Hello Renku Team,
I am working on the SV deployment of Renku. I chose to update the template version of the following project: https://sv-renku.epfl.ch/projects/pulver/ensembl-tss-clustering-r/
But since I tried that, trying to launch Renku using any commit (the last one or ones before the template update) leads to an image build failure. Could you please help ?
Thanks !
Here is the error log:
Running with gitlab-runner 14.2.0 (58ba2b95)
on sv-renku-git-run.epfl.ch cMGas78W
Preparing the "docker" executor 00:02
Using Docker executor with image docker:stable ...
Pulling docker image docker:stable ...
Using docker image sha256:b0757c55a1fdbb59c378fd34dde3e12bd25f68094dd69546cf5ca00ddbaa7a33 for docker:stable with digest docker@sha256:fd4d028713fd05a1fb896412805daed82c4a0cc84331d8dad00cb596d7ce3e3a ...
Preparing environment 00:01
Running on runner-cmgas78w-project-435-concurrent-0 via e70a719a144d...
Getting source from Git repository
Fetching changes with git depth set to 50...
Reinitialized existing Git repository in /builds/pulver/ensembl-tss-clustering-r/.git/
Checking out 7ae8b358 as renku/autosave/pulver/master/dcb187c/7ae8b35...
Skipping Git submodules setup
Executing "step_script" stage of the job script 00:09
Using docker image sha256:b0757c55a1fdbb59c378fd34dde3e12bd25f68094dd69546cf5ca00ddbaa7a33 for docker:stable with digest docker@sha256:fd4d028713fd05a1fb896412805daed82c4a0cc84331d8dad00cb596d7ce3e3a ...
$ docker login -u gitlab-ci-token -p $CI_JOB_TOKEN http://$CI_REGISTRY
WARNING! Using --password via the CLI is insecure. Use --password-stdin.
WARNING! Your password will be stored unencrypted in /root/.docker/config.json.
Configure a credential helper to remove this warning. See
https://docs.docker.com/engine/reference/commandline/login/#credentials-store
Login Succeeded
$ CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7)
$ docker build --tag $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA_7 .
Step 1/7 : FROM renku/renkulab-bioc:RELEASE_3_12-0.7.5
---> d9ada51fe1e4
Step 2/7 : COPY install.R /tmp/
---> Using cache
---> b5cff42447da
Step 3/7 : RUN R -f /tmp/install.R
---> Using cache
---> fe431e678234
Step 4/7 : COPY requirements.txt /tmp/
---> Using cache
---> 91701e307f73
Step 5/7 : RUN pip3 install -r /tmp/requirements.txt
---> Using cache
---> 876a3813e9c4
Step 6/7 : ARG RENKU_VERSION=0.14.2
---> Using cache
---> a7a6f3082a75
Step 7/7 : RUN if [ -n "$RENKU_VERSION" ] ; then pipx uninstall renku && pipx install --force renku==${RENKU_VERSION} ; fi
---> Running in a64a42c47abe
upgrading shared libraries...
uninstalled renku! ✨ 🌟 ✨
Fatal error from pip prevented installation. Full pip output in file:
/home/rstudio/.local/pipx/logs/cmd_2021-09-22_07.12.10_pip_errors.log
pip seemed to fail to build package:
rdflib-jsonld<0.6.0,>=0.5.0
Some possibly relevant errors from pip install:
ERROR: Could not find a version that satisfies the requirement rdflib-jsonld<0.6.0,>=0.5.0 (from renku) (from versions: 0.2, 0.3, 0.4.0, 0.5.0, 0.6.0, 0.6.1, 0.6.2)
ERROR: No matching distribution found for rdflib-jsonld<0.6.0,>=0.5.0
Error installing renku from spec 'renku==0.14.2'.
creating virtual environment...
installing renku from spec 'renku==0.14.2'...
The command '/bin/sh -c if [ -n "$RENKU_VERSION" ] ; then pipx uninstall renku && pipx install --force renku==${RENKU_VERSION} ; fi' returned a non-zero code: 1
Cleaning up file based variables 00:01
ERROR: Job failed: exit code 1