Trying to create a docker container for a shiny app and rgdal isn’t installing properly.
Ubuntu ver:
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 18.04.5 LTS
Release: 18.04
Codename: bionic
I’m using renv with the system like https://www.statworx.com/de/blog/how-to-dockerize-shinyapps/
The Dockerfile looks like this:
cat Dockerfile
#get the base image
#FROM rocker/shiny:latest
#try with r-ver to make it smaller
FROM rocker/r-ver:latest
# system libraries of general use
## install debian packages
RUN apt-get update -qq && apt-get -y --no-install-recommends install
libxml2-dev
libcairo2-dev
libsqlite3-dev
libpq-dev
libssh2-1-dev
unixodbc-dev
r-cran-v8
libv8-dev
net-tools
libprotobuf-dev
protobuf-compiler
libjq-dev
libudunits2-0
libudunits2-dev
libcurl4-gnutls-dev
libssl-dev
# libhdf4-0
# libhdf4-dev
libhdf5-dev
gdal-bin libgdal-dev
# libgdal27
proj-bin libproj-dev
# libgdal-dev
# libgdal20
libgeos-dev
libnetcdf-dev
# libproj-dev
## update system libraries
RUN apt-get update &&
apt-get upgrade -y &&
apt-get clean
# copy necessary files
## renv.lock file
COPY /tfwm-public-dashboard/renv.lock ./renv.lock
# install renv & restore packages
RUN Rscript -e 'install.packages("renv")'
RUN Rscript -e 'renv::restore()'
## app folder
COPY /tfwm-public-dashboard ./app
# expose port
EXPOSE 3838
# run app on container start
CMD ["R", "-e", "shiny::runApp('/tfwm-public-dashboard', host = '0.0.0.0', port = 3838)"]
I’ve commented out dependencies that conflicted when installed, or I added from other solutions and they appeared to have no effect on it.
The error I get after all the other r packages appear to load fine is:
Installing rgdal [1.3-6] ...
Error: install of package 'rgdal' failed
FAILED
Error installing package 'rgdal':
=================================
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
** using staged installation
configure: R_HOME: /usr/local/lib/R
'config' variable 'CPP' is deprecated
configure: CC: gcc
configure: CXX: g++ -std=gnu++11
configure: C++11 support available
configure: rgdal: 1.3-6
checking for /usr/bin/svnversion... no
configure: svn revision: 773
checking for gdal-config... /usr/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 3.0.4
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
./configure: line 1979: ERROR:: command not found
./configure: line 1994: ERROR:: command not found
configure: Install failure: compilation and/or linkage problems.
configure: error: GDALAllRegister not found in libgdal.
ERROR: configuration failed for package ‘rgdal’
* removing ‘/usr/local/lib/R/site-library/.renv/1/rgdal’
Traceback (most recent calls last):
14: renv::restore()
13: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
12: renv_install(records, library)
11: renv_install_staged(records, library)
10: renv_install_default(records, library)
9: handler(package, renv_install_impl(record))
8: renv_install_impl(record)
7: withCallingHandlers(renv_install_package_local(record), error = function(e) {
vwritef("tFAILED")
writef(e$output)
})
6: renv_install_package_local(record)
5: renv_install_package_local_impl(package, path, library)
4: r_cmd_install(package, path, library)
3: r_exec(package, args, "install")
2: r_exec_error(package, output, label)
1: stop(error)
Execution halted
The command '/bin/sh -c Rscript -e 'renv::restore()'' returned a non-zero code: 1
I’ve looked at the other questions around this topic but they don’t seem to have the same error being thrown.
2
Answers
fixed it (kinda)
by going through other versions of rocker Dockerfiles and building a composite, mostly stealing from geospatial. Here is the set up for the docker container that allows the rgdal installation.
It’s hard to tell for sure, but based on that output + the associated configure script it seems like the C++ compiler is not being properly set or picked up:
My suspicion is that
${CXX}
is empty for some reason. You might need to try installing or using a newer version of thergdal
package.