I am trying to deploy Shiny App through Docker using windows 10 machine(8GB RAM).
Here is the Dockerfile :
# Base image https://hub.docker.com/u/rocker
FROM rocker/shiny:3.6.3
# system libraries of general use
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
libxml2-dev \
libcairo2-dev \
libsqlite3-dev \
libmariadbd-dev \
libmariadbclient-dev \
libpq-dev \
libssl-dev \
libcurl4-openssl-dev \
libssh2-1-dev \
unixodbc-dev \
&& install2.r --error \
--deps TRUE \
tidyverse \
dplyr \
devtools \
formatR \
remotes \
selectr \
caTools \
BiocManager \
&& rm -rf /tmp/downloaded_packages
# copy necessary files
## app folder
COPY /shinyapp/shinyapp.Rproj /srv/shiny-server/
COPY /shinyapp/ui.R /srv/shiny-server/
COPY /shinyapp/server.R /srv/shiny-server/
COPY /shinyapp/global.R /srv/shiny-server/
# install renv & restore packages
RUN Rscript -e 'install.packages("shiny", repos='http://cran.rstudio.com/')'
RUN Rscript -e 'install.packages("shinydashboard", repos='http://cran.rstudio.com/')'
RUN Rscript -e 'install.packages("glue", repos='http://cran.rstudio.com/')'
# expose port
EXPOSE 3838
RUN sudo chown -R shiny:shiny /srv/shiny-server
# run app on container start
CMD ["/usr/bin/shiny-server.sh"]
The Folder Structure is as follows :
Dockerfile
shinyapp ---> global.R ,
ui.R,
server.R
I tried troubleshooting and checked the name of the files. Everything is correct.
But still getting the error
Any help will be great !!
Follow this steps
/Users/myUserName/.docker
ls -a
rm -rf .token_seed
if it doesn't resolve the issue
remove '.token_seed.lock' file as well
Related
I am new to docker and not an IT-specialist. I try to install Kartoza Geoserver in Docker on Heroku, but so far no success. Does anyone has experience with this and can explain me the settings in the dockerfile and the steps specifically for a Heroku install?
So far I tried a build with a modified dockerfile but I always get the same error (in the log trail) when opening/launching geoserver on Heroku:
"Error: groupadd: cannot open /etc/group".
I guess it is an permission/privileges issue.
Any sharing of experience on modifying the docker file so that the image is read by Heroku would be helpfull.
Modifying the settings in the dockerfile:
Removed the port forwarding from dockerfile
Add RUN adduser -D myuser USER myuser to dockerfile
Result dockerfile:
#--------- Generic stuff all our Dockerfiles should start with so we get caching ------------
ARG IMAGE_VERSION=9.0.65-jdk11-openjdk-slim-buster
ARG JAVA_HOME=/usr/local/openjdk-11
FROM tomcat:$IMAGE_VERSION
LABEL maintainer="Tim Sutton<tim#linfiniti.com>"
ARG GS_VERSION=2.22.0
ARG WAR_URL=https://downloads.sourceforge.net/project/geoserver/GeoServer/${GS_VERSION}/geoserver-${GS_VERSION}-war.zip
ARG STABLE_PLUGIN_BASE_URL=https://sourceforge.net/projects/geoserver/files/GeoServer
ARG DOWNLOAD_ALL_STABLE_EXTENSIONS=1
ARG DOWNLOAD_ALL_COMMUNITY_EXTENSIONS=1
ARG HTTPS_PORT=8443
ENV DEBIAN_FRONTEND=noninteractive
#Install extra fonts to use with sld font markers
RUN adduser -D myuser
USER myuser
RUN set -eux; \
apt-get update; \
apt-get -y --no-install-recommends install \
locales gnupg2 wget ca-certificates rpl pwgen software-properties-common iputils-ping \
apt-transport-https curl gettext fonts-cantarell lmodern ttf-aenigma \
ttf-bitstream-vera ttf-sjfonts tv-fonts libapr1-dev libssl-dev \
wget zip unzip curl xsltproc certbot cabextract gettext postgresql-client figlet gosu gdal-bin; \
# Install gdal3 - bullseye doesn't build libgdal-java anymore so we can't upgrade
curl https://deb.meteo.guru/velivole-keyring.asc | apt-key add - \
&& echo "deb https://deb.meteo.guru/debian buster main" > /etc/apt/sources.list.d/meteo.guru.list \
