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Waldo Rivier
@waldorivier_gitlab
and I see that git as not load.
Thanks for Help and have a nice day.
Philippe Grosjean
@phgrosjean
Hi,
Today I am not able to build images that run RStudio. I got this, even on repositories that worked well last week:
Screenshot 2021-08-23 at 16.17.56.png
The log starts with this:
Screenshot 2021-08-23 at 16.15.36.png
Rok Roškar
@rokroskar
Hi @phgrosjean, sorry you're having trouble - could you give me some more info about what you are trying to do? If the project is public, could you share a link?
Philippe Grosjean
@phgrosjean
I just solved the problem. It is in https://renkulab.io/projects/sciviews/svbox-renku. My previous Docker file started from rocker/geospatial:4.0.5 and it worked fine until last Friday. But then rocker/geospatial apparently changed something that interfers with correct starting of RStudio. I changed the Docker file to start from renku/renkulab-r:4.0.5-0.8.0, and now it works again... except it takes 30min to build against <10min with rocker/geospatial. I'll try now with renku/renkulab-r:4.0.5-0.9.0 to be up-to-date. Thanks.
4 replies
Simon Blanchoud
@pintomollo
Hi all,
Simon Blanchoud
@pintomollo
I'm just starting with Renku and I'm running into a really basic issue. I'm trying to migrate my local code developed using Conda. I updated environment.yml to include my required packages (I've tried installing them manually too). I can indeed see them there (conda list) but I cannot access them. I mean if I try to import the package in a notebook or try to call the functions directly in the terminal, it always says "Name not defined". Thanks in advance :D
13 replies
Philippe Grosjean
@phgrosjean
Help! My problem is still there, and I really don't understand what is wrong. On 2021-08-25, I build a functional image (registry.renkulab.io/sciviews/svbox-renku:3c32dc5). There, RStudio works fine, and I have `/usr/lib/rstudio-server/bin/rserver --www-port=8787`that runs well, and I see this:

`ls -l /var/run/rstudio-server/revocation-list` that gives
`-rw------- 1 rstudio users 0 Aug 26 19:03 /var/run/rstudio-server/revocation-list`

All docker images I compiled after that have broken RStudio. So, I revert back to same `Dockerfile`, same `install.R`, same everything than the previous working one... and I still got a broken RStudio with the message

"500: Internal Error, could not start rstudio in time"

(this is registry.renkulab.io/sciviews/svbox-renku:d59816e). On a terminal from Jupyterlab, I have:

`/usr/lib/rstudio-server/bin/rserver --www-port=8787
27 Aug 2021 14:06:27 [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]; ...`
and

`ls -l /var/run/rstudio-server/revocation-list
-rw------- 1 rstudio-server rstudio-server 0 Aug 26 17:01 /var/run/rstudio-server/revocation-list`

Obviously, RStudio is started with the wrong (default) "rstudio-server" user, but it should be "rstudio". How two compilations of Docker images with same data could give two different results?
25 replies
Simon Blanchoud
@pintomollo
Hi, I have observed a really strange behavior with conda packages in Renku when editing the environment.yml file, namely that the package trinity (in bioconda) takes forever to install itself (I have tried to install them manually and it works well). I have tried it on a totally fresh project, and installing this package only. It always take more than 1h to build, while separately the dependencies of trinity take less than 5 min to build. Looking at the logs of the build in GitLab did not provide much information as it is stuck at the "Solving environment: ...working...". Is there a way to get some more details about what is causing this delay?
5 replies
Simon Blanchoud
@pintomollo
Hi, I am forking my project to several students and one of them has a seemingly endless stalling saying "Identifying project number". I have checked in Github and the project seems to be forked properly and the docker image was build successfully. Link to the session is here: https://renkulab.io/projects/18027263/maristem-omics/sessions
6 replies
Simon Blanchoud
@pintomollo
Hi there, yet another issue here. My last build do not complete properly, while the only thing I think I have changed was a minor spelling mistake in one of my notebook. The error is a bit surprising as it relates to pip, which I do not use at least explicitly, and to the renku package itself.
Screenshot_2021-09-07_16-35-03.png
8 replies
Olivier Levitt
@olevitt
Hi ! I'm trying to deploy renku on our (on-premise) kubernetes cluster. I started by running make-values.sh providing my gitlab url & application credentials. Then I installed renku using helm providing the generated values. Every pod runs fine except for the renku-gateway-auth one which fails with "Obtaining public key from https://<redacted>/auth/realms/Renku" which leads me to believe that something is wrong with the keycloak configuration (note that I have not done any specific configuration except for the make-values.sh). Browsing https://<redacted>/auth/realms/Renku gets me a keycloak page with "We are sorry...
Page not found".
Any tips on what to configure for keycloak ?
11 replies
Simon Blanchoud
@pintomollo
Hi, I'm trying to run some R code inside my Jupyter notebook, currently with little success. I've decided to use rpy2 (installed through conda) and I have installed the necessary R packages through install.R. Both work fine, but apparently separately. If I run :

