Dockerizing a shiny app with an error in the building process

huangapple
go评论101阅读模式
英文:

Dockerizing a shiny app with an error in the building process

问题

I built a shiny app couple of months ago and i've been trying to deploy it into a docker for a while...with no success. I checked some other questions like [this one][1] and some other webs, youtube videos but I always get errors builing it.

一段时间前，我创建了一个Shiny应用程序，一直在尝试将其部署到Docker中...但一直没有成功。我查看了一些类似于[这个问题][1]以及其他一些网站和YouTube视频，但每次构建时都会出现错误。

One of the things I saw different is the structure of the app. Most of them, not all, have the simplest structure:

其中一个我发现不同的是应用程序的结构。大多数应用程序，而不是全部，都具有最简单的结构：

  • app
    |
    |-ui.R
    |-server.R
    dockerfile

一个名为app的文件夹，其中包含ui和server两个文件，以及与文件夹同级的dockerfile。

My structure is a little bit different.

我的结构略有不同。

  • app
    • renv
      • library
      • activate.R
      • settings.json
    • src
      • Carga_datos.R
      • packages.R
      • Descriptivo_aplicacion.R
    • www
      • image.png
    • server.R
    • ui.R
    • app.R
  • dockerfile

我的结构略有不同。

My last try with the dockerfile was:

我最后一次尝试使用Dockerfile如下：

  1. FROM rocker/shiny:latest
  3. RUN apt-get update -qq && apt-get -y --no-install-recommends install \
  4.     libxml2-dev \
  5.     libxml2 \
  6.     libcairo2-dev \
  7.     libsqlite3-dev \
  8.     libmariadbd-dev \
  9.     libpq-dev \
  10.     libssh2-1-dev \
  11.     unixodbc-dev \
  12.     libcurl4-openssl-dev \
  13.     libssl-dev
  15. ## update system libraries
  16. RUN apt-get update && \
  17.     apt-get upgrade -y && \
  18.     apt-get -y install r-cran-curl && \
  19.     apt-get clean
  21. # copy necessary files
  22. ## renv.lock file
  23. COPY /app/renv.lock ./renv.lock
  25. ## app folder
  26. COPY /app ./app
  28. # install renv & restore packages
  29. RUN Rscript -e 'install.packages("renv")'
  30. RUN Rscript -e 'renv::restore()'
  32. # expose port
  33. EXPOSE 3838
  35. # run app on container start
  36. CMD ["R", "-e", "shiny::runApp('/app', host = '0.0.0.0', port = 3838)"]

我的最后一次尝试使用Dockerfile如下：

  1. FROM rocker/shiny:latest
  3. RUN apt-get update -qq && apt-get -y --no-install-recommends install \
  4.     libxml2-dev \
  5.     libxml2 \
  6.     libcairo2-dev \
  7.     libsqlite3-dev \
  8.     libmariadbd-dev \
  9.     libpq-dev \
  10.     libssh2-1-dev \
  11.     unixodbc-dev \
  12.     libcurl4-openssl-dev \
  13.     libssl-dev
  15. ## update system libraries
  16. RUN apt-get update && \
  17.     apt-get upgrade -y && \
  18.     apt-get -y install r-cran-curl && \
  19.     apt-get clean
  21. # copy necessary files
  22. ## renv.lock file
  23. COPY /app/renv.lock ./renv.lock
  25. ## app folder
  26. COPY /app ./app
  28. # install renv & restore packages
  29. RUN Rscript -e 'install.packages("renv")'
  30. RUN Rscript -e 'renv::restore()'
  32. # expose port
  33. EXPOSE 3838
  35. # run app on container start
  36. CMD ["R", "-e", "shiny::runApp('/app', host = '0.0.0.0', port = 3838)"]

Errors had been changing, every time I try to create the container with the sentence:

错误一直在变化，每次我尝试使用以下命令创建容器时：

  1. docker build -t actividades .
  3. docker build -t actividades .

I cannot see the error, to be honest.

老实说，我看不到错误。

Thank in advanced and in case more information is needed...happy to share, even to create a repo in github and give access to the code, no problem at all.

