James W. MacDonald
2024-Oct-15 13:21 UTC
[R-sig-Debian] 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 at r-project.org> On Behalf Of
Gerber, Lauren J
Sent: Tuesday, October 15, 2024 9:15 AM
To: r-sig-debian at r-project.org
Cc: dirk at 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 "$PATH:/usr/bin/geckodriver"
ENV HOME "/root/"
RUN apt-get update \
&& apt install -y \
software-properties-common \
dirmngr \
gnupg2 \
wget \
build-essential \
libcurl4-openssl-dev \
libxml2-dev \
libasound2 \
# libasound2t64 \
python3 \
python3-pip \
python3.11-venv \
# python3.12-venv \
git-all \
lsb-release \
libxml-twig-perl \
libc6-dev \
vim \
&& wget -q -O -
https://urldefense.com/v3/__https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc__;!!K-Hz7m0Vt54!j4qWJp3neZb132HVgGwaZ3mog2adnEcdl8X0OTb3wuUcviOwwus9E8QSsmCmKta8dZ-FmpzQOKC7qePXnj1qvC-XQQ$
\
| 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 at helsinki.fi
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On 15 October 2024 at 13:21, James W. MacDonald wrote:
| Don't you have to load BiocManager before using it?
Correct. The most minimal 'proof' I can offer is that after
docker run --rm -ti rocker/r2u:noble
the one line 'two-command' wrapping both R CMD INSTALL for BiocManager
plus
calling BiocManager::install() for ggbreak, ie
time (install.r BiocManager; installBioc.r ggbreak)
finishes in 16 seconds from my machine (on decent connectivity) installing 35
(binary) packages in total on Ubuntu 24.04 ending in
[... stuff omitted ...]
'getOption("repos")' replaces Bioconductor standard
repositories, see
'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Installing package(s) 'BiocVersion', 'ggbreak'
[... two screens full of logs omitted]
Setting up r-cran-ggbreak (0.1.2-1.ca2404.1) ...
real 0m16.012s
user 0m8.481s
sys 0m2.769s
This uses binaries thanks to r2u [1] but you can of course do it 'by
hand'
from source too if you ensure you have all your ducks in a row as all
packages are in good standing at CRAN and BioConductor. Doing it
incrementally and carefully perusing your build logs should get you there.
Dirk
[1] More about r2u is at https://eddelbuettel.github.io/r2u/
--
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
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 at helsinki.fi
From: James W. MacDonald <jmacdon at uw.edu>
Date: Tuesday, 15. October 2024 at 16.22
To: Gerber, Lauren J <lauren.gerber at helsinki.fi>, r-sig-debian at
r-project.org <r-sig-debian at r-project.org>
Cc: dirk at eddelbuettel.com <dirk at 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 at r-project.org> On Behalf Of
Gerber, Lauren J
Sent: Tuesday, October 15, 2024 9:15 AM
To: r-sig-debian at r-project.org
Cc: dirk at 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 at helsinki.fi
[[alternative HTML version deleted]]
[[alternative HTML version deleted]]
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