assert_package() didn't return min version

[ddsjoberg]

print(gtsummary:::assert_package("emmeans"))
#> NULL

^{Created on 2022-07-19 by the reprex package (v2.0.1)}

[larmarange]

Similarly, broom.helpers::.get_min_version_required() doesn't work in GitHub actions (see examples in https://larmarange.github.io/broom.helpers/reference/assert_package.html ) while it's working properly locally on my PC.

[ddsjoberg]

I think it'll work better to use installed.packages() which stores the min version numbers (as opposed parsing the DESCRIPTION file).

[larmarange]

I'm not sure to see your point. You will still have to parse the DESCRIPTION of the package returned by installed.packages() to know the minimum version required by a specific package.

[ddsjoberg]

The returned object from installed.packages() includes the information in Imports, Suggests, etc.

df_pkg_details <-
  installed.packages() |> 
  tibble::as_tibble() |> 
  dplyr::filter(Package == "gtsummary") |> 
  dplyr::select(Depends, Imports, LinkingTo, Suggests, Enhances)
df_pkg_details$Suggests
#> [1] "aod (>= 1.3.1), broom.mixed (>= 0.2.7), car (>= 3.0-11),\ncmprsk, covr, effectsize (>= 0.6.0), emmeans (>= 1.7.3),\nflextable (>= 0.6.10), geepack, GGally (>= 2.1.0), Hmisc,\nhuxtable (>= 5.4.0), insight (>= 0.15.0), kableExtra (>=\n1.3.4), lme4, mgcv, mice (>= 3.10.0), nnet, officer, openxlsx,\nparameters (>= 0.18.1), parsnip (>= 0.1.7), rmarkdown, sandwich\n(>= 3.0.1), scales, smd (>= 0.6.6), spelling (>= 2.2), survey,\nsurvival (>= 3.2-11), testthat (>= 3.0.4), tidycmprsk (>=\n0.1.2), workflows (>= 0.2.4)"

^{Created on 2022-07-19 by the reprex package (v2.0.1)}

[larmarange]

Would something like that be useful in broom.helpers ?

library(tidyverse)

.get_dependencies <- function(pkg = "broom.helpers") {
  utils::installed.packages() %>%
    tibble::as_tibble() %>%
    dplyr::filter(.data$Package == .env$pkg) %>%
    dplyr::select(dplyr::all_of(c("Imports", "Depends", "Suggests", "Enhances", "LinkingTo"))) %>%
    tidyr::pivot_longer(dplyr::everything(), values_to = "package", names_to = "dependency_type") %>%
    tidyr::separate_rows(.data$package, sep = ",") %>%
    dplyr::mutate(package = stringr::str_squish(.data$package)) %>%
    tidyr::separate(.data$package, into = c("package", "version"), sep = " ", extra = "merge", fill = "right") %>%
    dplyr::filter(!is.na(.data$package))
}

.get_dependencies() %>% knitr::kable()

dependency_type	package	version
Imports	broom	NA
Imports	cli	NA
Imports	dplyr	NA
Imports	labelled	NA
Imports	lifecycle	NA
Imports	purrr	NA
Imports	rlang	(>= 1.0.1)
Imports	stats	NA
Imports	stringr	NA
Imports	tibble	NA
Imports	tidyr	NA
Depends	R	(>= 3.4)
Suggests	biglm	NA
Suggests	biglmm	NA
Suggests	brms	(>= 2.13.0)
Suggests	broom.mixed	NA
Suggests	cmprsk	NA
Suggests	covr	NA
Suggests	datasets	NA
Suggests	emmeans	NA
Suggests	fixest	(>= 0.10.0)
Suggests	forcats	NA
Suggests	gam	NA
Suggests	gee	NA
Suggests	geepack	NA
Suggests	ggplot2	NA
Suggests	glmmTMB	NA
Suggests	glue	NA
Suggests	gt	NA
Suggests	gtsummary	NA
Suggests	knitr	NA
Suggests	lavaan	NA
Suggests	lfe	NA
Suggests	lme4	(>= 1.1.28)
Suggests	MASS	NA
Suggests	mgcv	NA
Suggests	mice	NA
Suggests	nnet	NA
Suggests	ordinal	NA
Suggests	parameters	NA
Suggests	parsnip	NA
Suggests	plm	NA
Suggests	rmarkdown	NA
Suggests	rstanarm	NA
Suggests	spelling	NA
Suggests	survey	NA
Suggests	survival	NA
Suggests	testthat	NA
Suggests	tidycmprsk	NA
Suggests	VGAM	NA

.get_dependencies("gtsummary") %>% knitr::kable()

dependency_type	package	version
Imports	broom	(>= 0.8.0)
Imports	broom.helpers	(>= 1.7.0.9003)
Imports	cli	(>= 3.1.1)
Imports	dplyr	(>= 1.0.7)
Imports	forcats	(>= 0.5.1)
Imports	glue	(>= 1.6.0)
Imports	gt	(>= 0.6.0)
Imports	knitr	(>= 1.37)
Imports	lifecycle	(>= 1.0.1)
Imports	purrr	(>= 0.3.4)
Imports	rlang	(>= 0.4.12)
Imports	stringr	(>= 1.4.0)
Imports	tibble	(>= 3.1.6)
Imports	tidyr	(>= 1.1.4)
Depends	R	(>= 3.4)
Suggests	aod	(>= 1.3.1)
Suggests	broom.mixed	(>= 0.2.7)
Suggests	car	(>= 3.0-11)
Suggests	cmprsk	NA
Suggests	covr	NA
Suggests	effectsize	(>= 0.6.0)
Suggests	emmeans	(>= 1.7.3)
Suggests	flextable	(>= 0.6.10)
Suggests	geepack	NA
Suggests	GGally	(>= 2.1.0)
Suggests	Hmisc	NA
Suggests	huxtable	(>= 5.4.0)
Suggests	insight	(>= 0.15.0)
Suggests	kableExtra	(>= 1.3.4)
Suggests	lme4	NA
Suggests	mgcv	NA
Suggests	mice	(>= 3.10.0)
Suggests	nnet	NA
Suggests	officer	NA
Suggests	openxlsx	NA
Suggests	parameters	(>= 0.18.1)
Suggests	parsnip	(>= 0.1.7)
Suggests	rmarkdown	NA
Suggests	sandwich	(>= 3.0.1)
Suggests	scales	NA
Suggests	smd	(>= 0.6.6)
Suggests	spelling	(>= 2.2)
Suggests	survey	NA
Suggests	survival	(>= 3.2-11)
Suggests	testthat	(>= 3.0.4)
Suggests	tidycmprsk	(>= 0.1.2)
Suggests	workflows	(>= 0.2.4)

^{Created on 2022-07-19 by the reprex package (v2.0.1)}

[ddsjoberg]

I think this a great function to include, and we can update .get_min_version_required() to pull the information from here, rather than parsing DESCRIPTION.

[larmarange]

You may have a look at larmarange/broom.helpers#171

New function .get_package_dependencies() returning a tibble with all dependencies, minimum version and comparison operator.

.get_min_version_required() now returns the comparison operator as an attribute

The comparison operator is taken into account by .asset_package()