I run as root or return to the original user, it was correct.

I tried run start-notebook.sh manually, the first time it was failed, then the second time it was successfully.

beakerx@716d9a8334ca:~$ cd /usr/local/bin/
beakerx@716d9a8334ca:/usr/local/bin$ ls
start-notebook.sh  start-singleuser.sh  start.sh
beakerx@716d9a8334ca:/usr/local/bin$ 
beakerx@716d9a8334ca:/usr/local/bin$ 
beakerx@716d9a8334ca:/usr/local/bin$ start-notebook.sh 
Execute the command
Traceback (most recent call last):
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/traitlets.py", line 528, in get
    value = obj._trait_values[self.name]
KeyError: 'runtime_dir'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/opt/conda/envs/beakerx/bin/jupyter-notebook", line 6, in <module>
    sys.exit(notebook.notebookapp.main())
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyter_core/application.py", line 266, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/config/application.py", line 657, in launch_instance
    app.initialize(argv)
  File "<decorator-gen-7>", line 2, in initialize
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/config/application.py", line 87, in catch_config_error
    return method(app, *args, **kwargs)
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/notebook/notebookapp.py", line 1505, in initialize
    self.init_configurables()
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/notebook/notebookapp.py", line 1209, in init_configurables
    connection_dir=self.runtime_dir,
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/traitlets.py", line 556, in __get__
    return self.get(obj, cls)
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/traitlets.py", line 535, in get
    value = self._validate(obj, dynamic_default())
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyter_core/application.py", line 99, in _runtime_dir_default
    ensure_dir_exists(rd, mode=0o700)
  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyter_core/utils/__init__.py", line 13, in ensure_dir_exists
    os.makedirs(path, mode=mode)
  File "/opt/conda/envs/beakerx/lib/python3.6/os.py", line 220, in makedirs
    mkdir(name, mode)
PermissionError: [Errno 13] Permission denied: '/home/beakerx/.local/share/jupyter/runtime'
beakerx@716d9a8334ca:/usr/local/bin$ ll /home/beakerx/.local/share/jupyter/runtime
ls: cannot access '/home/beakerx/.local/share/jupyter/runtime': Permission denied
beakerx@716d9a8334ca:/usr/local/bin$ ll /home/beakerx/.local/share/jupyter/       
ls: cannot access '/home/beakerx/.local/share/jupyter/kernels': Permission denied
total 8
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ./
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ../
d????????? ? ?       ?          ?            ? kernels/
beakerx@716d9a8334ca:/usr/local/bin$ ll /home/beakerx/.local/share/        
total 12
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ./
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ../
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyter/
beakerx@716d9a8334ca:/usr/local/bin$ su
Password: 
root@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/jupyter/runtime
ls: cannot access '/home/beakerx/.local/share/jupyter/runtime': No such file or directory
root@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/jupyter/       
total 4
drwxr-xr-x 18 beakerx beakerx 4096 Sep  6 00:51 kernels
root@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/        
total 4
drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyter
root@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/jupyter/kernels/
total 16
drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp11
drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp14
drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp17
drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp1z
root@716d9a8334ca:/usr/local/bin# exit
exit
beakerx@716d9a8334ca:/usr/local/bin$ id
uid=1000(beakerx) gid=1000(beakerx) groups=1000(beakerx)
beakerx@716d9a8334ca:/usr/local/bin$ start-notebook.sh 
Execute the command
[I 01:20:56.433 NotebookApp] Writing notebook server cookie secret to /home/beakerx/.local/share/jupyter/runtime/notebook_cookie_secret
[W 01:20:56.567 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.
[I 01:20:56.647 NotebookApp] [beakerx] enabled
[I 01:20:56.736 NotebookApp] JupyterLab beta preview extension loaded from /opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyterlab
[I 01:20:56.736 NotebookApp] JupyterLab application directory is /opt/conda/envs/beakerx/share/jupyter/lab
[I 01:20:56.971 NotebookApp] Serving notebooks from local directory: /usr/local/bin
[I 01:20:56.971 NotebookApp] 0 active kernels
[I 01:20:56.971 NotebookApp] The Jupyter Notebook is running at:
[I 01:20:56.971 NotebookApp] http://[all ip addresses on your system]:8888/?token=1b94f5bf7e14e4ed5defece6870addc630d81eb8aae85990
[I 01:20:56.971 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 01:20:56.972 NotebookApp] 

