Hi All,
Does anyone have experience successfully installing and loading the R package
�ggbreak� in a Docker container?
I ask because I have successfully used the �ggbreak� package in a script
outside the Docker container (on my local computer), but for some reason, I get
the following error message when trying to load it using library(ggbreak) or
library(�ggbreak�) inside the same script that has been copied to the Docker
container:
Error in library(ggbreak) : there is no package called 'ggbreak'
Execution halted
I have tried installing �ggbreak� using Bioconductor, the �ggbreak� GitHub
repo, and the standard install.packages() function in R, and none have helped.
The image is building successfully; the issue is specifically when I run the
container, which generates the above error message. I am wondering if I am
missing some type of dependency upstream, or something else.
Please see the contents of the Dockerfile below:
FROM selenium/standalone-firefox:127.0
USER root
ENV SE_OFFLINE=true
ENV PATH "$PATH:/usr/bin/geckodriver"
ENV HOME "/root/"
RUN apt-get update \
&& apt install -y \
software-properties-common \
dirmngr \
gnupg2 \
wget \
build-essential \
libcurl4-openssl-dev \
libxml2-dev \
libasound2 \
# libasound2t64 \
python3 \
python3-pip \
python3.11-venv \
# python3.12-venv \
git-all \
lsb-release \
libxml-twig-perl \
libc6-dev \
vim \
&& wget -q -O -
https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc \
| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& add-apt-repository -y "ppa:marutter/rrutter4.0"
RUN apt-get update -y \
&& apt-get install -y r-base\
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/*
RUN pip3 install --upgrade pip wheel setuptools>5
RUN pip3 install pandas
RUN pip3 install openpyxl
RUN pip3 install selenium-firefox
RUN pip3 install --no-cache-dir --upgrade rbase
RUN pip3 install webdriver-manager
RUN pip3 install 'rpy2>=3.5.12'
RUN pip3 install xlsxwriter
# Install additional R packages
# RUN R -e "install.packages(c('tools', 'ggplot2', 'ggbreak', 'ggrepel',
'stringr'), repos='http://cran.us.r-project.org')"
RUN R -e "install.packages('tools', repos='http://cran.us.r-project.org')"
RUN R -e "install.packages('ggplot2', repos='http://cran.us.r-project.org')"
# RUN R -e "install.packages('ggbreak', repos='http://cran.us.r-project.org')"
# RUN R -e "install.packages('remotes', repos='http://cran.rstudio.com/')"
# RUN R -e "remotes::install_github('YuLab-SMU/ggbreak')"
RUN R -e "install.packages('ggrepel', repos='http://cran.us.r-project.org')"
RUN R -e "install.packages('stringr', repos='http://cran.us.r-project.org')"
RUN R -e "install.packages('BiocManager', repos='http://cran.us.r-project.org')"
RUN R -e "BiocManager::install('ggbreak')"
# Create an app directory
RUN mkdir /app
RUN mkdir /volume_w_htmls
RUN mkdir /volume
RUN mkdir /volume2
RUN mkdir /home/seluser/Downloads
# Set the working directory
WORKDIR /app
# Copy bash script to Docker image
COPY ./webscraping_combined_boxplots.sh /app/webscraping_combined_boxplots.sh
# Make bash script executable
RUN chmod +x /app/webscraping_combined_boxplots.sh
ENTRYPOINT ["/app/webscraping_combined_boxplots.sh"]
CMD ["param1", "param2", "param3", "param4", "param5", "param6", "param7",
"param8", "param9", "param10", "param11", "param12", "param13", "param14",
"param15", "param16", "param17", "param18", "param19"]
Would you please advise?
Thank you in advance for your help.
Br,
Lauren
--
Lauren J. Gerber
Bioinformatician
Precision Systems Medicine (Kallioniemi) Research Group
iCAN � Digital Precision Cancer Medicine Flagship
Institute for Molecular Medicine Finland (FIMM)
Nordic EMBL Partnership for Molecular Medicine
Biomedicum Helsinki 2U, D301a1
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland
lauren.ger...@helsinki.fi
[[alternative HTML version deleted]]
_______________________________________________
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
