search

CSCfi / rstudio-openshift

MIT License
7 stars 15 forks source link

Require 4.0.3 for latest Bioconductor 3.12 #2

Closed vondoRishi closed 3 years ago

vondoRishi commented 3 years ago

Hi,

I like to use Bioconductor 3.12 which requires R 4.0.3. I have tried to use "rocker/tidyverse:4.0.3" in the Dockerfile. However, it has caused an error similar to this issue.

Now I am using "rocker/tidyverse:4.0.2" but it would be nice to have a solution for R 4.0.3

Thanks

koetjen commented 3 years ago

Hi,

I've rebuilt the rocker installation for R 4.0.3 to support Bioconductor 3.12 on our cluster by resetting to RStudio 1.3. It's available to pull at koetjen/rstudio:4.0.3

Dockerfile:


FROM rocker/r-ver:4.0.3-cuda10.1
LABEL org.label-schema.license="GPL-2.0" \
      org.label-schema.vcs-url="https://github.com/rocker-org/rocker-versioned" \
      org.label-schema.vendor="Rocker Project" \
      maintainer="Carl Boettiger <cboettig@ropensci.org>"
ENV S6_VERSION=v2.0.0.1
ENV RSTUDIO_VERSION=1.3.1093
ENV PANDOC_VERSION=default
ENV TENSORFLOW_VERSION=gpu
ENV KERAS_VERSION=default
ENV PATH=/usr/lib/rstudio-server/bin:$PATH
RUN /rocker_scripts/install_rstudio.sh
RUN /rocker_scripts/install_pandoc.sh
RUN /rocker_scripts/install_tidyverse.sh
RUN /rocker_scripts/install_tensorflow.sh
RUN /rocker_scripts/install_verse.sh
RUN /rocker_scripts/install_geospatial.sh
EXPOSE 8787
CMD ["/init"]
vondoRishi commented 3 years ago

Thanks a lot. Additionally, I have added few more lines to add shiny-server. Please let me know if you have any comments regarding this.

FROM rocker/r-ver:4.0.3-cuda10.1 LABEL org.label-schema.license="GPL-2.0" \ org.label-schema.vcs-url="https://github.com/rocker-org/rocker-versioned" \ org.label-schema.vendor="Rocker Project" \ maintainer="Carl Boettiger cboettig@ropensci.org" ENV S6_VERSION=v2.0.0.1 ENV RSTUDIO_VERSION=1.3.1093 ENV PANDOC_VERSION=default ENV TENSORFLOW_VERSION=gpu ENV KERAS_VERSION=default ENV SHINY_SERVER_VERSION=latest ENV PATH=/usr/lib/rstudio-server/bin:$PATH RUN /rocker_scripts/install_rstudio.sh RUN /rocker_scripts/install_pandoc.sh RUN /rocker_scripts/install_tidyverse.sh RUN /rocker_scripts/install_tensorflow.sh RUN /rocker_scripts/install_verse.sh RUN /rocker_scripts/install_geospatial.sh RUN /rocker_scripts/install_shiny_server.sh EXPOSE 3838 8787 CMD ["/init"]