Package 'pacs' reference manual

Title:	Supplementary Tools for R Packages Developers
Description:	Supplementary utils for CRAN maintainers and R packages developers. Validating the library, packages and lock files. Exploring a complexity of a specific package like evaluating its size in bytes with all dependencies. The shiny app complexity could be explored too. Assessing the life duration of a specific package version. Checking a CRAN package check page status for any errors and warnings. Retrieving a DESCRIPTION or NAMESPACE file for any package version. Comparing DESCRIPTION or NAMESPACE files between different package versions. Getting a list of all releases for a specific package. The Bioconductor is partly supported.
Authors:	Maciej Nasinski [aut, cre]
Maintainer:	Maciej Nasinski <[email protected]>
License:	GPL (>= 3)
Version:	0.6.0
Built:	2024-10-27 06:21:16 UTC
Source:	https://github.com/polkas/pacs

The shiny app dependencies

Description

the shiny app dependencies packages are checked recursively. The c("Depends", "Imports", "LinkingTo") DESCRIPTION files fields are checked recursively. The required dependencies have to be installed in the local repository. The default arguments setup is recommended.

Usage

app_deps(
  path = ".",
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  local = TRUE,
  base = FALSE,
  description_v = FALSE,
  recursive = TRUE,
  repos = biocran_repos()
)
app_deps(
  path = ".",
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  local = TRUE,
  base = FALSE,
  description_v = FALSE,
  recursive = TRUE,
  repos = biocran_repos()
)

Arguments

`path`	`character` path to the shiny app. Default: `"."`
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`local`	`logical` if to use local repository (or newest remote packages). Default: TRUE
`base`	`logical` if to add base packages too. If `TRUE` then `pacs::pacs_base()` are taken into account. Default: `FALSE`
`description_v`	`logical` if the dependencies version should be taken from description files, minimal required. By default installed versions are taken. Default: `FALSE`
`recursive`	`logical` if to assess the dependencies recursively. Default: TRUE
`repos`	`character` vector base URLs of the repositories to use. By default checking CRAN and newest Bioconductor per R version. Default `pacs::biocran_repos()`

Value

character vector with dependency packages or data.frame when checking recursively.

Note

renv package has to be installed.

Examples

## Not run: 
library(renv)
# Please update the path to the custom shiny app
app_path <- system.file("examples/04_mpg", package = "shiny")
pacs::app_deps(app_path)
pacs::app_deps(app_path, recursive = FALSE)

## End(Not run)
## Not run: 
library(renv)
# Please update the path to the custom shiny app
app_path <- system.file("examples/04_mpg", package = "shiny")
pacs::app_deps(app_path)
pacs::app_deps(app_path, recursive = FALSE)

## End(Not run)

Size of the shiny app

Description

The size of shiny app is a sum of dependencies packages and the app directory. The app dependencies packages are checked recursively, and only in local repository. The default arguments setup is recommended.

Usage

app_size(
  path = ".",
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  recursive = TRUE
)
app_size(
  path = ".",
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  recursive = TRUE
)

Arguments

`path`	`character` path to the shiny app. Default: `"."`
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`recursive`	`logical` if to assess the dependencies recursively. Default: TRUE

Value

numeric size in bytes, to get MB ten divide by 10**6.

Note

renv package has to be installed. base packages (pacs::pacs_base()) are not taken into account.

Examples

## Not run: 
library(renv)
# Please update the path to the shiny app
cat(pacs::app_size(system.file("examples/04_mpg", package = "shiny")) / 10**6, "MB")

## End(Not run)
## Not run: 
library(renv)
# Please update the path to the shiny app
cat(pacs::app_size(system.file("examples/04_mpg", package = "shiny")) / 10**6, "MB")

## End(Not run)

Retrieving all Bioconductor releases

Description

Retrieving all Bioconductor releases. The data is downloaded from ⁠https://www.bioconductor.org/about/release-announcements/⁠.

