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Published 20 hours ago • verified publisher icon jupyterhub

RStudio user interface not working for R 3.6 using runtime.txt

Open aplamada opened this issue 2 years ago • 6 comments

Bug description

The project has just a runtime.txt with the content

$ cat runtime.txt 
r-3.6-2022-01-01

How to reproduce

  1. Build a container using repo2docker
$ jupyter-repo2docker  --user-name jovyan --user-id 1000 .
  1. Try to use the RStudio user interface

Expected behaviour

RStudio should appear.
It works fine with r-4.1, or using conda.

Actual behaviour

I get an error. Please see the logs

Click to expand! 
[W 16:17:28.269 NotebookApp] 500 GET /rstudio/ (172.17.0.1): could not start rstudio in time
[E 16:17:28.293 NotebookApp] {
      "Host": "127.0.0.1:53884",
      "Connection": "keep-alive",
      "Sec-Ch-Ua": "\" Not A;Brand\";v=\"99\", \"Chromium\";v=\"99\", \"Google Chrome\";v=\"99\"",
      "Sec-Ch-Ua-Mobile": "?0",
      "Sec-Ch-Ua-Platform": "\"macOS\"",
      "Upgrade-Insecure-Requests": "1",
      "Dnt": "1",
      "User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/99.0.4844.83 Safari/537.36",
      "Accept": "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.9",
      "Sec-Fetch-Site": "same-origin",
      "Sec-Fetch-Mode": "navigate",
      "Sec-Fetch-User": "?1",
      "Sec-Fetch-Dest": "document",
      "Referer": "http://127.0.0.1:53884/lab",
      "Accept-Encoding": "gzip, deflate, br",
      "Accept-Language": "en-CH,en-GB;q=0.9,en-US;q=0.8,en;q=0.7,ro;q=0.6,de;q=0.5",
      "Cookie": "port-token=1faed3183265; csrf-token=50b8eac7-c44e-4217-bc3b-54e4432ae404; persist-auth=0; user-id=jovyan|Tue%2C%2022%20Mar%202022%2017%3A15%3A54%20GMT|DkN3O7I3mbO%2FWHAtK9w8HWNSbsFDF8vW1w3BDKLcxdM%3D; user-list-id=9c16856330a7400cbbbba228392a5d83|Tue%2C%2022%20Mar%202022%2017%3A15%3A54%20GMT|LnQ0Gs2SZ9QKUsj7Icj9GXpVWZ1gczaZ%2FDYHerlsaWQ%3D; _xsrf=2|472da1bf|ef27fa61a82f579bdd71091761205945|1647525932; username-127-0-0-1-64319=\"2|1:0|10:1647525974|24:username-127-0-0-1-64319|44:ZTBkNDEwZjkyZjhhNGVhMDkxZmUxZmI2MzZjNzBjZGY=|e9a06fb1a05b3750bbe4d036c7627098e89ec86f9bb6606b1d313f76b47d0b5c\"; username-127-0-0-1-64937=\"2|1:0|10:1647527149|24:username-127-0-0-1-64937|44:NjdmOGJlYTJiZTlhNGYwY2E2NjUyNDU1ZDgyNDBjMmU=|3516d99484fadc73074752854abd769540c877b13be31a5b857be5fd9e352761\"; username-127-0-0-1-49172=\"2|1:0|10:1647530679|24:username-127-0-0-1-49172|44:M2FhNjc3ZGQxZTU5NDJjNzkyMjA3YjZmNDhmY2I4NWE=|6a3544e2bedbafc6626bcfae15a087ffe527b176b09ae17d76e222f745d5ebb9\"; username-127-0-0-1-51344=\"2|1:0|10:1647533631|24:username-127-0-0-1-51344|44:ZmJlZmQ1NDMyZjNiNDgwNGFiZTlhMmU4NDc4ZDQ5YjQ=|09e0f0a1ded7a8918b37609dda5b9b1188c682990989b05c3a703cbc7635ad9c\"; username-127-0-0-1-51702=\"2|1:0|10:1647533986|24:username-127-0-0-1-51702|44:YmUyNGJiNzhiYzgyNDE1ZWIxZjNlYzk4MDdhODg5ZTU=|624d798fd3f07b0cd6361b88d21ec4e7307da92c3fd70979de7740f7514d610c\"; username-127-0-0-1-52229=\"2|1:0|10:1647534460|24:username-127-0-0-1-52229|44:YzdjMGE0OTNkYjQ4NDQzMzllYTRmMjY3MmNkNWUwODc=|a22fb145fb2123f8c14a881e1ccd27de52f248255355eda087245b275627006d\"; username-127-0-0-1-53266=\"2|1:0|10:1647538764|24:username-127-0-0-1-53266|44:MzI3YjNiY2Q4OTQzNDYxNjlmNjQxODUyNjJlYzJjNmU=|299aa43326edf6721b37f6761b99ce64703cb3ba3e9d4c9e8570cc558ec4a587\"; username-127-0-0-1-54835=\"2|1:0|10:1647544227|24:username-127-0-0-1-54835|44:NzRhNWIzYzJlMTYwNDY4ODljZGUxMWQyMmMxNDM4Mzc=|738a726b9aa08acc86bc8260ba7b11e45bb11a97aedaffc8350f1fbdcfd4b4af\"; username-127-0-0-1-55854=\"2|1:0|10:1647595025|24:username-127-0-0-1-55854|44:OGRjOWY3MjVjMGZmNDM1Njg3NzUwMGMwYjU0NTI3ZTU=|71e032938cfaab6881cdaee73ea871d232f2162455d44d96115815f8e4fe1c7a\"; username-127-0-0-1-57049=\"2|1:0|10:1647597236|24:username-127-0-0-1-57049|44:N2I4ZTU5MzBlZGM2NDMwMWI0M2VhOGRhNWI4ZGU1OTY=|ab963ba701bd3368050d6b36cc34a1b972db9891a54d8c440b86bc08577780fb\"; username-127-0-0-1-55622=\"2|1:0|10:1647954489|24:username-127-0-0-1-55622|44:OWE0N2M4NWZmYzg4NDEwYjg2ZjQ1YzBjZDVjOGVjYWU=|8f6fe2ed72e746b81e7c924c5806dc9e538dae175473d22b5c678ec6f4e0c05b\"; username-127-0-0-1-56254=\"2|1:0|10:1647955076|24:username-127-0-0-1-56254|44:YzIwYjJjN2U2MTI4NDM5MWFiZTBlNGMyZDQ0YmQ0MGQ=|8194b13548d9b5b0b2202de62c57b869ea18fd8613356fb24445240b65382552\"; username-127-0-0-1-50222=\"2|1:0|10:1647957351|24:username-127-0-0-1-50222|44:NTM5MzhhOTQ0ZWRlNGM4YjlhMDZlNGY1YTY1ODVlYTg=|62e1adcc3133a7aafbf773f2ff7665ce6b8e2eb1338274b8a437da230bc55a00\"; username-127-0-0-1-50655=\"2|1:0|10:1647959301|24:username-127-0-0-1-50655|44:NjJjOTczZmEzMDg2NGM2ZWJlNjYxMzMzYmZlY2YzYmY=|b45329798893a38efc70f8fa5040a4ad927b2eb677f2a58570e782eb6c7ee699\"; username-127-0-0-1-52337=\"2|1:0|10:1647963057|24:username-127-0-0-1-52337|44:ZDEyNjI4ZWY1ODM4NDRkYThmYzNjZWNiYWYyMWU3Y2Y=|1c9b14e6fbd955da4f08f1d08970bf249dd9717e9e19222e69563da658653891\"; username-127-0-0-1-52897=\"2|1:0|10:1647963954|24:username-127-0-0-1-52897|44:ZWYwZTk3MDRmMGM0NDc0ODkzYzFkODY4Y2YzOTA4N2E=|54a042e403e03db2a859501c26ce60c47872ce44de5855624c8fad42dce57794\"; username-127-0-0-1-53382=\"2|1:0|10:1647965144|24:username-127-0-0-1-53382|44:YzI1ZmM5MWU3NTU2NGJlNWE4N2M1ZDJhMWI1NDdhMzA=|179c2c471eb3f3334b523264d327b487bd80786016b11194dd94b40ed90347fc\"; username-127-0-0-1-53819=\"2|1:0|10:1647965758|24:username-127-0-0-1-53819|44:MDRkOWJlZjA4OTQwNGYyMmI1YzU2YzZhNTVjN2Q5N2Y=|817fbd7ac8a1701d11933ceaf8ed9757dafd901a89e72b19c89bdbcd4be3a606\"; username-127-0-0-1-53884=\"2|1:0|10:1647965842|24:username-127-0-0-1-53884|44:YTM1ZjY0MjBhYTVkNDkxNjk2N2MyNmZlMjJlYWNhODM=|57f41705947e30d7947d65e976cf3aa601ff2b2344e4d8c7099e0d03557f8cc2\""
    }
[E 16:17:28.293 NotebookApp] 500 GET /rstudio/ (172.17.0.1) 5332.050000ms referer=http://127.0.0.1:53884/lab

