[R-sig-Debian] R Package: 'ggbreak' in Dockerfile
Gerber, Lauren J
|@uren@gerber @end|ng |rom he|@|nk|@||
Tue Oct 15 15:51:02 CEST 2024
Hi James,
I just tried fixing my script and added library(BiocManager) before library(ggbreak), then rebuilt the image, and am still getting the same error.
Error in library(ggbreak) : there is no package called 'ggbreak'
Execution halted
I will say that when I ran docker exec docker_container_id R -e "installed.packages()" I get the following:
Package LibPath Version
BiocManager "BiocManager" "/usr/local/lib/R/site-library" "1.30.25"
BiocVersion "BiocVersion" "/usr/local/lib/R/site-library" "3.19.1"
R6 "R6" "/usr/local/lib/R/site-library" "2.5.1"
RColorBrewer "RColorBrewer" "/usr/local/lib/R/site-library" "1.1-3"
Rcpp "Rcpp" "/usr/local/lib/R/site-library" "1.0.13"
cli "cli" "/usr/local/lib/R/site-library" "3.6.3"
colorspace "colorspace" "/usr/local/lib/R/site-library" "2.1-1"
digest "digest" "/usr/local/lib/R/site-library" "0.6.37"
dplyr "dplyr" "/usr/local/lib/R/site-library" "1.1.4"
fansi "fansi" "/usr/local/lib/R/site-library" "1.0.6"
farver "farver" "/usr/local/lib/R/site-library" "2.1.2"
generics "generics" "/usr/local/lib/R/site-library" "0.1.3"
ggplot2 "ggplot2" "/usr/local/lib/R/site-library" "3.5.1"
ggrepel "ggrepel" "/usr/local/lib/R/site-library" "0.9.6"
glue "glue" "/usr/local/lib/R/site-library" "1.8.0"
gridGraphics "gridGraphics" "/usr/local/lib/R/site-library" "0.5-1"
gtable "gtable" "/usr/local/lib/R/site-library" "0.3.5"
isoband "isoband" "/usr/local/lib/R/site-library" "0.2.7"
labeling "labeling" "/usr/local/lib/R/site-library" "0.4.3"
lifecycle "lifecycle" "/usr/local/lib/R/site-library" "1.0.4"
magrittr "magrittr" "/usr/local/lib/R/site-library" "2.0.3"
munsell "munsell" "/usr/local/lib/R/site-library" "0.5.1"
patchwork "patchwork" "/usr/local/lib/R/site-library" "1.3.0"
pillar "pillar" "/usr/local/lib/R/site-library" "1.9.0"
pkgconfig "pkgconfig" "/usr/local/lib/R/site-library" "2.0.3"
rlang "rlang" "/usr/local/lib/R/site-library" "1.1.4"
scales "scales" "/usr/local/lib/R/site-library" "1.3.0"
stringi "stringi" "/usr/local/lib/R/site-library" "1.8.4"
stringr "stringr" "/usr/local/lib/R/site-library" "1.5.1"
tibble "tibble" "/usr/local/lib/R/site-library" "3.2.1"
tidyselect "tidyselect" "/usr/local/lib/R/site-library" "1.2.1"
utf8 "utf8" "/usr/local/lib/R/site-library" "1.2.4"
vctrs "vctrs" "/usr/local/lib/R/site-library" "0.6.5"
viridisLite "viridisLite" "/usr/local/lib/R/site-library" "0.4.2"
withr "withr" "/usr/local/lib/R/site-library" "3.0.1"
KernSmooth "KernSmooth" "/usr/lib/R/library" "2.23-24"
MASS "MASS" "/usr/lib/R/library" "7.3-61"
Matrix "Matrix" "/usr/lib/R/library" "1.6-5"
base "base" "/usr/lib/R/library" "4.4.1"
boot "boot" "/usr/lib/R/library" "1.3-30"
class "class" "/usr/lib/R/library" "7.3-22"
cluster "cluster" "/usr/lib/R/library" "2.1.6"
codetools "codetools" "/usr/lib/R/library" "0.2-19"
compiler "compiler" "/usr/lib/R/library" "4.4.1"
datasets "datasets" "/usr/lib/R/library" "4.4.1"
foreign "foreign" "/usr/lib/R/library" "0.8-86"
grDevices "grDevices" "/usr/lib/R/library" "4.4.1"
graphics "graphics" "/usr/lib/R/library" "4.4.1"
grid "grid" "/usr/lib/R/library" "4.4.1"
lattice "lattice" "/usr/lib/R/library" "0.22-5"
methods "methods" "/usr/lib/R/library" "4.4.1"
mgcv "mgcv" "/usr/lib/R/library" "1.9-1"
nlme "nlme" "/usr/lib/R/library" "3.1-165"
nnet "nnet" "/usr/lib/R/library" "7.3-19"
parallel "parallel" "/usr/lib/R/library" "4.4.1"
rpart "rpart" "/usr/lib/R/library" "4.1.23"
spatial "spatial" "/usr/lib/R/library" "7.3-15"
splines "splines" "/usr/lib/R/library" "4.4.1"
stats "stats" "/usr/lib/R/library" "4.4.1"
stats4 "stats4" "/usr/lib/R/library" "4.4.1"
survival "survival" "/usr/lib/R/library" "3.7-0"
tcltk "tcltk" "/usr/lib/R/library" "4.4.1"
tools "tools" "/usr/lib/R/library" "4.4.1"
utils "utils" "/usr/lib/R/library" "4.4.1"
As you can see, ggbreak is not there. Please let me know if you have any additional thoughts.