    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://localhost:8888/?token=1b94f5bf7e14e4ed5defece6870addc630d81eb8aae85990

JavaScript
 
beakerx@716d9a8334ca:~$ cd /usr/local/bin/beakerx@716d9a8334ca:/usr/local/bin$ lsstart-notebook.sh  start-singleuser.sh  start.shbeakerx@716d9a8334ca:/usr/local/bin$ beakerx@716d9a8334ca:/usr/local/bin$ beakerx@716d9a8334ca:/usr/local/bin$ start-notebook.sh Execute the commandTraceback (most recent call last):  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/traitlets.py", line 528, in get    value = obj._trait_values[self.name]KeyError: 'runtime_dir'​During handling of the above exception, another exception occurred:​Traceback (most recent call last):  File "/opt/conda/envs/beakerx/bin/jupyter-notebook", line 6, in <module>    sys.exit(notebook.notebookapp.main())  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyter_core/application.py", line 266, in launch_instance    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/config/application.py", line 657, in launch_instance    app.initialize(argv)  File "<decorator-gen-7>", line 2, in initialize  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/config/application.py", line 87, in catch_config_error    return method(app, *args, **kwargs)  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/notebook/notebookapp.py", line 1505, in initialize    self.init_configurables()  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/notebook/notebookapp.py", line 1209, in init_configurables    connection_dir=self.runtime_dir,  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/traitlets.py", line 556, in __get__    return self.get(obj, cls)  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/traitlets/traitlets.py", line 535, in get    value = self._validate(obj, dynamic_default())  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyter_core/application.py", line 99, in _runtime_dir_default    ensure_dir_exists(rd, mode=0o700)  File "/opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyter_core/utils/__init__.py", line 13, in ensure_dir_exists    os.makedirs(path, mode=mode)  File "/opt/conda/envs/beakerx/lib/python3.6/os.py", line 220, in makedirs    mkdir(name, mode)PermissionError: [Errno 13] Permission denied: '/home/beakerx/.local/share/jupyter/runtime'beakerx@716d9a8334ca:/usr/local/bin$ ll /home/beakerx/.local/share/jupyter/runtimels: cannot access '/home/beakerx/.local/share/jupyter/runtime': Permission deniedbeakerx@716d9a8334ca:/usr/local/bin$ ll /home/beakerx/.local/share/jupyter/       ls: cannot access '/home/beakerx/.local/share/jupyter/kernels': Permission deniedtotal 8drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ./drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ../d????????? ? ?       ?          ?            ? kernels/beakerx@716d9a8334ca:/usr/local/bin$ ll /home/beakerx/.local/share/        total 12drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ./drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 ../drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyter/beakerx@716d9a8334ca:/usr/local/bin$ suPassword: root@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/jupyter/runtimels: cannot access '/home/beakerx/.local/share/jupyter/runtime': No such file or directoryroot@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/jupyter/       total 4drwxr-xr-x 18 beakerx beakerx 4096 Sep  6 00:51 kernelsroot@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/        total 4drwxr-xr-x 6 beakerx beakerx 4096 Sep  6 00:51 jupyterroot@716d9a8334ca:/usr/local/bin# ls -l /home/beakerx/.local/share/jupyter/kernels/total 16drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp11drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp14drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp17drwxr-xr-x 2 beakerx beakerx 4096 Sep  6 00:51 cling-cpp1zroot@716d9a8334ca:/usr/local/bin# exitexitbeakerx@716d9a8334ca:/usr/local/bin$ iduid=1000(beakerx) gid=1000(beakerx) groups=1000(beakerx)beakerx@716d9a8334ca:/usr/local/bin$ start-notebook.sh Execute the command[I 01:20:56.433 NotebookApp] Writing notebook server cookie secret to /home/beakerx/.local/share/jupyter/runtime/notebook_cookie_secret[W 01:20:56.567 NotebookApp] WARNING: The notebook server is listening on all IP addresses and not using encryption. This is not recommended.[I 01:20:56.647 NotebookApp] [beakerx] enabled[I 01:20:56.736 NotebookApp] JupyterLab beta preview extension loaded from /opt/conda/envs/beakerx/lib/python3.6/site-packages/jupyterlab[I 01:20:56.736 NotebookApp] JupyterLab application directory is /opt/conda/envs/beakerx/share/jupyter/lab[I 01:20:56.971 NotebookApp] Serving notebooks from local directory: /usr/local/bin[I 01:20:56.971 NotebookApp] 0 active kernels[I 01:20:56.971 NotebookApp] The Jupyter Notebook is running at:[I 01:20:56.971 NotebookApp] http://[all ip addresses on your system]:8888/?token=1b94f5bf7e14e4ed5defece6870addc630d81eb8aae85990[I 01:20:56.971 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).[C 01:20:56.972 NotebookApp] ​    Copy/paste this URL into your browser when you connect for the first time,    to login with a token:        http://localhost:8888/?token=1b94f5bf7e14e4ed5defece6870addc630d81eb8aae85990​