Your personal set up

  • OS: macOS
  • Docker version: 20.10.13, build a224086
  • repo2docker version 2022.02.0

I think the problem is independent of OS or Docker version.

aplamada avatar Mar 22 '22 16:03 aplamada

Thank you for opening your first issue in this project! Engagement like this is essential for open source projects! :hugs:
If you haven't done so already, check out Jupyter's Code of Conduct. Also, please try to follow the issue template as it helps other other community members to contribute more effectively. welcome You can meet the other Jovyans by joining our Discourse forum. There is also an intro thread there where you can stop by and say Hi! :wave:
Welcome to the Jupyter community! :tada:

welcome[bot] avatar Mar 22 '22 16:03 welcome[bot]

@yuvipanda Can you remember what errors you ran into with older versions of R? https://github.com/jupyterhub/repo2docker/blob/66f608e207a30b88bad40c7076ecd1809e1dab92/repo2docker/buildpacks/_r_base.py#L17-L29

The RStudio FAQ claims the latest version supports R 3.0.1 https://support.rstudio.com/hc/en-us/articles/200486548-Frequently-Asked-Questions

manics avatar Mar 22 '22 16:03 manics

@manics hmm, I don't fully remember :| I think maybe https://github.com/jupyterhub/repo2docker/issues/1041 was manifesting in reverse wrt the graphics engine? Closest guess.

yuvipanda avatar Mar 23 '22 04:03 yuvipanda

@manics and @yuvipanda Thanks for your input. Regarding the if statement - I found something mentioned on #1099. I am trying to fix it in #1148.

aplamada avatar Mar 28 '22 08:03 aplamada

@ryanlovett do you remember why we split which versions of RStudio are available in different R versions?

Thanks for working on this, @aplamada!

yuvipanda avatar Mar 28 '22 17:03 yuvipanda

@yuvipanda In the case of #1041, RStudio would still launch. For this issue, it'd be interesting to see the output of the rserver command when run manually.

(perhaps simpervisor's start can be passed params to preserve stdout/stderr)

ryanlovett avatar Mar 28 '22 19:03 ryanlovett