run_app and datasets not recognized as exported when using docker files

[moodymudskipper]

I created a golem app and tested the deployment on shinyapp.io where it worked smoothly.

Then I created a docker file and tried to deploy it but for some reason it told me run_app wasn't an exported function.

This was fixed by replacing in the docker file mypkg::run_app() by mypkg:::run_app() (adding third :).

This is puzzling to me as the "#' @export" line is definitely there (I didn't tweak the boilerplate), and again, this works locally and on shinyapps.io.

Then I ran into issues because my datasets were not recognized, this could be solved by replacing the last line of the docker file by :

CMD R -e 'data(dataset1,package = "mypkg");data(dataset2,package = "mypkg");options("shiny.port"=80,shiny.host="0.0.0.0");mypkg:::run_app()'

This kind of namespace issues happened to me in the past when passing in my package expressions to functions from other packages that would use NSE.

Finally a simple solution could solve all at once, just add a library call to attach my package.

CMD R -e 'library(mypkg);run_app()'

[jtrecenti]

@moodymudskipper I also had this problem and solved adding mypkg::dataset every time my dataset is called. In a shiny with many modules this could be painful, so I would suggest creating reactive() objects to store the mypkg::dataset calls and call the reactive when you need the data.

There are other options here: https://coolbutuseless.github.io/2018/12/10/r-packages-internal-and-external-data/

Good luck!

[ColinFay]

Note to self: try and see if using "Lazyload: false" in the DESCRIPTION changes that

[maxheld83]

I think this might be related to https://github.com/ThinkR-open/golem/issues/413.

[ColinFay]

For some reason I haven't clearly identified yet, some internal dataset are not recognized, and the best way to do this is to explicitely namespace them, which is not a viable solution.

Issue right now is that I haven't find a way yet to reprex this reliably. I'll keep you posted on this :)

[psolymos]

Hi all, I have run into this issue recently, and I am glad to see a few options out there. The mypkg::dataset is cumbersome, but CMD R -e 'library(mypkg);run_app()' in the Dockerfile is what I did and is the most straightforward solution.

I also feel that there is a difference between {golem} approach and runApp() from app directory, that is the use of the global.R file. I use the global.R file to load packages (like the library(mypkg) in CMD), load and pre-process data sets that should be available globally, set global variables (which is covered by get_golem_config()).

In the Docker context, a way would be to use CMD Rscript index.R and use the index.R file to load necessary objects:

options("shiny.port"=80,shiny.host="0.0.0.0")
library(mypkg)
mydata <- t(myotherdata)
run_app()

Question would be how to automate this part given that the build_zone is removed after package install. I can see having it in inst/app/index.R with the following template:

options("shiny.port"=80,shiny.host="0.0.0.0")
mypkg::run_app()

And with these lines added to the Dockerfile:

...
RUN rm -rf ./build_zone
COPY inst/app/index.R .
EXPOSE 80
CMD Rscript index.R

Users can then edit the index.R file as they would the global.R.

Of course one can do this without {golem} following course. I just wanted to throw this into the mix because this might be an overlooked consequence of the early decision of "you don't need global.R in {golem}" (see https://github.com/ThinkR-open/golem/issues/6). @ColinFay what do you think?

[VincentGuyader]

Hi all,

Do you have an example where doing "library(mypkg);run_app()" does not solve all the problems with data?

in my opinion (but I may be wrong) if you need to source a file, there is a problem in the package (you have to play with the Lazyload parameters)

[ColinFay]

Hey,

Please see : https://github.com/ThinkR-open/golem/issues/413#issuecomment-2182500403

TLDR: add explicit namespacing pkg::dataset to your dataset, because pkg::function() doesn’t have access to the dataset before you library("pkg").