rocker/binder basic example gives 'jupyter-notebook' not found error #147

fmannhardt · 2021-04-19T08:48:14Z

I am trying to run the simple example provided on this page:
https://hub.docker.com/r/rocker/binder

It gives the following error:

> docker run -p 8888:8888 rocker/binder
Unable to find image 'rocker/binder:latest' locally
latest: Pulling from rocker/binder
a70d879fa598: Already exists
c4394a92d1f8: Already exists
10e6159c56c0: Already exists
833bebb909e4: Pull complete
9bceb8b50184: Pull complete
e925a327b30d: Pull complete
01c3425e0ade: Pull complete
aa899054de42: Pull complete
3073722381fa: Pull complete
c11e2f8a575b: Pull complete
1b74c9d06d50: Pull complete
5081f19c4c6e: Pull complete
Digest: sha256:9ea13371c43d83c161da413669846eb5d19e67e7245686d2926c99ef99e07849
Status: Downloaded newer image for rocker/binder:latest
Traceback (most recent call last):
  File "/usr/local/bin/jupyter", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.8/dist-packages/jupyter_core/command.py", line 285, in main
    command = _jupyter_abspath(subcommand)
  File "/usr/local/lib/python3.8/dist-packages/jupyter_core/command.py", line 124, in _jupyter_abspath
    raise Exception(
Exception: Jupyter command `jupyter-notebook` not found.

The text was updated successfully, but these errors were encountered:

eitsupi · 2021-04-19T10:23:44Z

It may be due to the fact that jupyter-server-proxy, which is required when installing jupyter-rsession-proxy, no longer installs notebook.
jupyterhub/jupyter-server-proxy@48eec72

$ docker run --rm -it rocker/binder pip list
Package                Version
---------------------- -----------
aiohttp                3.7.4.post0
anyio                  2.2.0
appdirs                1.4.3
argon2-cffi            20.1.0
async-generator        1.10
async-timeout          3.0.1
attrs                  20.3.0
bleach                 3.3.0
cffi                   1.14.5
chardet                4.0.0
defusedxml             0.7.1
distlib                0.3.1
entrypoints            0.3
filelock               3.0.12
GDAL                   3.0.4
idna                   3.1
importlib-metadata     1.5.0
ipython-genutils       0.2.0
Jinja2                 2.11.3
jsonschema             3.2.0
jupyter-client         6.1.12
jupyter-core           4.7.1
jupyter-rsession-proxy 1.2
jupyter-server         1.6.1
jupyter-server-proxy   3.0.2
jupyterlab-pygments    0.1.2
MarkupSafe             1.1.1
mistune                0.8.4
more-itertools         4.2.0
multidict              5.1.0
nbclient               0.5.3
nbconvert              6.0.7
nbformat               5.1.3
nest-asyncio           1.5.1
numpy                  1.17.4
packaging              20.9
pandocfilters          1.4.3
pip                    21.0.1
prometheus-client      0.10.1
ptyprocess             0.7.0
pycparser              2.20
Pygments               2.8.1
pyparsing              2.4.7
pyrsistent             0.17.3
python-dateutil        2.8.1
pyzmq                  22.0.3
Send2Trash             1.5.0
setuptools             56.0.0
simpervisor            0.4
six                    1.14.0
sniffio                1.2.0
terminado              0.9.4
testpath               0.4.4
tornado                6.1
traitlets              5.0.5
typing-extensions      3.7.4.3
virtualenv             20.4.3
webencodings           0.5.1
wheel                  0.34.2
yarl                   1.6.3
zipp                   1.0.0

fmannhardt · 2021-04-19T10:56:23Z

I can confirm that it is fixed by changing:
pip3 install --no-cache-dir jupyter-rsession-proxy
to:
pip3 install --no-cache-dir jupyter-rsession-proxy jupyterlab~=3.0 notebook==5.*
here:

rocker-versioned2/scripts/install_binder.sh

Line 24 in 96d41e9

pip3 install --no-cache-dir jupyter-rsession-proxy

I still don't get a R Kernel in the Jupyter Notebook though and a error 500 : Internal Server Error when trying to access RStudio, Maybe related to this issue here:
#88

(This is all using 4.x R)

fmannhardt · 2021-04-19T11:27:03Z

Something is wrong in the way the IRkernel::installspec call is done. I simply added (to the end of my Dockerfile:

RUN R --quiet -e "IRkernel::installspec()"

and now the R Kernel shows up and works.

fmannhardt · 2021-04-19T11:28:20Z

Starting RStudio the errors look like:

19 Apr 2021 11:27:16 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:16 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:16 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:16 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:16 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:16 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:16 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:16 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:16 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:17 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:17 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:17 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:17 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:17 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:17 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:17 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:17 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:17 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:17 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:17 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:17 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:18 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:18 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:18 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:18 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:18 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:18 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:18 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:18 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:18 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:19 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:19 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:19 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:19 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:19 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:19 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:19 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:19 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:19 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:19 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:19 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:19 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:20 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:20 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:20 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:20 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:20 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:20 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
19 Apr 2021 11:27:20 [rserver] ERROR system error 1 (Operation not permitted) [path: /var/run/rstudio-server/revocation-list, description: Could not set revocation file permissions to 600 for file: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::system::changeFileMode(const rstudio::core::FilePath&, mode_t) src/cpp/server/ServerMain.cpp:62; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:531
19 Apr 2021 11:27:20 [rserver] ERROR Could not read revocation list; LOGGED FROM: rstudio::core::Error rstudio::server::auth::handler::initialize() src/cpp/server/auth/ServerAuthHandler.cpp:539
19 Apr 2021 11:27:20 [rserver] ERROR system error 2 (No such file or directory) [path: /var/run/rstudio-server/revocation-list]; OCCURRED AT rstudio::core::Error rstudio::core::FilePath::openForRead(std::shared_ptr<std::basic_istream<char> >&) const src/cpp/shared_core/FilePath.cpp:1150; LOGGED FROM: int main(int, char* const*) src/cpp/server/ServerMain.cpp:674
[W 11:27:21.056 NotebookApp] 500 GET /rstudio/ (172.17.0.1): could not start rstudio in time