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.gerber using helsinki.fi
From: James W. MacDonald <jmacdon using uw.edu>
Date: Tuesday, 15. October 2024 at 16.22
To: Gerber, Lauren J <lauren.gerber using helsinki.fi>, r-sig-debian using r-project.org <r-sig-debian using r-project.org>
Cc: dirk using eddelbuettel.com <dirk using eddelbuettel.com>
Subject: RE: R Package: 'ggbreak' in Dockerfile
Don't you have to load BiocManager before using it?
-----Original Message-----
From: R-SIG-Debian <r-sig-debian-bounces using r-project.org> On Behalf Of Gerber, Lauren J
Sent: Tuesday, October 15, 2024 9:15 AM
To: r-sig-debian using r-project.org
Cc: dirk using eddelbuettel.com
Subject: Re: [R-sig-Debian] R Package: 'ggbreak' in Dockerfile
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 "$PATH:/usr/bin/geckodriver"
ENV HOME "/root/"
RUN apt-get update \
&& apt install -y \
software-properties-common \
dirmngr \
gnupg2 \
wget \
build-essential \
libcurl4-openssl-dev \
libxml2-dev \
libasound2 \
# libasound2t64 \
python3 \
python3-pip \
python3.11-venv \
# python3.12-venv \
git-all \
lsb-release \
libxml-twig-perl \
libc6-dev \
vim \
&& wget -q -O - https://urldefense.com/v3/__https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj1qvC-XQQ$<https://urldefense.com/v3/__https:/cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj1qvC-XQQ$> \
| tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
&& add-apt-repository -y "ppa:marutter/rrutter4.0"
RUN apt-get update -y \
&& apt-get install -y r-base\
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/* /tmp/*
RUN pip3 install --upgrade pip wheel setuptools>5 RUN pip3 install pandas RUN pip3 install openpyxl RUN pip3 install selenium-firefox RUN pip3 install --no-cache-dir --upgrade rbase RUN pip3 install webdriver-manager RUN pip3 install 'rpy2>=3.5.12'
RUN pip3 install xlsxwriter
# Install additional R packages
# RUN R -e "install.packages(c('tools', 'ggplot2', 'ggbreak', 'ggrepel', 'stringr'), repos='https://urldefense.com/v3/__http://cran.us.r-project.org__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj0ggNUwsA$ ')"
RUN R -e "install.packages('tools', repos='https://urldefense.com/v3/__http://cran.us.r-project.org__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj0ggNUwsA$ ')"
RUN R -e "install.packages('ggplot2', repos='https://urldefense.com/v3/__http://cran.us.r-project.org__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj0ggNUwsA$ ')"
# RUN R -e "install.packages('ggbreak', repos='https://urldefense.com/v3/__http://cran.us.r-project.org__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj0ggNUwsA$ ')"
# RUN R -e "install.packages('remotes', repos='https://urldefense.com/v3/__http://cran.rstudio.com/__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj1ACvaCfA$ ')"
# RUN R -e "remotes::install_github('YuLab-SMU/ggbreak')"
RUN R -e "install.packages('ggrepel', repos='https://urldefense.com/v3/__http://cran.us.r-project.org__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj0ggNUwsA$ ')"
RUN R -e "install.packages('stringr', repos='https://urldefense.com/v3/__http://cran.us.r-project.org__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj0ggNUwsA$ ')"
RUN R -e "install.packages('BiocManager', repos='https://urldefense.com/v3/__http://cran.us.r-project.org__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj0ggNUwsA$ ')"
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.gerber using helsinki.fi
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