提前感谢，如果需要更多信息...乐意分享，甚至创建一个GitHub仓库并提供代码访问权限，完全没问题。

EDIT:

编辑：

I am adding the last part of the message error:

我添加错误消息的最后部分：

  1. #0 2987.8 Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng
  2. #0 2987.8 --------------------------- [ANTICONF] --------------------------------
  3. #0 2987.8 Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
  4. #0 2987.8  * deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
  5. #0 2987.8  * rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
  6. #0 2987.8  * csw: libharfbuzz_dev libfribidi_dev (Solaris)
  7. #0 2987.8  * brew: harfbuzz fribidi (OSX)
  8. #0 2987.8 If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in your
  9. #0 2987.8 PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-config
  10. #0 2987.8 is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
  11. #0 2987.8 R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
  12. #0 2987.8 -------------------------- [ERROR MESSAGE] ---------------------------
  13. #0 2987.8 <stdin>:1:10: fatal error: hb-ft.h: No such file or directory
  14. #0 2987.8 compilation terminated.
  15. #0 2987.8 --------------------------------------------------------------------
  16. #0 2987.8 ERROR: configuration failed for package ‘textshaping’
  17. #0 2987.8 * removing ‘/usr/local/lib/R/site-library/.renv/1/textshaping’
  18. #0 2987.8 Error: install of package 'textshaping' failed [error code 1]
  19. #0 2987.9 Traceback (most recent calls last):
  20. #0 2987.9 12: renv::restore()
  21. #0 2987.9 11: renv_restore_run
  23. <details>
  24. <summary>英文:</summary>
  26. I built a shiny app couple of months ago and i&#39;ve been trying to deploy it into a docker for a while...with no success. I checked some other questions like [this one][1] and some other webs, youtube videos but I always get errors builing it.
  28. One of the things I saw different is the structure of the app. Most of them, not all, have the simplest structure: 
  30. -app &lt;br/&gt;
  31. |&lt;br/&gt;
  32. |-ui.R &lt;br/&gt;
  33. |-server.R &lt;br/&gt;
  34. dockerfile
  36. A folder called app with both files, ui and server and at the level of the folder the dockerfile. 
  38. My structure is a little bit different.
  40. - app&lt;br/&gt;
  41.     * renv &lt;br/&gt;
  42.         * library
  43.         * activate.R
  44.         * settings.json
  45.     * src&lt;br/&gt;
  46.         * Carga_datos.R &lt;br/&gt;
  47.         * packages.R &lt;br/&gt;
  48.         * Descriptivo_aplicacion.R &lt;br/&gt;
  49.     * www &lt;br/&gt;
  50.         * image.png 
  51.     * server.R&lt;br/&gt;
  52.     * ui.R &lt;br/&gt;
  53.     * app.R &lt;br/&gt;
  54. - dockerfile
  56. My last try with the dockerfile was:

FROM rocker/shiny:latest

RUN apt-get update -qq && apt-get -y --no-install-recommends install
libxml2-dev
libxml2
libcairo2-dev
libsqlite3-dev
libmariadbd-dev
libpq-dev
libssh2-1-dev
unixodbc-dev
libcurl4-openssl-dev
libssl-dev

update system libraries

RUN apt-get update &&
apt-get upgrade -y &&
apt-get -y install r-cran-curl &&
apt-get clean

copy necessary files

renv.lock file

COPY /app/renv.lock ./renv.lock

app folder

COPY /app ./app

install renv & restore packages

RUN Rscript -e 'install.packages("renv")'
RUN Rscript -e 'renv::restore()'

expose port

EXPOSE 3838

run app on container start

CMD ["R", "-e", "shiny::runApp('/app', host = '0.0.0.0', port = 3838)"]

  1.     Errors had been changing, every time I try to create the container with the sentence:

docker build -t actividades .

  2. I cannot see the error, to be honest.
  4. Thank in advanced and in case more information is needed...happy to share, even to create a repo in github and give access to the code, no problem at all.
  6. EDIT: 
  8. I am adding the last part of the message error:

#0 2987.8 Using PKG_LIBS=-lfreetype -lharfbuzz -lfribidi -lpng
#0 2987.8 --------------------------- [ANTICONF] --------------------------------
#0 2987.8 Configuration failed to find the harfbuzz freetype2 fribidi library. Try installing:
#0 2987.8 * deb: libharfbuzz-dev libfribidi-dev (Debian, Ubuntu, etc)
#0 2987.8 * rpm: harfbuzz-devel fribidi-devel (Fedora, EPEL)
#0 2987.8 * csw: libharfbuzz_dev libfribidi_dev (Solaris)
#0 2987.8 * brew: harfbuzz fribidi (OSX)
#0 2987.8 If harfbuzz freetype2 fribidi is already installed, check that 'pkg-config' is in your
#0 2987.8 PATH and PKG_CONFIG_PATH contains a harfbuzz freetype2 fribidi.pc file. If pkg-config
#0 2987.8 is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
#0 2987.8 R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
#0 2987.8 -------------------------- [ERROR MESSAGE] ---------------------------
#0 2987.8 <stdin>:1:10: fatal error: hb-ft.h: No such file or directory
#0 2987.8 compilation terminated.
#0 2987.8 --------------------------------------------------------------------
#0 2987.8 ERROR: configuration failed for package ‘textshaping’
#0 2987.8 * removing ‘/usr/local/lib/R/site-library/.renv/1/textshaping’
#0 2987.8 Error: install of package 'textshaping' failed [error code 1]
#0 2987.9 Traceback (most recent calls last):
#0 2987.9 12: renv::restore()
#0 2987.9 11: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
#0 2987.9 10: renv_install_impl(records)
#0 2987.9 9: renv_install_staged(records)
#0 2987.9 8: renv_install_default(records)
#0 2987.9 7: handler(package, renv_install_package(record))
#0 2987.9 6: renv_install_package(record)
#0 2987.9 5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
#0 2987.9 vwritef("\tFAILED")
#0 2987.9 writef(e$output)
#0 2987.9 })
#0 2987.9 4: renv_install_package_impl(record)
#0 2987.9 3: r_cmd_install(package, path)
#0 2987.9 2: r_exec_error(package, output, "install", status)
#0 2987.9 1: stop(error)
#0 2989.1 Execution halted

Dockerfile:32

30 | # install renv & restore packages
31 | RUN Rscript -e 'install.packages("renv")'
32 | >>> RUN Rscript -e 'renv::restore()'
33 |
34 | # expose port

ERROR: failed to solve: process "/bin/sh -c Rscript -e 'renv::restore()'" did not complete successfully: exit code: 1

  2. EDIT 2:
  4. Now the dockerfile is compiled, I added:

install renv & restore packages

RUN R -e "install.packages(c('leaflet', 'dplyr', 'httr', 'jsonlite', 'shinyWidgets', 'shiny', 'stringr', 'tidyverse', 'htmltools', 'leaflet.extras', 'leaflet.extras2', 'raster', 'plotly', 'crosstalk', 'shinydashboard', 'later', 'htmlwidgets'), repos='https://cloud.r-project.org/')"

  1. As suggested by Hailey but now when I try to execute the image:

docker run --rm -p 3838:3838 actividades

  2. Everything looks fine but when I access to ```localhost:3838``` I got the error: ```object &#39;tidyverse&#39; not found``` which is included in the list of the packages to be installed. Any idea?
  4. Thank you in advance because the problem is evolving :)
  6.  
  8.   [1]: https://stackoverflow.com/questions/44406631/deploy-shiny-app-in-rocker-shiny-docker
  10. </details>
  13. # 答案1
  14. **得分**: 1
  16. The docker image is not able to access your R environment to download packages. Instead of using `renv`, try to download each package in your Dockerfile. For example:
  18.     RUN R -e "install.packages(c('shiny', 'rmarkdown'), repos='https://cloud.r-project.org/')"
  21. <details>
  22. <summary>英文:</summary>
  24. The docker image is not able to access your R environment to download packages. Instead of using `renv`, try to download each package in your Dockerfile. For example:
  26.     RUN R -e &quot;install.packages(c(&#39;shiny&#39;, &#39;rmarkdown&#39;), repos=&#39;https://cloud.r-project.org/&#39;)&quot;
  28. </details>

huangapple
  • 本文由 发表于 2023年5月17日 17:03:12
  • 转载请务必保留本文链接：https://go.coder-hub.com/76270326.html
  • r
  • shiny
匿名

发表评论

匿名网友

:?: :razz: :sad: :evil: :!: :smile: :oops: :grin: :eek: :shock: :???: :cool: :lol: :mad: :twisted: :roll: :wink: :idea: :arrow: :neutral: :cry: :mrgreen:

确定