Wrong entry point with Rstudio

RenkuLab
1

Hi all

I have forked 2 projects and started new environments in both the forks and parent project. For all of them the entry point for rstudio is no longer the project folder but the rstudio home folder, /home/rstudio instead of /home/rstudio/work/project_name.

Not sure if that is related, but looking at the logs for the new session they all show the same errors:

fatal: repository '//renku-env.git' does not exist
find: ‘/tmp/renku-env’: No such file or directory
OK
You are using renku version 0.16.0, however version 0.16.2 is available.
You should consider upgrading ...
/home/rstudio//.Rproj
chown: changing ownership of '/home/rstudio/.rstudio/projects_settings/next-session-project': Operation not permitted
chown: changing ownership of '/home/rstudio/.rstudio/projects_settings': Operation not permitted

Side effect of this: when forking and opening a new session no new project_name.rproj project file is created. Because there is no valid project to open the git plugin is also disabled. Opening a project at least enables git and activates the desired project.

cheers

1 Like
2

Hi @a_user,
thanks for reporting this. Yes, we have changed the way we mount the volume which holds the cloned repo into the user session to avoid some symbolic link which was somewhat confusing. However, the change should not manifest in the way you’ve described, at least not for projects which are based on our more recent base images. Could you maybe point me to the project you have forked?

3

So the solution to this problem contains two steps:

  1. Bump the used base image to the latest (ie 0.10.1) version. You do this by editing your Dockerfile, for example by replacing
    ARG RENKU_BASE_IMAGE=renku/renkulab-r:4.0.5-0.8.0 with ARG RENKU_BASE_IMAGE=renku/renkulab-r:4.0.5-0.10.1.

  2. Due recent problems with breaking changes in dependencies of the renku python package, we also changed the way we install renku in the images. When updating to a 0.10.1 base image, you will therefore also have to replace the last block in your Dockerfile

########################################################
# Do not edit this section and do not add anything below

# Install renku from pypi or from github if it's a dev version
RUN if [ -n "$RENKU_VERSION" ] ; then \
        currentversion=$(pipx list | sed -n "s/^\s*package\srenku\s\([^,]\+\),.*$/\1/p") ; \
        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
            pipx uninstall renku ; \
            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\3/p"); \
            if [ -n "$gitversion" ] ; then \
                pipx install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
            else \
                pipx install --force renku==${RENKU_VERSION} ;\
            fi \
        fi \
    fi

########################################################

with

########################################################
# Do not edit this section and do not add anything below

# Install renku from pypi or from github if it's a dev version
RUN if [ -n "$RENKU_VERSION" ] ; then \
        source .renku/venv/bin/activate ; \
        currentversion=$(renku --version) ; \
        if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
            pip uninstall renku -y ; \
            gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; \
            if [ -n "$gitversion" ] ; then \
                pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
            else \
                pip install --force renku==${RENKU_VERSION} ;\
            fi \
        fi \
    fi

########################################################

This should fix the problems described by the @a_user.

1 Like
4

Hi Andreas

This does indeed solve the issue. Thanks a lot.

cheers

1 Like