Close #1940 Removing unnecessary runtime development-related dependencies

[zdz2101]

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• Place Closes #<insert_issue_number> into the beginning of your Pull Request Title (Use Edit button in top-right if you need to update)
• Code is formatted according to the tidyverse style guide. Run styler::style_file() to style R and Rmd files
• Updated relevant unit tests or have written new unit tests, which should consider realistic data scenarios and edge cases, e.g. empty datasets, errors, boundary cases etc. - See Unit Test Guide
• If you removed/replaced any function and/or function parameters, did you fully follow the deprecation guidance?
• Update to all relevant roxygen headers and examples, including keywords and families. Refer to the categorization of functions to tag appropriate keyword/family.
• Run devtools::document() so all .Rd files in the man folder and the NAMESPACE file in the project root are updated appropriately
• Address any updates needed for vignettes and/or templates
• Update NEWS.md if the changes pertain to a user-facing function (i.e. it has an @export tag) or documentation aimed at users (rather than developers)
• Build admiral site pkgdown::build_site() and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.
• Address or fix all lintr warnings and errors - lintr::lint_package()
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[github-actions]

Package	Line Rate	Health
admiral	98%	✔
Summary	98% (4215 / 4287)	✔

[zdz2101]

@galachad Similar to how you accomplished #1942, do you know why only the 4.1 version is failing here for the exclusion or library(rmarkdown)?

[bms63]

ummm... I would of thought devtools:document() was needed to make the admiral-package.Rd file with this update?

[bms63]

Hi @cicdguy any ideas on 4.1 failing check for vignettes?

[zdz2101]

ummm... I would of thought devtools:document() was needed to make the admiral-package.Rd file with this update?

pretty sure devtools::document() is just a wrapper for roxygen2 which according to the sacred text, ie R Packages (2e)

[bms63]

I was thinking that when you update the desciprtion file you need to update the .Rd file that is generated from it. I guess I was mistaken

[bms63]

Did we want to try and clean up the dependencies still? @ddsjoberg and @zdz2101

Perhaps a Wednesday topic and then we can get this PR done?

[zdz2101]

Did we want to try and clean up the dependencies still? @ddsjoberg and @zdz2101

Perhaps a Wednesday topic and then we can get this PR done?

^agreed, brief wednesday discussion should suffice

[manciniedoardo]

Tagging @galachad to look at failing check.

[galachad]

Hi @zdz2101, looks like we need the rmarkdown package in suggest as it's used for output of vignette: output: rmarkdown::html_vignette.

In my opinion we should keep rmarkdown package in Suggest as we are using rmarkdown::html_vignette and having rmarkdown in suggest is default behaviour for all packages.

I'm not sure why it's only occur on 4.1 but my suspicion is the changes in devtools between 2.4.3-2.4.4.

[bms63]

Do you mind removing magrittr, tidyselect and I think we can drop tibble as well??

[zdz2101]

Do you mind removing magrittr, tidyselect and I think we can drop tibble as well??

This actually brings up a good point of implicit dependencies, if we require admiraldev and admiraldev lists these all out (how we're getting by with the dplyr >1), should we be redundantly be keeping them here in admiral ?

[bms63]

Do you mind removing magrittr, tidyselect and I think we can drop tibble as well??

This actually brings up a good point of implicit dependencies, if we require admiraldev and admiraldev lists these all out (how we're getting by with the dplyr >1), should we be redundantly be keeping them here in admiral ?

I think we should keep the main ones for sure. People check the description file and having them over at admiraldev would be another page to track this stuff down??? @ddsjoberg

[zdz2101]

Do you mind removing magrittr, tidyselect and I think we can drop tibble as well??

This actually brings up a good point of implicit dependencies, if we require admiraldev and admiraldev lists these all out (how we're getting by with the dplyr >1), should we be redundantly be keeping them here in admiral ?

I think we should keep the main ones for sure. People check the description file and having them over at admiraldev would be another page to track this stuff down??? @ddsjoberg

Nvm, I was given quite an amount of grief playing around as is, I think anything declared in our R/admiral_package.R file needs to be included, those 3^ listed above need to be included

[bundfussr]

Do you mind removing magrittr, tidyselect and I think we can drop tibble as well??

This actually brings up a good point of implicit dependencies, if we require admiraldev and admiraldev lists these all out (how we're getting by with the dplyr >1), should we be redundantly be keeping them here in admiral ?

I think we should keep the main ones for sure. People check the description file and having them over at admiraldev would be another page to track this stuff down??? @ddsjoberg

I would not rely on implicit dependencies. I think if we call a function in admiral code, we should add the package and the required version to Imports:. I.e., I would require dplyr > 1 also in admiral because we are calling across().

If we remove magrittr, tidyselect, and tibble from Imports:, we would need to update admiral-package.R as well and import the functions from dplyr. However, I am not sure if we should rely on reexports. Using the original packages looks cleaner to me.

[ddsjoberg]

Correct, we cannot rely on implicit dependencies: CRAN would reject us!

We can simple update to re-export functions from dplyr, however: simple and easy, while reducing the number of pkgs listed in our description. I would personally re-export from dplyr, but if you feel strongly against it, either way is fine.

[bms63]

Hi all, @manciniedoardo @bundfussr @ddsjoberg @zdz2101

I think I am losing track of what we were trying to do here.

So if we drop magrittr and tidyselect from the Imports we will need to update the admiral-pacakge.R as seen below to re-export those functions?

[ddsjoberg]

The @importFrom only imports the function for use within the package. We'd want to also export the functions. This is commonly done in a reexport.R script. Here's an example:
https://github.com/pharmaverse/ggsurvfit/blob/main/R/reexport.R

#' @importFrom survival survfit
#' @export
survival::survfit

#' @importFrom survival Surv
#' @export
survival::Surv

#' @importFrom dplyr %>%
#' @export
dplyr::`%>%`

[bundfussr]

So if we drop magrittr and tidyselect from the Imports we will need to update the admiral-pacakge.R as seen below to re-export those functions?

It is not related to re-exporting. I think if we remove magrittr from Imports: but keep @importFrom magrittr %>%, R-CMD check will complain.

[bms63]

i say lets just leave this issue for after the release as I am still a little confused.

apologies for my limited technical knowledge!!

[bms63]

@zdz2101 and @ddsjoberg this one is good to go correct?

[zdz2101]

@zdz2101 and @ddsjoberg this one is good to go correct?

For just Suggestions, yes I believe we mentioned we'll make separate issue for Imports

[bms63]

LGTM!