If I modified Dockerfile (move up USER beakerx)

FROM beakerx/beakerx

MAINTAINER liudonghua123 <liudonghua123@gmail.com>

# not works
#RUN conda install xeus-cling notebook -c QuantStack -c conda-forge -y --quiet

USER root
# install gcc7
RUN add-apt-repository -y ppa:jonathonf/gcc-7.2
RUN apt-get update -y
RUN apt-get install -y gcc-7

# revert to beakerx user
USER beakerx
ARG CLING_FILENAME=cling_2018-09-04_ubuntu16
RUN echo "use ${CLING_FILENAME} for build"
# add the prebuild cling packages
ADD ${CLING_FILENAME}.tar.bz2 /home/beakerx
ENV PATH=/home/beakerx/${CLING_FILENAME}/bin:$PATH
USER root
RUN pip install --upgrade pip
# install steps, https://github.com/root-project/cling/tree/master/tools/Jupyter
RUN cd /home/beakerx/${CLING_FILENAME}/share/cling/Jupyter/kernel && pip install -e . && jupyter-kernelspec install --user cling-cpp17 && jupyter-kernelspec install --user cling-cpp1z && jupyter-kernelspec install --user cling-cpp14 && jupyter-kernelspec install --user cling-cpp11
RUN ln -s /usr/bin/gcc-7 /usr/bin/gcc

RUN echo "root:root" | chpasswd
RUN echo "beakerx:beakerx" | chpasswd
RUN usermod -aG sudo beakerx

RUN echo beakerx | sudo -S chown -R beakerx:beakerx /home/beakerx/
RUN echo beakerx | sudo -S find /home/beakerx/ -type d -exec chmod 755 {} ;
RUN echo beakerx | sudo -S find /home/beakerx/ -type f -exec chmod 644 {} ;

USER beakerx

RUN id
RUn ls -la /home/beakerx/.local
RUn ls -la /home/beakerx/.local/share

JavaScript
 
FROM beakerx/beakerx​MAINTAINER liudonghua123 <liudonghua123@gmail.com>​# not works#RUN conda install xeus-cling notebook -c QuantStack -c conda-forge -y --quiet​USER root# install gcc7RUN add-apt-repository -y ppa:jonathonf/gcc-7.2RUN apt-get update -yRUN apt-get install -y gcc-7​# revert to beakerx userUSER beakerxARG CLING_FILENAME=cling_2018-09-04_ubuntu16RUN echo "use ${CLING_FILENAME} for build"# add the prebuild cling packagesADD ${CLING_FILENAME}.tar.bz2 /home/beakerxENV PATH=/home/beakerx/${CLING_FILENAME}/bin:$PATHUSER rootRUN pip install --upgrade pip# install steps, https://github.com/root-project/cling/tree/master/tools/JupyterRUN cd /home/beakerx/${CLING_FILENAME}/share/cling/Jupyter/kernel && pip install -e . && jupyter-kernelspec install --user cling-cpp17 && jupyter-kernelspec install --user cling-cpp1z && jupyter-kernelspec install --user cling-cpp14 && jupyter-kernelspec install --user cling-cpp11RUN ln -s /usr/bin/gcc-7 /usr/bin/gcc​RUN echo "root:root" | chpasswdRUN echo "beakerx:beakerx" | chpasswdRUN usermod -aG sudo beakerx​RUN echo beakerx | sudo -S chown -R beakerx:beakerx /home/beakerx/RUN echo beakerx | sudo -S find /home/beakerx/ -type d -exec chmod 755 {} ;RUN echo beakerx | sudo -S find /home/beakerx/ -type f -exec chmod 644 {} ;​USER beakerx​RUN idRUn ls -la /home/beakerx/.localRUn ls -la /home/beakerx/.local/share​

Then some errors occurred (ls -la /home/beakerx/.local).