%run -m rpy2.situation

rpy2 version:
3.4.5
Python version:
3.9.5 | packaged by conda-forge | (default, Jun 19 2021, 00:32:32)
[GCC 9.3.0]
Looking for R's HOME:
Environment variable R_HOME: /usr/local/lib/R
Calling R RHOME: /opt/conda/lib/R
Environment variable R_LIBS_USER: None
Warning: The environment variable R_HOME differs from the default R in the PATH.
R's additions to LD_LIBRARY_PATH:
/usr/local/lib/R/lib
R version:
In the PATH: R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
include:
['/usr/local/lib/R/include']
libraries:
['R', 'pcre2-8', 'lzma', 'bz2', 'z', 'rt', 'dl', 'm', 'icuuc', 'icui18n']
library_dirs:
['/usr/local/lib', '/usr/local/lib/R/lib']
extra_compile_args:
[]
extra_link_args:
['-Wl,--export-dynamic', '-fopenmp']

I believe this shows that there are two separate installations. I can run the rpy2 one by changing the R_HOME variable (os.environ['R_HOME'] = '/opt/conda/lib/R') but I then do not have access to the packages installed by R. So my question is, should I just add the R folder to my library folder to use the packages installed by install.R, or is there a more direct way to use the exact same R from the start? I have tried to set the home to the conda folder inside install.R, but it tells me that the folder is not writable.

Thank

13 replies
Simon Blanchoud
@pintomollo
Screenshot_2021-09-14_18-38-58.png
Hi again :D
I seem to have corrupted a bit my project somehow. It does not prevent it from working (or so that I can notice), but at every commit, I get a lot of errors like these above.
3 replies
Eric Pohl
@pohleric
Hello, I have a question on how students can fork a certain environment. I did the following: 1) Create an environment with a docker file X1, 2) have a group of students A (last year's students) fork this environment X1, 3) forked the environment X1 myself and make adjustments for a new course X2, 4) have my new students B (this year's course) fork X2.
The problem is now that students who attended the first course cannot properly fork X2. They end up getting X1 even though they choose to fork X2. This is probably a gitter question. Does anyone know what to do so students A (now in group B) can fork X2?
5 replies
Antonio Pérez
@aperezvelasco

Hi there! I have tried to clone a repository from a challenge names "s2s-ai-challenge" and it gives me an authentication error when using the renku clone command:
renku clone https://renkulab.io/gitlab/antonioperezvelasco/s2s-ai-challenge-predictia.git

I have tried to use my e-mail and my username with the corresponden password, but I'm not able to solve the error

1 reply
Eric Pohl
@pohleric

I have two out of 38 students who told me they could not save their work. They would get the attached message when they try to git push the tracked, and committed changes. Any help is appreciated:

Locking support detected on remote "origin". Consider enabling it with: $ git config lfs.https://renku.unifr.ch/gitlab/<student_name>/sp21-sgg-00272.git/info/lfs.locksverify true To https://renku.unifr.ch/gitlab/<student_name>/sp21-sgg-00272.git ! [rejected] HEAD -> master (fetch first) error: failed to push some refs to 'https://renku.unifr.ch/gitlab/<student_name>/sp21-sgg-00272.git' hint: Updates were rejected because the remote contains work that you do hint: not have locally. This is usually caused by another repository pushing hint: to the same ref. You may want to first integrate the remote changes hint: (e.g., 'git pull ...') before pushing again. hint: See the 'Note about fast-forwards' in 'git push --help' for details.

3 replies
Tasko Olevski
@olevski

Hello everyone, as you may have noticed by the recent notifications, we are planning to release a new version of Renku on renkulab.io tomorrow afternoon at 16:00 CET. This new version of Renku brings significant changes and improvements but it also requires us to shut down all active user sessions before doing the upgrade. Therefore please make sure you shut down any active sessions you may have on renkulab.io by 16:00 CET tomorrow (November 4th). If you leave any sessions running when we start the update process any data or code in them that has not been saved will be lost.

Please let me know if you have any questions or concerns. The update process should be finished within a few hours at most. We do not anticipate that similar interruptions will occur any time in the near future.

2 replies
Pamela
@pameladelgado

Dear renkulab users,

the Renkulab 0.10.0 rollout went fine and you can now enjoy working with Renku again :tada:

Also, in case you were not aware: there was a small outage this morning on renkulab.io, see the post-mortem, if you had open sessions it's possible that unsaved work was kept in an auto-saved branch on your project. See this post for more details on how to potentially recover unsaved work and how the auto-save feature works.

Geert van Geest
@GeertvanGeest

Hi! I'm rather new to renku, and I'm trying to build an image based on this environment.yml: https://renkulab.io/gitlab/geert.vangeest/ngs-introduction-training/-/blob/master/environment.yml . However, during building it gives the following error:

UnavailableInvalidChannel: The channel is not accessible or is invalid.
  channel name: bioconda
  channel url: https://conda.anaconda.org/bioconda
  error code: 404
You will need to adjust your conda configuration to proceed.
Use `conda config --show channels` to view your configuration's current state,
and use `conda config --show-sources` to view config file locations.

e.g. adding conda config --add channels bioconda to the Dockerfile did not help. How should I proceed?

9 replies
markrobinsonuzh
@markrobinsonuzh
Screenshot 2021-11-09 at 15.01.08.png
Hi, I'm trying to run a (fairly standard?) instance, but it's been waiting this point (screenshot above) for a long time. I ran one earlier this morning and it was fine. The project is here: https://renkulab.io/projects/mark.robinson/sta426hs2021-r .. Any ideas?
31 replies
Pol del Aguila Pla
@poldap
Hi. Noob question here. I wanted to try to get a bit more resources for a session and now I am stuck waiting. I'd rather reduce the resources and work now than wait, but I can not launch a new one or modify the one that is waiting to start.
project: https://renkulab.io/projects/pol.delaguilapla/lp-stability-examples (nothing to remark, just started it)
3 replies