Additional dependencies via Config/Needs/

[ms609]

Following on from #459, I am using install_deps('soft', 'Config/Needs/coverage') in a continuous integration workflow.

This installs my package's dependencies, and any package listed in Config/Needs/coverage: but not the dependencies of the latter.

Specifically, my DESCRIPTION includes Config/Needs/coverage: covr, but install_deps does not install packages from "covr"'s imports, such as "rex", so when I run the script I see "package not installed: 'rex'". I believe that this behaviour differs from that of 'soft': dependencies of soft dependencies are installed.

A possible workaround is to list all the "covr" dependencies under "Config/Needs/coverage:", but this would require me to keep this up to date as dependencies change in the future, which seems inelegant.

[jimhester]

Can you give an example workflow and build log which is failing to install the second order dependencies?

[ms609]

Here we go:

Commit

Workflow file

DESCRIPTION file

Build log

[dragosmg]

Let me start by thanking you all for the hard work you put into this package.

I have encountered a similar issue. I am currently working on the Arrow R package and wanted to add Config/Needs/website: pkgdown to our DESCRIPTION file.

In this context, my expectation is that using remotes::install_deps(dependencies = "Config/Needs/Website") installs both pkgdown and its dependencies*. However, only pkgdown gets installed. Our CI pipeline building the pkgdown website fails due to, for example, fs or memoise not being available - log can be seen here, but the key part seems to be this one:

> pkgdown::build_site(install = FALSE)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called 'memoise'
Calls: loadNamespace ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
1
Error: `docker-compose --file /home/runner/work/arrow/arrow/docker-compose.yml run --rm ubuntu-docs` exited with a non-zero exit code 1, see the process log above.

Somewhat of a reprex (I call this from inside the RStudio project corresponding to the package):

remove.packages(c("pkgdown", "fs", "memoise"))
remotes::install_deps(".", dependencies = "Config/Needs/website")
packageVersion("pkgdown")
packageVersion("fs")
packageVersion("memoise")

It might be worth mentioning that both dependencies = c("hard", "Config/Needs/website")) and dependencies = c("soft", "Config/Needs/website")) do the job, i.e. install pkgdown and its dependencies:

remove.packages(c("pkgdown", "fs", "memoise"))
remotes::install_deps(".", dependencies = c("hard", "Config/Needs/website"))
packageVersion("pkgdown")
packageVersion("fs")
packageVersion("memoise")

but that feels a bit hacky to me as this use case is not clearly stated in the docs and, as a consequence, it makes it a bit difficult to depend on this behaviour.

* I cannot see a scenario in which I would want to install only pkgdown (without its dependencies) as that would mean it's virtually unusable.

[gaborcsardi]

I suggest you use the v2 tag of r-lib/actions which should not have these issues: https://github.com/r-lib/actions#releases-and-tags

[dragosmg]

Thanks for your reply, Gábor! In this case (Arrow), we use both GHA and other CI workflows - the CI pipelines are a bit more complex. This is only one step in a much bigger picture. I don't think we would be able to switch everything to GHA and use r-lib/actions.

[dragosmg]

A follow-up question: does this mean that, for the time being, the only way to use Config/Needs/... reliably is with pak?

[gaborcsardi]

If you trust yourself that this is a bug in remotes, then it seems so.

[jimhester]

I am not sure what the objection to dependencies = c("soft", "Config/Needs/website")) is. Without the soft this is essentially equivalent to install_github("r-lib/pkgdown", dependencies = FALSE), e.g. it would only install pkgdown and not any of its dependencies, which is exactly the behavior you describe. Using c("soft", "Config/Needs/website") is the intended usage.

[dragosmg]

I did not mention this as I'm still trying to figure out if I can (consistently) reproduce an issue I noticed / perceived with "soft" (which directed me towards "hard" and, what I think it was a non-intended use of "hard"). I found "soft" to be slightly different from TRUE as in "soft" is much more recursive. Running install_deps(".", dependencies = c("soft", "Config/Needs/website")) from arrow resulted in the installation of hundreds, if not thousands of (mostly binary) packages over more than 1 hour on a Mac. This made me think I did something wrong and somehow "soft" might not be the behaviour / functionality I was looking for.

[jimhester]

so the way TRUE works is it gives you the 1st order soft dependencies and the 2nd order hard dependencies. soft gives you all of the recursive soft dependencies even the N order dependencies, so you are right, you end up basically installing all of CRAN.

So I guess above I should have written 'hard' rather than 'soft'.

[dragosmg]

@jimhester Thanks for confirming what I noticed. In conclusion, using c("hard", "Config/Needs/website") would not fall under unintended use and, thus, should be appropriate for our use case.
Do you think it might be worth including something similar to your explanation above in the docs for the dependencies argument? As it stands the docs say:

The value "soft" means the same as TRUE,

which I read as "soft" is the equivalent of TRUE.

[jonkeane]

Also, I'm curious if there is a way to have the same behavior as dependencies = TRUE and install one (or more) of the Config/Needs fields at the same time?

We could do remotes::install_deps(dependencies = TRUE) and remotes:: install_deps(dependencies =c("hard", "Config/Needs/website")) to accomplish that, but I wonder if having a direct way of doing that with one call to install_deps() would be nice?

[dragosmg]

I ran a small experiment to understand the differences between "soft", "hard" and TRUE a bit better.

Conclusion:

• TRUE is definitely different from "soft", and
• the combination we need (TRUE + "Config/Needs/website") cannot be achieved with a single function call. (i.e. it is different from c("hard", "Config/Needs/website")).

Details

Investigation results:

test	description	number of packages installed
1	dependencies = TRUE	64
2	dependencies = 'hard'	12
3	dependencies = c('hard', 'Config/Needs/website')	61
4	dependencies = 'soft'	1819
5	dependencies = c('soft', 'Config/Needs/website')	1819
6	dependencies = c('Config/Needs/website')	1

I excluded dependencies = "soft" & combinations of "soft" since they are too recursive and end up installing an excessive number of packages.
dependencies = "hard" & dependencies = "Config/Needs/website" are too narrow.
I compared dependencies = TRUE to dependencies = c("hard", "Config/Needs/website"). While the overall number of installed packages looks promising (64 vs 61), there isn't complete overlap.

indicator	value
packages exclusive to test 1	21
packages exclusive to test 3	18
packages in common	43

We can safely conclude that dependencies = c("hard", "Config/Needs/website") is not equal to dependencies = TRUE + dependencies = c("Config/Needs/website").
We definitely need "Config/Needs/website" - in our case pkgdown and its dependencies, but in combination with dependencies = "hard" it is too narrow in scope, while with dependencies = "soft" it is much too wide.

How I got there?

• I removed all installed packages from the system library (with the exception of "base" and "recommended"packages)
• I installed remotes and rstudioapi in the system library
• each test installed packages to its own folder (configured via the R_LIBS_USER environment variable) with the R session being restarted for each run
• I then compared the contents of the 6 libraries

[gaborcsardi]

Hopefully the situation is better now with pak?