Usage

bio_releases()
bio_releases()

Value

data.frame with the same structure as the html table on ⁠https://www.bioconductor.org/about/release-announcements/⁠.

Note

Results are cached for 30 minutes with memoise package.

Examples

## Not run: 
pacs::bio_releases()

## End(Not run)
## Not run: 
pacs::bio_releases()

## End(Not run)

CRAN and Bioconductor repositories

Description

CRAN and Bioconductor repositories. The newest Bioconductor release for the specific R version is assumed.

Usage

biocran_repos(version = NULL)
biocran_repos(version = NULL)

Arguments

version

character the Bioconductor release. By default the newest Bioconductor release for the specific R version is assumed, if not available only CRAN repository is returned. Available Bioconductor versions for your R version could be checked with pacs::bio_releases(). Default NULL

Value

⁠named character⁠ vector of repositories.

Note

The Internet connection is needed to get Bioconductor repositories.

Examples

## Not run: 
pacs::biocran_repos()

## End(Not run)
## Not run: 
pacs::biocran_repos()

## End(Not run)

Retrieving all R CRAN packages check pages statuses.

Description

Retrieving all R CRAN packages check pages statuses. The data is downloaded from ⁠https://cran.r-project.org/web/checks/check_summary_by_package.html⁠.

Usage

checked_packages()
checked_packages()

Value

data.frame with the same structure as the html table on ⁠https://cran.r-project.org/web/checks/check_summary_by_package.html⁠.

Note

Results are cached for 30 minutes with memoise package. Some packages could be duplicated as not all tests are performed for a new version so two versions still coexists. Checks with asterisks (*) indicate that checking was not fully performed, this is a case for less than 1% of all packages.

Examples

## Not run: 
pacs::checked_packages()

## End(Not run)
## Not run: 
pacs::checked_packages()

## End(Not run)

Maximum version across the vector

Description

Reduce function over the utils::compareVersion

Usage

compareVersionsMax(vec, na.rm = TRUE)
compareVersionsMax(vec, na.rm = TRUE)

Arguments

`vec`	`character` vector.
`na.rm`	`logical` if to remove `NA` values.

Value

character maximum version

Examples

compareVersionsMax(c("1.1.1", "0.2.0"))
compareVersionsMax(c("1.1.1", "0.2.0"))

Minimum version across the vector

Description

Reduce function over the utils::compareVersion

Usage

compareVersionsMin(vec, na.rm = TRUE)
compareVersionsMin(vec, na.rm = TRUE)

Arguments

`vec`	`character` vector.
`na.rm`	`logical` if to remove `NA` values.

Value

character minimal version

Examples

compareVersionsMin(c("1.1.1", "0.2.0"))
compareVersionsMin(c("1.1.1", "0.2.0"))

Retrieving all R CRAN servers flavors

Description

Retrieving all R CRAN servers flavors. The data is downloaded from ⁠https://cran.r-project.org/web/checks/check_flavors.html⁠.

Usage

cran_flavors()
cran_flavors()

Value

data.frame with the same structure as the html table on ⁠https://cran.r-project.org/web/checks/check_flavors.html⁠.

Note

Results are cached for 30 minutes with memoise package.

Examples

## Not run: 
pacs::cran_flavors()

## End(Not run)
## Not run: 
pacs::cran_flavors()

## End(Not run)

Size of the package

Description

size of package.

Usage

dir_size(path = ".", recursive = TRUE)
dir_size(path = ".", recursive = TRUE)

Arguments

`path`	`character` path to the shiny app. Default: `"."`
`recursive`	`logical` if to assess the dependencies recursively. Default: TRUE

Value

numeric size in bytes, to get MB ten divide by 10**6.

