diff --git a/source/user_guide/FAQ_user.rst b/source/user_guide/FAQ_user.rst index 4b7777ce99b170f5b3f877a8dc83cc08041f9fbc..8e8c19ae099601ac4127575b31896121fb7187a1 100644 --- a/source/user_guide/FAQ_user.rst +++ b/source/user_guide/FAQ_user.rst @@ -49,10 +49,10 @@ or if you get the "503 Service unavailable" page when trying to access to your a | If so, read :ref:`Private registry helm` to indicate that the registry is private, and then provide the credentials with :ref:`Define registry token`. -How to fix build error during docker-compose during R packages installation ? +How to fix build error during docker compose during R packages installation ? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -During the build of docker image following ``docker-compose`` command line, it's possible that installation error occur. +During the build of docker image following ``docker compose`` command line, it's possible that installation error occur. Example : @@ -129,14 +129,98 @@ In order to install it inside your container, you just add it in the ``Dockefile libgdal-dev \ && rm -rf /var/lib/apt/lists/* -After modification, you have just to run again the ``docker-compose`` command line ( see dedicated section :ref:`run locally<run_locally>` ). +After modification, you have just to run again the ``docker compose`` command line ( see dedicated section :ref:`run locally<run_locally>` ). .. code-block:: bash - docker-compose up --build + docker compose up --build +How to fix infinite installing R package during docker compose ? How to install "tidyverse" R packages ? +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +When you run a "docker compose" command, if the step "installation of R package" doesn't finish without error, like in this example with the installation of R package "tidyverse" + +.. tabs:: + + .. code-tab:: console + :caption: local terminal + :linenos: + :emphasize-lines: 2,12,17 + + + docker compose up --build + [+] Building 2138.3s (8/15) + => [shiny-k8s-toolkit internal] load build definition from Dockerfile + => => transferring dockerfile: 1.30kB + => [shiny-k8s-toolkit internal] load metadata for registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.4.0 + => [shiny-k8s-toolkit internal] load .dockerignore + => => transferring context: 2B + => [shiny-k8s-toolkit 1/11] FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.4.0 + => [shiny-k8s-toolkit internal] load build contex=> => transferring context: 22.23kB + => CACHED [shiny-k8s-toolkit 2/11] WORKDIR /srv/shiny-server/ + => CACHED [shiny-k8s-toolkit 3/11] COPY ./my_packages_to_install.csv /opt/scripts/packages_to_install.csv + => [shiny-k8s-toolkit 5/11] RUN Rscript /opt/scripts/install_r_packages.R + => => # i No downloads are needed + => => # v 1 pkg + 68 deps: kept 57 [1.1s] + => => # [1] "Installation done!!" + => => # [1] "Installation of: " + => => # [1] "tidyverse" + + +You need to install some system dependencies in your docker image. Please check the dependencies needed with the R command ``pak::pkg_sysreqs("tidyverse")`` + +.. tabs:: + + .. code-tab:: R + :caption: R console + :linenos: + :selected: + + pak::pkg_system_requirements("tidyverse") + "apt-get install -y libcurl4-openssl-dev libssl-dev make zlib1g-dev pandoc libfreetype6-dev libjpeg-dev libpng-dev libtiff-dev libicu-dev libfontconfig1-dev libfribidi-dev libharfbuzz-dev libxml2-dev" + +Add the dependenciesin the ``Dockerfile`` file like bellow : + + +.. tabs:: + + .. code-tab:: Dockerfile + :caption: Dockerfile + :linenos: + :selected: + + # Add workdir information + WORKDIR /srv/shiny-server/ + + # Build image from the base image, previously configured for you + # Full list of images can be found at + # https://hub.pages.pasteur.fr/shiny-k8s/user_guide/configure_image.html#image-list + FROM registry-gitlab.pasteur.fr/hub/shiny-k8s/r:4.4.0 + + # Add workdir information + WORKDIR /srv/shiny-server/ + + # Install additional dependencies, uncomment the block if you have one, and edit/duplicate line 12 + RUN apt-get update \ + && apt-get install -y \ + libcurl4-openssl-dev \ + libssl-dev \ + make \ + zlib1g-dev \ + pandoc \ + libfreetype6-dev \ + libjpeg-dev \ + libpng-dev \ + libtiff-dev \ + libicu-dev \ + libfontconfig1-dev \ + libfribidi-dev \ + libharfbuzz-dev \ + libxml2-dev \ + && rm -rf /var/lib/apt/lists/* + .. _update_chart_dependency: How to upgrade my helm dependency / I can't enable a feature ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~