&& apt-get update \
&& apt-get -y --no-install-recommends install gdal-bin libgdal-java; \
dpkg-divert --local --rename --add /sbin/initctl \
&& (echo "Yes, do as I say!" | apt-get remove --force-yes login) \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*; \
# verify that the binary works
gosu nobody true
ENV \
JAVA_HOME=${JAVA_HOME} \
DEBIAN_FRONTEND=noninteractive \
GEOSERVER_DATA_DIR=/opt/geoserver/data_dir \
GDAL_DATA=/usr/share/gdal \
LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/tomcat/native-jni-lib:/usr/lib/jni:/usr/local/apr/lib:/opt/libjpeg-turbo/lib64:/usr/lib:/usr/lib/x86_64-linux-gnu" \
FOOTPRINTS_DATA_DIR=/opt/footprints_dir \
GEOWEBCACHE_CACHE_DIR=/opt/geoserver/data_dir/gwc \
CERT_DIR=/etc/certs \
RANDFILE=/etc/certs/.rnd \
FONTS_DIR=/opt/fonts \
GEOSERVER_HOME=/geoserver \
EXTRA_CONFIG_DIR=/settings \
COMMUNITY_PLUGINS_DIR=/community_plugins \
STABLE_PLUGINS_DIR=/stable_plugins
WORKDIR /scripts
ADD resources /tmp/resources
ADD build_data /build_data
ADD scripts /scripts
RUN echo $GS_VERSION > /scripts/geoserver_version.txt ;\
chmod +x /scripts/*.sh;/scripts/setup.sh \
&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN echo 'figlet -t "Kartoza Docker GeoServer"' >> ~/.bashrc
WORKDIR ${GEOSERVER_HOME}
ENTRYPOINT ["/bin/bash", "/scripts/entrypoint.sh"]
Then build it with argument --platform linux/amd64 (I use arm64 architecture). Then pushed it to Heroku. All the time I get the same error.
I am getting the following error inside my docker container:
How can I update my dockerfile, so that while building the container it builds with a version of wkhtmltopdf with patched Qt.
Following is my dockerfile:
...
RUN apt-get install -y wkhtmltopdf
RUN apt-get install -y xvfb
COPY requirements.txt requirements.txt
RUN pip3 install -r requirements.txt
...
Installing the following dependencies with wkhtmltopdf worked out for me:
...
RUN apt-get update
RUN apt-get install -y xvfb
RUN apt-get install -y wget
RUN apt-get install -y openssl build-essential xorg libssl1.0-dev
RUN wget https://github.com/wkhtmltopdf/wkhtmltopdf/releases/download/0.12.4/wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
RUN tar xvJf wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
RUN cp wkhtmltox/bin/wkhtmlto* /usr/bin/
...
FROM php:7.4-fpm
# Install dependencies, libssl1.1-dev ?
RUN apt-get update && apt-get install -y \
xvfb \
wget \
openssl \
xorg \
libssl1.1 \
build-essential \
libpng-dev \
libjpeg62-turbo-dev \
libfreetype6-dev \
locales \
zip \
jpegoptim optipng pngquant gifsicle \
vim \
unzip \
git \
curl \
libzip-dev \
dcmtk \
nginx \
supervisor
RUN wget https://github.com/wkhtmltopdf/wkhtmltopdf/releases/download/0.12.4/wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
RUN tar xvJf wkhtmltox-0.12.4_linux-generic-amd64.tar.xz
RUN cp wkhtmltox/bin/wkhtmlto* /usr/bin/
# Clear cache
RUN apt-get clean && rm -rf /var/lib/apt/lists/*
COPY php.ini /usr/local/etc/php/php.ini
# adjustments to php.ini base on the production version.
# Install extensions and configure
RUN docker-php-ext-configure gd --with-freetype --with-jpeg
RUN docker-php-ext-configure zip
RUN docker-php-ext-install pdo_mysql zip exif pcntl gd sockets
# RUN sed -E -i -e 's/max_execution_time = 1200/max_execution_time = 120/' /etc/php.ini \
# && sed -E -i -e 's/memory_limit = 128M/memory_limit = 512M/' /etc/php.ini \
# && sed -E -i -e 's/post_max_size = 8M/post_max_size = 64M/' /etc/php.ini \
# && sed -E -i -e 's/upload_max_filesize = 2M/upload_max_filesize = 64M/' /etc/php.ini
# php artisan storage:link
# THAT NEEDS TO BE RUN FROM THE nginx-home/LaravelPortal/ directory to symlink the storage directory. NEED to figure out how to do that.