Examples

## Not run: 
cat(pacs::dir_size(system.file(package = "stats")) / 10**6, "MB")

## End(Not run)
## Not run: 
cat(pacs::dir_size(system.file(package = "stats")) / 10**6, "MB")

## End(Not run)

Validate the local library

Description

Checking if installed packages have correct versions taking into account all DESCRIPTION files requirements. Moreover identifying which packages are newest releases. Optionally we could add life duration and CRAN check page status for each package.

Usage

lib_validate(
  lib.loc = .libPaths(),
  fields = c("Depends", "Imports", "LinkingTo"),
  lifeduration = FALSE,
  checkred = list(scope = character(0), flavors = NULL),
  built = FALSE,
  repos = biocran_repos()
)
lib_validate(
  lib.loc = .libPaths(),
  fields = c("Depends", "Imports", "LinkingTo"),
  lifeduration = FALSE,
  checkred = list(scope = character(0), flavors = NULL),
  built = FALSE,
  repos = biocran_repos()
)

Arguments

`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`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)`
`built`	`logical` if to add an R version under which each package was installed. Useful mainly for a local usage. Packages installed with a previous version of R could not work correctly with the new version of R. Default: `FALSE`
`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 4/6/8/9/10 columns.

Package: character a package name.
Version.expected.min: character expected by DESCRIPTION files minimal version. "" means not specified so the newest version.
Version.have: character installed package version.
version_status: 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.
built: character package was built under this R version
built_status: integer if the package was built under the current R version, then 1 (good) and for older R versions 0 (possibly bad). A package built under older R version or mix of packages built under different versions could bring possible failures.
newest: logical (Internet needed) if the installed version is the newest one. For Bioconductor if is the newest one per R version.
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. pacs::checked_packages is used to quickly retrieve all statuses at once.
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. When turn on the lifeduration options, calculations might be time consuming for libraries bigger than 500 packages. Results are cached for 30 minutes with memoise package. BioConductor packages are tested only in available scope, checkred is not assessed for them. 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: 
pacs::lib_validate()
pacs::lib_validate(checkred = list(scope = c("ERROR", "FAIL", "WARN")))
pacs::lib_validate(checkred = list(
  scope = c("ERROR", "FAIL"),
  flavors = pacs::match_flavors()
))
# activate lifeduration argument, could be time consuming for bigger libraries.
pacs::lib_validate(
  lifeduration = TRUE,
  checkred = list(scope = c("ERROR", "FAIL"))
)
# only R CRAN repository
pacs::lib_validate(repos = "https://cran.rstudio.com/")

## End(Not run)
## Not run: 
pacs::lib_validate()
pacs::lib_validate(checkred = list(scope = c("ERROR", "FAIL", "WARN")))
pacs::lib_validate(checkred = list(
  scope = c("ERROR", "FAIL"),
  flavors = pacs::match_flavors()
))
# activate lifeduration argument, could be time consuming for bigger libraries.
pacs::lib_validate(
  lifeduration = TRUE,
  checkred = list(scope = c("ERROR", "FAIL"))
)
# only R CRAN repository
pacs::lib_validate(repos = "https://cran.rstudio.com/")

## End(Not run)

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()
)
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)
## 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)

Get all matched CRAN servers to the local `OS`

Description

CRAN servers matched to the local OS.

Usage

match_flavors()
match_flavors()

Value

character vector matched server names.

Note

The Internet connection is needed to use the function.

Examples

## Not run: 
pacs::match_flavors()

## End(Not run)
## Not run: 
pacs::match_flavors()

## End(Not run)

Retrieving the R CRAN package check page

Description

Retrieving the R CRAN package check page.

Usage

pac_checkpage(pac)
pac_checkpage(pac)

Arguments

pac

character a package name.

Value

data.frame.

Note

Results are cached for 30 minutes with memoise package. If you need to check many packages at once then is recommended usage of pacs::checked_packages. Please as a courtesy to the R CRAN, don't overload their server by constantly using this function.

