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 [[alternative HTML version deleted]]
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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