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  • Sep 24 09:48
    pameladelgado review_requested #2276
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Erol Orel
@triphon:matrix.org
[m]
Hi Gavin, Thank you for your help. Yes this is definitely a git problem. I will probably end up doing what you are suggesting :-) Thanks for helping!
Gavin Lee
@gavin-k-lee

Alternatively, you can "Revert" to a point in time when the CI/CD passed. The last time a commit worked was here: https://renkulab.io/gitlab/erol.orel/topic-modelling/-/commit/004ed41228aac54b3bd14f9f7aaab6cb4927e0fd

and after you did a merge, git was broken.

Mattias de Hollander
@mdehollander
I was wondering if it is possible to choose the R version when starting RStudio via RenkuLab? Currently it starts with R 4.0.0. Also I see that there are newer versions of RStudio that for example using renv as default in stead of packrat. There are Rocker images support the latest R and RStudio versions. Are there any plans to update the Rocker version in RenkuLab and (even better) let the end user choose the R version? I looked at github for open issue, but did not find any. Thanks!
12 replies
Aaron Spring
@aaronspring

Hi,
I work on https://renkulab.io/projects/aaron.spring/s2s-ai-challenge-template. I can create an environment, the docker image is available, but I cannot launch and the following error, which I do not understand. Working on AS_initial branch, but happens on all branches.

An error occurred when trying to start a new Interactive environment. Error message: "Renku API error", Stack trace: "o@https://renkulab.io/static/js/2.661f982d.chunk.js:2:2214652 a/<@https://renkulab.io/static/js/2.661f982d.chunk.js:2:4567 a@https://renkulab.io/static/js/main.32a029ec.chunk.js:2:16699 kt@https://renkulab.io/static/js/main.32a029ec.chunk.js:2:16969 Ga/</</<@https://renkulab.io/static/js/main.32a029ec.chunk.js:2:81568 “

6 replies
Aaron Spring
@aaronspring
how do you work in gitlab with/without notifications? I am very used to the github style in-browser notifications, which still does not work right? what are your workarounds? email notifications?
4 replies
Aaron Spring
@aaronspring
how is the best way to fork a project, make it private and clone a local version? Tried https://renkulab.io/gitlab/help/ssh/README#generate-an-ssh-key-pair ssh -T git@renkulab.io git@renkulab.io: Permission denied (publickey) working on this template: https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/README.md
13 replies
Aaron Spring
@aaronspring
I think I found a small error with the renkulab website. when I click on the number of forks in a renku projects, I get an error page. when I click on the number of forks in gitlab, I get the list of forks as expected.
4 replies
Luca Pegoraro
@lpego
Hey there, I have a question about authentication for Renku/Gitlab, is this the right place to ask?
10 replies
Aaron Spring
@aaronspring
Hi all, I’d like to run a short notebook in CI for merge requests. Is this possible? I have no experience with docker so far and started this MR: https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/merge_requests/11/diffs Help appreciated.
11 replies
rezaulwre
@rezaulwre
Hi all, I have a renku project in which I added my team-members with a "Developer" status. But they can't access my project or script. Can anyone suggest me how to do that? Thanks, Muhammad
Rok Roškar
@rokroskar
heads up, the Renku team is hiring! See the discourse post for the details and feel free to reach out to me if there are any questions about the roles.
Pulktho
@Pulktho_gitlab
Hi all, unfortunately I can't login to my Renku/Gitlab account anymore. Same as @lpego, I get the Error 422. @rokroskar can you help me out?
6 replies
Aaron Spring
@aaronspring

Hi, since this storage setting of 16GB max was introduced (and I updated to renku=0.16 today), I cannot run this notebook anymore on renkulab.io: https://renkulab.io/gitlab/aaron.spring/s2s-ai-challenge-template/-/blob/master/notebooks/ML_train_and_predict.ipynb

Traceback:
...
Error updating the git index:
Error cleaning LFS object: write /work/s2s-ai-challenge-template/.git/lfs/tmp/210917465: no space left on device
error: packet write failed
error: external filter 'git-lfs filter-process --skip' failed
fatal: data/ecmwf_forecast-input_2020_biweekly_deterministic.zarr/t2m/0.0.0.0.0: clean filter 'lfs’ failed

exit status 128

The files I am pulling are less than 16 GB.

2 replies
Aaron Spring
@aaronspring
image.png
Tasko Olevski
@olevski
Hi Aaron do you know how much space you need for it?
I can add a 32GB option
Aaron Spring
@aaronspring
image.png
The data I want to pull (here on a different machine) is actually much less than 16 GB
8.8 GB in total
Tasko Olevski
@olevski
Let me try just temporarily resizing your session
Do you already have the session active?
Aaron Spring
@aaronspring
yep but I can restart. Should I do automatic fetch of LFS data or not?
31 replies
Pamela
@pameladelgado
Hi all,
we want to call to your attention to the maintenance that renkulab.io will be undergoing later today (at 10:30AM CEST for 2 hours).
During this time all services will be unavailable and all user sessions will be killed without the possibility of recovery.
We take the opportunity to remind you to subscribe to our status page if you wish to receive notifications about future maintenance.
Thank you for using renku!
Waldo Rivier
@waldorivier_gitlab
image.png
Hi everybody, I got the same issue
6 replies
image.png
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