Examples

## Not run: 
pacs::pac_checkpage("dplyr")

## End(Not run)
## Not run: 
pacs::pac_checkpage("dplyr")

## End(Not run)

Checking the R CRAN package check page status

Description

using package R CRAN check page to validate if there are ANY errors and/or fails and/or warnings and/or notes.

Usage

pac_checkred(pac, scope = c("ERROR", "FAIL"), flavors = NULL)
pac_checkred(pac, scope = c("ERROR", "FAIL"), flavors = NULL)

Arguments

`pac`	`character` a package name.
`scope`	`character` vector scope of the check, accepted values c("ERROR", "FAIL", "WARN", "NOTE"). Default: `c("ERROR", "FAIL")`
`flavors`	`character` vector of CRAN server names to consider, possible names could be get with `pacs::cran_flavors()$Flavor`. The `pacs::match_flavors()` function could be used to get CRAN server names matched for your local `OS`. By default all CRAN machines are considered `NULL` value. Default: `NULL`

Value

logical if the package fail under specified criteria.

Note

Results are cached for 30 minutes with memoise package. If you need to check many packages at once then is recommended usage of pacs::checked_packages. The used repository ⁠https://cran.rstudio.com/⁠. Please as a courtesy to the R CRAN, don't overload their server by constantly using this function.

Examples

## Not run: 
pacs::pac_checkred("dplyr")
pacs::pac_checkred("dplyr", scope = c("ERROR"))
pacs::pac_checkred("dplyr",
  scope = c("ERROR", "FAIL", "WARN"),
  flavors = pacs::match_flavors()
)

## End(Not run)
## Not run: 
pacs::pac_checkred("dplyr")
pacs::pac_checkred("dplyr", scope = c("ERROR"))
pacs::pac_checkred("dplyr",
  scope = c("ERROR", "FAIL", "WARN"),
  flavors = pacs::match_flavors()
)

## End(Not run)

Compare NAMESPACE exports between specific CRAN packages versions

Description

using the remote github CRAN mirror to compare NAMESPACE exports between specific packages versions.

Usage

pac_compare_namespace(
  pac,
  old = NULL,
  new = NULL,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)
pac_compare_namespace(
  pac,
  old = NULL,
  new = NULL,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)

Arguments

`pac`	`character` a package name.
`old`	`character` an old version of package, default local version. Default: `NULL`
`new`	`character` a new version of package, default newest version. Default: `NULL`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`repos`	`character` vector repositories URLs to use. Used only for the validation. Default `⁠https://cran.rstudio.com/⁠`

Value

list with c("imports", "exports", "exportPatterns", "importClasses", "importMethods", "exportClasses", "exportMethods", "exportClassPatterns", "dynlibs", "S3methods") slots, and added and removed ones for each of them.

Examples

## Not run: 
pacs::pac_compare_namespace("shiny", "1.0.0", "1.6.0")
pacs::pac_compare_namespace("shiny", "1.0.0", "1.6.0")$exports
# local version to newest one
pacs::pac_compare_namespace("shiny")

## End(Not run)
## Not run: 
pacs::pac_compare_namespace("shiny", "1.0.0", "1.6.0")
pacs::pac_compare_namespace("shiny", "1.0.0", "1.6.0")$exports
# local version to newest one
pacs::pac_compare_namespace("shiny")

## End(Not run)

Compare NEWS files between specific CRAN packages versions

Description

using the remote github CRAN mirror to compare NEWS files between specific packages versions.

Usage

pac_compare_news(
  pac,
  old = NULL,
  new = NULL,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)
pac_compare_news(
  pac,
  old = NULL,
  new = NULL,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)

Arguments

`pac`	`character` a package name.
`old`	`character` an old version of package, default local version. Default: `NULL`
`new`	`character` a new version of package, default newest version. Default: `NULL`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`repos`	`character` vector repositories URLs to use. Used only for the validation. Default `⁠https://cran.rstudio.com/⁠`

Value

character with NEWS content between specific versions.

