rawrr::buildRawrrExe() fails

[SamThilmany]

I have created a Docker container based on rocker/r2u for my statistical analyses. Unfortunately, rawrr is not included in the pool of r2u packages and therefore has to be installed manually.
I have attempted to do so both in the Dockerfile and in the terminal of the finished container and failed in both cases. The rawrr package can be installed, but the rawrr::buildRawrrExe() process fails. According to the error message, a log file was stored under /root/.cache/R/rawrr/rawrrassembly/rawrr_build.log.*, but this file does not exist.

Here is the full error message:

Attempting to build 'rawrr.exe', one time setup ...
Error in rawrr::buildRawrrExe() : 
  Building 'rawrr.exe' failed. For details see the build report, supposed to be saved in:
'/root/.cache/R/rawrr/rawrrassembly/rawrr_build.log.9fa3cd0ef28'
Call 'rawrr::installRawrrExe()' to download and install a precompiled version
from a remote location. Note this requires internet connection.
In addition: Warning message:
In system2(cmd, cmdArgs, wait = TRUE, stderr = TRUE, stdout = TRUE) :
  running command ''xbuild' /p:OutputPath='/root/.cache/R/rawrr/rawrrassembly'/ /p:AdditionalLibPaths='/root/.cache/R/rawrr/rawrrassembly' /v:diagnostic /flp:LogFile='/root/.cache/R/rawrr/rawrrassembly/rawrr_build.log.9fa3cd0ef28' rawrr.csproj 2>&1' had status 134
Execution halted

Do you know what the problem might be?

---

Dockerfile

# Use the r2u image as the base
FROM rocker/r2u

# Switch to the root user
USER root

# Set the working directory to /app
WORKDIR /app

# Install Mono
RUN apt-get update && \
    apt-get install -y --no-install-recommends \
    mono-mcs \
    mono-xbuild

# Install Jupyter Notebook and IRkernel
RUN apt-get update && apt-get install -y --no-install-recommends \
    python3 \
    python3-pip

RUN pip3 install --upgrade pip && \
    pip3 install jupyter

RUN apt-get install -y --no-install-recommends \
    r-cran-irkernel

RUN Rscript -e "IRkernel::installspec(user = FALSE)"

# Install R Packages
RUN apt-get install -y --no-install-recommends \
    r-cran-tidyverse \
    r-cran-showtext \
    r-cran-ggally \
    r-cran-cowplot \
    r-cran-ggrepel \
    r-cran-doparallel \
    r-cran-combinat \
    r-cran-biocmanager \
    r-bioc-limma \
    r-bioc-clusterprofiler \
    r-bioc-annotationdbi \
    r-bioc-org.hs.eg.db

# Install rawrr
RUN R -e "BiocManager::install('rawrr', update = TRUE, ask = FALSE)" \
    R -e "tools::R_user_dir('rawrr', which = 'cache')" \
    R -e "rawrr::installRawFileReaderDLLs()" \
    R -e "rawrr::buildRawrrExe()"

# Expose the Jupyter Notebook port
EXPOSE 8888

# Create JupyterLab configuration directory
RUN mkdir -p /etc/jupyter

# Add JupyterLab configuration to save notebooks in /app/notebooks
RUN echo "c.NotebookApp.notebook_dir = '/app/notebooks'" >> /etc/jupyter/jupyter_lab_config.py
RUN echo "c.MappingKernelManager.kernel_cmd_timeout = 3600" >> /etc/jupyter/jupyter_notebook_config.py

# # Command to run Jupyter Notebook
CMD ["jupyter", "lab", "--ip=0.0.0.0", "--port=8888", "--no-browser", "--allow-root"]

docker-compose.yml

version: '3'

services:
  jupyter:
    build:
      context: ..
      dockerfile: ./jupyter-r/Dockerfile
    ports:
      - "8888:8888"
    volumes:
      - ../notebooks:/app/notebooks  # Mount a local folder to store notebooks
    environment:
      - TZ=UTC+1  # Set the container timezone
    image: jupyter_r
    container_name: jupyter_r

[tobiasko]

Hi @SamThilmany,

I am unfortunately not to familiar with building docker containers. Does the location /root/.cache/R/rawrr/rawrrassembly/ exist for the file system of the docker container? Can you place a file there using the command line of the container (is it writeable)? Have you tested the basic functionality of the mono compiler? Was is correctly build/installed in the container? On which platform do you run the docker container (OS)?

Have you ever tried to install rawrr in a bioc docker container?

https://www.bioconductor.org/help/docker/

Does it show the same behaviour?

Sorry for the many question.

Best,
Tobi

[tobiasko]

The mono project homepage shows some basic tests for the mono compiler

https://www.mono-project.com/docs/getting-started/mono-basics/

[tobiasko]

I think it would be nice to develop a recipe for rawrr application within containers.

[SamThilmany]

Hi @tobiasko,

Given that rocker/r2u is currently (and will likely remain) fixed on the AMD64 system architecture, I encountered significant slowness in my Docker container since I'm running it on an ARM64 host system. Consequently, I decided to completely rebuild my container using debian:bookworm as the base image and installing only the necessary components for my specific use-case, including rawrr.

In this updated environment, buildRawrrExe() successfully completed its task on the first attempt. This leads me to suspect that there may have been issues with the Rosetta translation from AMD64 to ARM64, causing the previous build to fail. I intend to upload the Dockerfile on GitHub and will provide a link to it in this thread to ensure others can access a functional Docker container with rawrr. If there's interest, I can adapt the Dockerfile to include only the essential requirements for running rawrr as a contribution to this project.

[tobiasko]

Maybe it would even make sense to publish your docker image on docker hub? A container image based on Debian Bookworm might be interesting for people that don't like the bioconductor containers for some reason.

[tobiasko]

The bioc containers incl. stuff like RStudio server, which is of course a cool thing for people that depend on an IDE, but there is for sure also people how prefer a stripped down minimal image.

https://github.com/Bioconductor/bioconductor_docker