Seems like a wrong permissions issue?

mark-andrews · 2021-05-30T18:46:10Z

Following @fmannhardt's advice, I dealt with the Jupyter command jupyter-notebook not found. issue, and got a Jupyter session working, but when i try to launch RStudio, I encountered the same Rstudio server error as described by @fmannhardt.

Does anyone have any advice on how to deal with that problem?

Robinlovelace · 2021-08-05T16:10:54Z

I have also noticed this issue. Very keen to see discussion of this, there have been issues with RStudio/Binder for ages and I think rocker-versioned2 could be the ideal place to address some of them with solutions that benefit many people.

eitsupi · 2021-08-14T09:45:14Z

Handling pip packages has been a problem for a long time, but now that the wiki records the installed pip packages for each image, I think it's possible to make destructive changes now.
I think it's a good idea to add the missing packages to install_binder.sh as a first step.

eitsupi · 2021-12-16T11:09:23Z

This issue seems resolved by #309.
rocker/binder:latest seems work correctly.
https://github.com/rocker-org/rocker-versioned2/wiki/binder_6fac4d6e57c3

cboettig · 2021-12-16T17:25:29Z

🎉 🎉

Thanks @yuvipanda, @ryanlovett and @eitsupi for all the work here. Very nice to have this fixed, updated in the build scripts and the fixed version automatically deployed. 🚀

yuvipanda · 2021-12-16T20:49:48Z

Yay! Thanks for the merge, @cboettig! Can this issue be closed now?

cboettig · 2021-12-16T21:02:54Z

probably, I was just waiting to confirm on my end at https://mybinder.org/v2/gh/rocker-org/binder/master?urlpath=rstudio but currently keep seeing timeouts there... ?

ryanlovett · 2021-12-16T21:17:48Z

I noticed something similar when I had tried rocker/binder + notebook a week or so ago. I don't think it is binder infrastructure. There was a javascript console error indicating something wrong with an HTTP header, so I suspected one of the jupyter proxy layers. However the proxies worked outside of rocker in a more minimal image. In any case, I still haven't a chance to explore further.

yuvipanda · 2021-12-17T06:31:23Z

https://github.com/yuvipanda/rstudio-binder-template works fine for me. I'm 100% convinced that is rocker-org/binder failing because the image was already built, and hence used the older, non-working rocker/binder:latest image. Maybe we can switch to a tag?

eitsupi · 2021-12-17T14:35:31Z

I don't really understand how mybinder works, but comparing https://github.com/yuvipanda/rstudio-binder-template/tree/411ca6a00fc2bd2ed390e23f8bdf439f4d28c128 and https://github.com/rocker-org/binder/tree/82a50434cddf87eb78ec20279120076ed4763be2, the path to the Dockerfile is different.
Is there a possible impact from this?

I did not see any option to set the path to the Dockerfile when creating the URL.
https://mybinder.org/

eitsupi · 2021-12-17T15:21:40Z

I tried playing with my fork (move the Dockerfile to the root), but I could not get RStudio Server to start...

This repo no longer builds newer versions of https://hub.docker.com/r/rocker/binder - those come from https://github.com/rocker-org/rocker-versioned2. I've an example template that works in https://github.com/yuvipanda/rocker-binder-template. This repo builds the images where R < 4.x. Needed a few changes to work: 1. Pin to older jupyter-rsession-proxy. Newer version only works with newer RStudio 2. Explicitly install notebook package, as jupyter-rsession-proxy no longer brings that in by default 3. Use jupyter server as the command to start, rather than jupyter notebook. This should have no functional difference, but it means you can remove the notebook package if you don't want to use jupyter notebooks. Ref rocker-org/rocker-versioned2#147

yuvipanda · 2021-12-20T09:25:44Z

I opened rocker-org/binder#46 to fix that repo. However, newer versions of the binder image are built from this repo, and don't need anything to fix. Maybe the rocker/binder repo should be converted into an example instead? Maybe https://github.com/yuvipanda/rocker-binder-template can be merged into it?

cboettig · 2021-12-20T18:12:19Z

@yuvipanda yes, that's a great idea! Do you want to send a PR for that?

eitsupi · 2022-02-19T07:33:09Z

I think this issue has been resolved by #309, so I close it.

louisaslett mentioned this issue Jun 1, 2021

Run locally on docker failing rocker-org/binder#45

Closed

eitsupi mentioned this issue Aug 2, 2021

[Tracking] Build system automation #181

Closed

36 tasks

yuvipanda mentioned this issue Dec 20, 2021

Pin to older rsession-proxy to work with R < 4.x rocker-org/binder#46

Closed

eitsupi closed this as completed Feb 19, 2022

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rocker/binder basic example gives 'jupyter-notebook' not found error #147

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rocker/binder basic example gives 'jupyter-notebook' not found error #147

rocker/binder basic example gives 'jupyter-notebook' not found error #147

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