# sudo docker exec -it orthanc-docker-dev_ris_php-fpm_1 /bin/bash
COPY default.conf /etc/nginx/conf.d/default.conf
COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
COPY entrypoint.sh /
ENTRYPOINT ["/bin/bash","/entrypoint.sh"]
I am trying to create a docker container for a shiny application. To do that, I have the following docker file:
# Start from an image containing R
FROM r-base:latest
# Install dependencies
RUN apt-get update && apt-get install -y \
sudo \
gdebi-core \
pandoc \
pandoc-citeproc \
libcurl4-gnutls-dev \
libcairo2-dev/unstable \
libxt-dev \
libssl-dev \
gsl-bin \
libgsl0-dev \
default-jdk
RUN wget --no-verbose https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/VERSION -O "version.txt" && \
VERSION=$(cat version.txt) && \
wget --no-verbose "https://s3.amazonaws.com/rstudio-shiny-server-os-build/ubuntu-12.04/x86_64/shiny-server-$VERSION-amd64.deb" -O ss-latest.deb && \
gdebi -n ss-latest.deb && \
rm -f version.txt ss-latest.deb
# I needed this for rJava-related errors
RUN R CMD javareconf
# Install R packages required by my app
RUN R -e "install.packages(c('shiny', 'xlsx', 'tidyr', 'DT', 'RColorBrewer', 'ggdendro', 'dendsort', 'grid', 'gridExtra', 'igraph', 'circlize', 'gplots', 'shinyFiles', 'shinydashboard', 'shinyjs', 'devtools', 'fpc', 'cluster', 'readr', 'CytobankAPI', 'stringr', 'dplyr', 'tibble'), repos='http://cran.rstudio.com/')"
# Install Bioconductor dependencies
RUN Rscript -e 'source("http://bioconductor.org/biocLite.R")' -e 'biocLite("ComplexHeatmap")'
# Remove Shiny example inherited from the base image
RUN rm -rf /srv/shiny-server/*
# copy the app to the image
COPY shiny-server.conf /etc/shiny-server/shiny-server.conf
RUN mkdir /srv/shiny-server/cytocluster/
COPY ./* /srv/shiny-server/cytocluster/
EXPOSE 3838
COPY shiny-server.sh /usr/bin/shiny-server.sh
RUN chmod +x /usr/bin/shiny-server.sh
CMD ["/usr/bin/shiny-server.sh"]
The image was created without any error but when I run:
docker run --rm -p 3838:3838 [image]
it just runs without the app coming up. Any suggestions/hints?
Many thanks in advance.
I tried to installed a LAMP stack with a DockerFile in a directory on my desktop /home/username/Desktop/docker/lamp/:
FROM ubuntu:16.04
VOLUME ["/var/www"]
RUN apt-get update && \
apt-get dist-upgrade -y && \
apt-get install -y \
apache2 \
php7.0 \
php7.0-cli \
libapache2-mod-php7.0 \
php7.0-gd \
php7.0-json \
php7.0-ldap \
php7.0-mbstring \
php7.0-mysql \
php7.0-pgsql \
php7.0-sqlite3 \
php7.0-xml \
php7.0-xsl \
php7.0-zip \
php7.0-soap
COPY apache_default /etc/apache2/sites-available/000-default.conf
COPY run /usr/local/bin/run
RUN chmod +x /usr/local/bin/run
RUN a2enmod rewrite
EXPOSE 80
CMD ["/usr/local/bin/run"]
Then on my terminal, I run it:
$ docker build -t docker-lamp .
Step 4 : COPY apache_default /etc/apache2/sites-available/000-default.conf
lstat apache_default: no such file or directory
What I have done wrong? How can I fix this?
First of all, are you 100% sure the files apache_default and run are in the same directory as the Dockerfile?
I'm trying to build a LAMP container and I have already built several containers: httpd 2.4.23, redis 3.0.7, mysql 5.6.30 by compiling them myself from source code downloaded archives. I have based all of these above on the debian container.
Now that I'm doing the php 5.6.20 container it complains that it does not know about apache and mysql.
Here is the Dockerfile for the php container:
FROM debian
RUN apt-get update
RUN apt-get install -y build-essential;
RUN apt-get install -y cmake;
RUN apt-get install -y libfreetype6-dev libjpeg-dev libpng12-dev libcurl4-openssl-dev libbz2-dev libxml2-dev libxslt-dev libgd2-xpm-dev php5-imap libz-dev
WORKDIR /usr/bin/
COPY php-5.6.20.tar.gz /usr/bin/
RUN gzip -d php-5.6.20.tar.gz
RUN tar -xvf php-5.6.20.tar
RUN ln -s php-5.6.20 php
WORKDIR /usr/bin/php/
RUN ./configure \
--prefix=/usr/bin/ \
--with-apxs2=/usr/bin/apache/bin/apxs \
--with-config-file-path=/usr/bin/php-5.6.20/ \
--enable-libgcc \
--with-mysqli=/usr/bin/mysql/mysql_config \
--with-zlib-dir=/usr \
--with-jpeg-dir=/usr \
--with-png-dir=/usr \
--with-gd \
--enable-gd-native-ttf \
--with-freetype-dir=/usr \
--enable-ftp \
--enable-xml \
--enable-zip \
--with-bz2 \
--enable-wddx \
--without-pear \
--enable-mbstring \
--with-curl
RUN make
RUN make install
I wonder if I should base it instead on: FROM httpd:2.4.23. But then I would need to base httpd on the mysql one, and / or on the redis one... I don't really like that setup.
