Update Proposal

[LeonKalderon]

Hello,

Many thanks for contributing the Broadsea images.

I am currently using Broadsea and I observed some things that may help improve the image.

In https://github.com/OHDSI/Broadsea/ repo you suggest adding for persistence the following volumes:

volumes:
      - ./home/rstudio:/home/rstudio
      - ./site-library:/usr/local/lib/R/site-library

By doing this, the volume is mounted on /usr/local/lib/R/site-library and the content in this directory is discarded. More specifically, this directory contains all the OHDSI libraries that have been installed through the image building process.
(

Broadsea-MethodsLibrary/Dockerfile

Line 18 in 46ab047

RUN installGithub.r \

).

I tried to solve this problem by moving all the libraries from /usr/local/lib/R/site-library to /usr/local/lib/R/library by adding one more step in the Dockerfile.

## Install OHDSI R packages
RUN installGithub.r \
	OHDSI/SqlRender \
	OHDSI/DatabaseConnector \
	OHDSI/OhdsiRTools \
	OHDSI/Achilles \
	OHDSI/Cyclops \
	OHDSI/FeatureExtraction \
	OHDSI/BigKnn \
	OHDSI/PatientLevelPrediction@development \
	OHDSI/CohortMethod \
	OHDSI/PublicOracle \
	hadley/xml2 \
	cloudyr/aws.s3 \
	OHDSI/OhdsiSharing \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds

RUN mv -v /usr/local/lib/R/site-library/* /usr/local/lib/R/library

It seems to work, but I do not know if this is a good practice.

Also, I noticed that the following packages that are required for building the predictive model packages that have been exported from Atlas are missing:
ff, ffbase, rvg, shiny, shinycssloaders, shinydashboard

Finally, I think that the image in DockerHub is a bit outdated and it would be nice to build and push a new image.
The previous week, R's XML library have been updated and requires R>=4.0. This library is a requirement for many OHDSI packages like PatientLevelPrediction and FeatureExtraction.

Sorry for this long issue, I can break it down to smaller ones if you'd like to proceed with any of these updates. Also I can open a PR with the changes.

Thanks :)