lock_validate {pacs}

Validate a specific renv lock file

Description

This function will be especially useful when renv lock file is built manually. Checking if packages in the lock file have correct versions taking into account their DESCRIPTION files requirements (c("Depends", "Imports", "LinkingTo")). Moreover identifying which packages are newest releases. Optionally we could add life duration and CRAN check page status for each dependency.

Usage

lock_validate(
  path,
  lifeduration = FALSE,
  checkred = list(scope = character(0), flavors = NULL),
  lib.loc = .libPaths(),
  repos = biocran_repos()
)

Arguments

path

character path to the shiny app. Default: "."

lifeduration

logical if to assess life duration for each package in the library. For installed newest releases of packages, a local evaluation is used. ⁠MEATCRAN CRANDB⁠ is used for libraries with less than 500 packages. Otherwise the direct web page download from CRAN is used. Default: 'FALSE“

checkred

list with two named fields, scope and flavor. scope of R CRAN check pages statuses to consider, any of c("ERROR", "FAIL", "WARN", "NOTE"). flavor is a vector of CRAN machines to consider, which might be retrieved with pacs::cran_flavors()$Flavor. By default an empty scope field deactivated assessment for checkred column, and NULL flavor will results in checking all machines. Default: list(scope = character(0), flavor = NULL)

lib.loc

character vector of search paths with local packages. Default: .libPaths()

repos

character vector of repositories URLs to use. By default checking CRAN and newest Bioconductor per R version. Default pacs::biocran_repos()

Value

data.frame with 2/6/7/8 columns.

Package

character a package name.

Version.expected.min

(conditional) (Internet needed) character expected by DESCRIPTION files minimal version. "" means not specified so the newest version.

Version.expected

character package version in the renv lock file.

version_status

(conditional) numeric -1/0/1 which comes from utils::compareVersion function. 0 means that we have the same version as required by DESCRIPTION files. -1 means we have too low version installed, this is an error. 1 means we have higher version.

newest

logical (Internet needed) if the installed version is the newest one.

cran

logical (Internet needed) if the package is on CRAN, version is not taken into account here.

checkred

(Optional) (Internet needed) logical if the NEWEST package contains any specified statuses on CRAN check page.

lifeduration

(Optional) (Internet needed) integer number of days a package was released.

Note

Version.expected.min column not count packages which are not a dependency for any package, so could not be find in DESCRIPTION files. Version.expected.min and version_status are assessed only if there are less than 500 packages in the lock file. When turn on the lifeduration option, calculations might be time consuming when there is more than 500 packages. The crandb R packages database is a part of METACRAN project, source: Csárdi G, Salmon M (2022). pkgsearch: Search and Query CRAN R Packages. ⁠https://github.com/r-hub/pkgsearch⁠, ⁠https://r-hub.github.io/pkgsearch/⁠.

Examples

## Not run: 
# path or url
url <- "https://raw.githubusercontent.com/Polkas/pacs/master/tests/testthat/files/renv_test.lock"
pacs::lock_validate(url)

pacs::lock_validate(
  url,
  checkred = list(scope = c("ERROR", "FAIL"), flavors = pacs::match_flavors())
)

pacs::lock_validate(
  url,
  lifeduration = TRUE,
  checkred = list(scope = c("ERROR", "FAIL"), flavors = NULL)
)

## End(Not run)