I have also installed Docker Compose but I wonder if it could be helpful in my situation.
UPDATE: Here is the fully working Dockerfile
FROM debian
RUN apt-get update
RUN apt-get install -y build-essential;
RUN apt-get install -y cmake;
RUN apt-get install -y openssl libssl-dev;
RUN apt-get install -y libpcre3 libpcre3-dev
WORKDIR /usr/bin/
COPY httpd-2.4.23.tar.gz /usr/bin/
RUN gzip -d httpd-2.4.23.tar.gz
RUN tar -xvf httpd-2.4.23.tar
RUN ln -s httpd-2.4.23 httpd
COPY apr-1.5.2.tar.gz /usr/bin/httpd/srclib/
COPY apr-util-1.5.4.tar.gz /usr/bin/httpd/srclib/
WORKDIR /usr/bin/httpd/srclib/
RUN gzip -d apr-1.5.2.tar.gz
RUN gzip -d apr-util-1.5.4.tar.gz
RUN tar -xvf apr-1.5.2.tar
RUN tar -xvf apr-util-1.5.4.tar
RUN ln -s apr-1.5.2 apr;
RUN ln -s apr-util-1.5.4 apr-util
WORKDIR /usr/bin/httpd/
RUN ./configure \
--prefix=/usr/bin/apache \
--enable-rewrite \
--enable-deflate \
--enable-ssl
RUN make
RUN make install
RUN apt-get update
RUN apt-get install -y libncurses-dev
COPY mysql-5.6.30.tar.gz /usr/bin/
WORKDIR /usr/bin/
RUN gzip -d mysql-5.6.30.tar.gz
RUN tar -xvf mysql-5.6.30.tar
RUN ln -s mysql-5.6.30 mysql
WORKDIR /usr/bin/mysql/
RUN mkdir install; mkdir install/data; mkdir install/var; mkdir install/etc; mkdir install/tmp
RUN cd /usr/bin/mysql/; cmake \
-DCMAKE_INSTALL_PREFIX=/usr/bin/mysql/install \
-DWITH_INNOBASE_STORAGE_ENGINE=1 \
-DMYSQL_DATADIR=/usr/bin/mysql/install/data \
-DDOWNLOAD_BOOST=1 \
-DWITH_BOOST=/usr/bin/mysql/install/boost \
-DMYSQL_UNIX_ADDR=/usr/bin/mysql/install/tmp/mysql.sock
RUN make
RUN make install
RUN apt-get update
RUN apt-get install -y libfreetype6-dev libjpeg-dev libpng12-dev libcurl4-openssl-dev libbz2-dev libxml2-dev libxslt-dev libgd2-xpm-dev php5-imap libz-dev
WORKDIR /usr/bin/
COPY php-5.6.20.tar.gz /usr/bin/
RUN gzip -d php-5.6.20.tar.gz
RUN tar -xvf php-5.6.20.tar
RUN ln -s php-5.6.20 php
WORKDIR /usr/bin/php/
RUN ./configure \
--prefix=/usr/bin/php \
--with-apxs2=/usr/bin/apache/bin/apxs \
--with-config-file-path=/usr/bin/php-5.6.20/ \
--enable-libgcc \
--with-mysqli=/usr/bin/mysql/install/bin/mysql_config \
--with-zlib-dir=/usr \
--with-jpeg-dir=/usr \
--with-png-dir=/usr \
--with-gd \
--enable-gd-native-ttf \
--with-freetype-dir=/usr \
--enable-ftp \
--enable-xml \
--enable-zip \
--with-bz2 \
--enable-wddx \
--without-pear \
--enable-mbstring \
--with-openssl
--with-curl
RUN make
RUN make install
ENTRYPOINT ["/usr/bin/apache/bin/apachectl", "start", "-D FOREGROUND"]
EXPOSE 80
# Build the container: docker build -t stephaneeybert/httpd:2.4.23 .
# Run the container: docker run -d -p 127.0.0.1:80:80 --name httpd stephaneeybert/httpd:2.4.23
# Check that the port is open: nmap -p 8081 localhost
If you need apache running in your container, you can install apache in your image with above Dockerfile, just as the same as you install the build-essential stuffs. Which means:
RUN apt-get install -y apache2
or similar command. If you also need the configure for this apache application, you can use ADD or COPY command to add your configure file from outside to inside of your container. More details can be found here.
If you need apache as an independent container, you can use docker-compse to achieve it. Start apache in another container, then use depends_on to config the dependency between your containers. You may use ports to change the port number of each container, so they can communicate between each other.