Step 18/25 : RUN usermod -aG sudo beakerx
 ---> Using cache
 ---> 2b341f8539b9
Step 19/25 : RUN echo beakerx | sudo -S chown -R beakerx:beakerx /home/beakerx/
 ---> Running in 8adb3c593f96
 ---> bd6237aa0196
Removing intermediate container 8adb3c593f96
Step 20/25 : RUN echo beakerx | sudo -S find /home/beakerx/ -type d -exec chmod 755 {} ;
 ---> Running in 5dc9ff3d8d1b
 ---> 98d3338124ce
Removing intermediate container 5dc9ff3d8d1b
Step 21/25 : RUN echo beakerx | sudo -S find /home/beakerx/ -type f -exec chmod 644 {} ;
 ---> Running in 63a4ce864b75
 ---> 0ca175cb1663
Removing intermediate container 63a4ce864b75
Step 22/25 : USER beakerx
 ---> Running in 42f8c91f6930
 ---> 94e9f6099aa3
Removing intermediate container 42f8c91f6930
Step 23/25 : RUN id
 ---> Running in 6f24ee8ce894
uid=1000(beakerx) gid=1000(beakerx) groups=1000(beakerx),27(sudo)
 ---> 58627cedc9de
Removing intermediate container 6f24ee8ce894
Step 24/25 : RUN ls -la /home/beakerx/.local
 ---> Running in cfd7bdd70666
ls: cannot access '/home/beakerx/.local/share': Permission denied
total 8
drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 03:08 .
drwxr-xr-x 43 beakerx beakerx 4096 Sep  6 03:09 ..
d?????????  ? ?       ?          ?            ? share
ERROR: Service 'beakerx-cling-prebuild' failed to build: The command '/bin/sh -c ls -la /home/beakerx/.local' returned a non-zero code: 1
ldh@ldh55:~/docker/cling/jupinger/beakerx-cling-prebuild$

JavaScript
 
Step 18/25 : RUN usermod -aG sudo beakerx ---> Using cache ---> 2b341f8539b9Step 19/25 : RUN echo beakerx | sudo -S chown -R beakerx:beakerx /home/beakerx/ ---> Running in 8adb3c593f96 ---> bd6237aa0196Removing intermediate container 8adb3c593f96Step 20/25 : RUN echo beakerx | sudo -S find /home/beakerx/ -type d -exec chmod 755 {} ; ---> Running in 5dc9ff3d8d1b ---> 98d3338124ceRemoving intermediate container 5dc9ff3d8d1bStep 21/25 : RUN echo beakerx | sudo -S find /home/beakerx/ -type f -exec chmod 644 {} ; ---> Running in 63a4ce864b75 ---> 0ca175cb1663Removing intermediate container 63a4ce864b75Step 22/25 : USER beakerx ---> Running in 42f8c91f6930 ---> 94e9f6099aa3Removing intermediate container 42f8c91f6930Step 23/25 : RUN id ---> Running in 6f24ee8ce894uid=1000(beakerx) gid=1000(beakerx) groups=1000(beakerx),27(sudo) ---> 58627cedc9deRemoving intermediate container 6f24ee8ce894Step 24/25 : RUN ls -la /home/beakerx/.local ---> Running in cfd7bdd70666ls: cannot access '/home/beakerx/.local/share': Permission deniedtotal 8drwxr-xr-x  6 beakerx beakerx 4096 Sep  6 03:08 .drwxr-xr-x 43 beakerx beakerx 4096 Sep  6 03:09 ..d?????????  ? ?       ?          ?            ? shareERROR: Service 'beakerx-cling-prebuild' failed to build: The command '/bin/sh -c ls -la /home/beakerx/.local' returned a non-zero code: 1ldh@ldh55:~/docker/cling/jupinger/beakerx-cling-prebuild$​

Answer

This problem is related to the storage-driver bug, see https://github.com/moby/moby/issues/28391, https://github.com/moby/moby/issues/20240. Currently I can only change storage-driver to overlay, use the default aufs or recommended overlay2 will break.

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Answer