I have a .Rmd along with a .sql file that is read by the .Rmd file that I’m trying to deploy in ShinyProxy. I am able to run this from within RStudio on my Mac.
The application loads, I can see it in ShinyProxy, but when I click on the application, it launches, then says please wait, then the error java.lang.StackOverflowError. I tried increasing the stack size with the JAVA_OPTS in the Dockerfile.
I do see this in shinyproxy.log:
java.lang.reflect.InvocationTargetException: null at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_332] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_332] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_332] at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_332] . . . . Caused by: javax.naming.NoInitialContextException: Need to specify class name in environment or system property, or as an applet parameter, or in an application resource file: java.naming.factory.initial at javax.naming.spi.NamingManager.getInitialContext(NamingManager.java:673) ~[na:1.8.0_332] at javax.naming.InitialContext.getDefaultInitCtx(InitialContext.java:313) ~[na:1.8.0_332] at javax.naming.InitialContext.getURLOrDefaultInitCtx(InitialContext.java:350) ~[na:1.8.0_332] at javax.naming.InitialContext.lookup(InitialContext.java:417) ~[na:1.8.0_332] ... 140 common frames omitted
Dockerfile:
FROM openanalytics/r-base
MAINTAINER John Reber "[email protected]"
ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64
RUN export JAVA_HOME
ENV JAVA_OPTS "-Xms4G -Xmx8G -Xss2G"
RUN export JAVA_OPTS
# Install Java for rJava
RUN apt-get update && \
apt-get install -y default-jdk && \
apt-get install -y default-jre && \
apt-get install -y ca-certificates-java && \
rm -rf /var/lib/apt/lists/*
RUN ["java", "-version"]
CMD javareconf
RUN apt-get update && apt-get install -y \
libcurl4-openssl-dev \
# libcurl4-gnutls-dev \
libssl-dev \
libxml2-dev && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update && apt-get install -y \
libharfbuzz0b && \
rm -rf /var/lib/apt/lists/*
RUN apt-get update && apt-get install -y \
sudo \
pandoc \
pandoc-citeproc \
libcairo2-dev \
libxt-dev \
libssh2-1-dev && \
rm -rf /var/lib/apt/lists/*
WORKDIR /opt/oracle
RUN apt-get update && apt-get install -y libaio1 wget unzip \
&& wget https://download.oracle.com/otn_software/linux/instantclient/instantclient-basiclite-linuxx64.zip \
&& unzip instantclient-basiclite-linuxx64.zip \
&& rm -f instantclient-basiclite-linuxx64.zip \
&& cd /opt/oracle/instantclient* \
&& rm -f *jdbc* *occi* *mysql* *README *jar uidrvci genezi adrci \
&& echo /opt/oracle/instantclient* > /etc/ld.so.conf.d/oracle-instantclient.conf \
&& ldconfig
WORKDIR /
RUN apt-get update && apt-get install -y \
libmysql++-dev \
unixodbc-dev \
libpq-dev && \
rm -rf /var/lib/apt/lists/*
#RUN apt-get update && apt-get install -y \
# libxml2 \
# libssl1.1 && \
# rm -rf /var/lib/apt/lists/*
CMD javareconf
RUN ["java", "-version"]
# install needed R packages
#RUN R -e "install.packages(c('flexdashboard', 'knitr', 'plotly', 'httpuv', 'shiny', 'rJava', 'RJDBC', 'dplyr', 'readr', 'DT', 'lubridate', 'rmarkdown'), dependencies = TRUE, repo='http://cran.r-project.org')"
RUN R -e "install.packages(c('shiny'), dependencies = TRUE, repo='https://cloud.r-project.org')"
RUN R -e "install.packages(c('flexdashboard', 'dplyr', 'rJava', 'RJDBC', 'readr', 'DT', 'lubridate', 'rmarkdown'), dependencies = TRUE, repo='https://cloud.r-project.org')"
# 'sysfonts','gifski', 'Cairo', 'tidyverse',
# make directory and copy Rmarkdown flexdashboard file in it
RUN mkdir -p /prmc
COPY prmc/PRMC.Rmd /prmc/PRMC.Rmd
#COPY prmc/PRMC_Local.Rmd /prmc/PRMC_Local.Rmd
COPY prmc/prmc.sql /prmc/prmc.sql
#COPY prmc/PRMC_ACCRUAL.csv /prmc/PRMC_ACCRUAL.csv
COPY prmc/ojdbc11.jar /prmc/ojdbc11.jar
# Copy Rprofile.site to the image
COPY Rprofile.site /usr/local/lib/R/etc/
# make all app files readable (solves issue when dev in Windows, but building in Ubuntu)
RUN chmod -R 755 /prmc
# expose port on Docker container
EXPOSE 3838
# run flexdashboard as localhost and on exposed port in Docker container
CMD ["R", "-e", "rmarkdown::run('/prmc/PRMC.Rmd', shiny_args = list(port = 3838, host = '0.0.0.0'))"]
application.xml:
proxy:
# title: Open Analytics Shiny Proxy
title: SKCC Open Analytics ShinyProxy
# logo-url: https://www.openanalytics.eu/shinyproxy/logo.png
logo-url: https://ewebapp01pa.jefferson.edu/includes/images/logo-2014.jpg
landing-page: /
heartbeat-rate: 10000
heartbeat-timeout: 60000
port: 8081
# authentication: keycloak
authentication: simple
admin-groups: admin
useForwardHeaders: true
# Example: 'simple' authentication configuration
users:
- name: jack
password: XXXXXXXX
groups: scientists, admin
- name: jeff
password: XXXXXXXXX
groups: mathematicians
# keycloak authentication
keycloak:
auth-server-url: https://kc.kcc.tju.edu/auth
realm: shinyproxy
public-client: true
resource: shinyproxy
credentials-secret: s2NwbneBKh10wG0fHjZjevGnLlNTt44h
use-resource-role-mappings: false
# Docker configuration
docker:
url: http://localhost:2375
port-range-start: 20000
specs:
- id: 01_hello
display-name: Hello Application
description: Application which demonstrates the basics of a Shiny app
container-cmd: ["R", "-e", "shinyproxy::run_01_hello()"]
container-image: openanalytics/shinyproxy-demo
access-groups: [scientists, mathematicians, analyze, admin]
# - id: 06_tabsets
# display-name: 06_tabsets
# description: Application 06_tabsets demonstration
# container-cmd: ["R", "-e", "shinyproxy::run_06_tabsets()"]
# container-image: openanalytics/shinyproxy-demo
# access-groups: []
## - id: euler
# display-name: Euler's number
# container-cmd: [ "R", "-e", "shiny::runApp('/root/euler')" ]
# container-image: openanalytics/shinyproxy-template
# access-groups: scientists
- id: prmc
display-name: PRMC Dashboard
description: (Protocol Review Monitoring Committee Dashboard)
docker-cmd: ["R", "-e rmarkdown::run('/prmc/PRMC.Rmd')"]
container-image: prmc_dashboard3
access-groups: [scientists, mathematicians, analyze, admin]
logging:
file:
name: shinyproxy.log
level:
root: DEBUG