Examples

## Not run: 
pacs::pac_compare_news("shiny", "1.0.0", "1.6.0")
# local version to newest one
pacs::pac_compare_news("shiny")

## End(Not run)
## Not run: 
pacs::pac_compare_news("shiny", "1.0.0", "1.6.0")
# local version to newest one
pacs::pac_compare_news("shiny")

## End(Not run)

Compare DESCRIPTION files dependencies between specific CRAN packages versions

Description

using the remote github CRAN mirror to compare DESCRIPTION files dependencies between specific packages versions.

Usage

pac_compare_versions(
  pac,
  old = NULL,
  new = NULL,
  fields = c("Imports", "Depends", "LinkingTo"),
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)
pac_compare_versions(
  pac,
  old = NULL,
  new = NULL,
  fields = c("Imports", "Depends", "LinkingTo"),
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)

Arguments

`pac`	`character` a package name.
`old`	`character` an old version of package, default local version. Default: `NULL`
`new`	`character` a new version of package, default newest version. Default: `NULL`
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`repos`	`character` vector repositories URLs to use. Used only for the validation. Default `⁠https://cran.rstudio.com/⁠`

Value

data.frame with 4 columns.

Package: character package names.
Version.OLD: character versions of dependencies required by an old package version.
Version.NEW: character versions of dependencies required by a new package version.
version_status: numeric -1/0/1 which comes from utils::compareVersion function. 0 means that both versions have the same requirement. -1 means that the new version remove this requirement. 1 means that the new version added a new requirement.

Examples

## Not run: 
pacs::pac_compare_versions("memoise", "0.2.1", "2.0.0")
pacs::pac_compare_versions("memoise", "0.2.1")
# local version to newest one
pacs::pac_compare_versions("memoise")

## End(Not run)
## Not run: 
pacs::pac_compare_versions("memoise", "0.2.1", "2.0.0")
pacs::pac_compare_versions("memoise", "0.2.1")
# local version to newest one
pacs::pac_compare_versions("memoise")

## End(Not run)

Package dependencies

Description

Package dependencies from DESCRIPTION files with installed or expected versions or newest released.

Usage

pac_deps(
  pac,
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  base = FALSE,
  local = TRUE,
  description_v = FALSE,
  attr = TRUE,
  recursive = TRUE,
  repos = biocran_repos()
)
pac_deps(
  pac,
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  base = FALSE,
  local = TRUE,
  description_v = FALSE,
  attr = TRUE,
  recursive = TRUE,
  repos = biocran_repos()
)

Arguments

`pac`	`character` a package name.
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`base`	`logical` if to add base packages too. If `TRUE` then `pacs::pacs_base()` are taken into account. Default: `FALSE`
`local`	logical if to use local repository (or newest remote packages). Default: TRUE
`description_v`	`logical` if the dependencies version should be taken from description files, minimal required. By default installed versions are taken. Default: `FALSE`
`attr`	`logical` if a package and its version should be added as an attribute of data.frame or for FALSE as an additional record. Default: TRUE
`recursive`	`logical` if to assess the dependencies recursively. Default: TRUE
`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 packages and their versions. Versions are taken from installed.packages or newest released.

Note

When function is invoked in the loop afterwards results could be aggregated like, stats::aggregate(results[, c("Version"), drop = FALSE], list(Package = results$Package), pacs::compareVersionsMax).

Examples

## Not run: 
pacs::pac_deps("stats", base = TRUE)$Package
pacs::pac_deps("memoise")$Package
pacs::pac_deps("memoise", description_v = FALSE)
# raw dependencies from DESCRIPTION file
pacs::pac_deps("memoise", description_v = TRUE, recursive = FALSE)
# raw dependencies from DESCRIPTION file - last release
pacs::pac_deps("memoise", description_v = TRUE, local = FALSE, recursive = FALSE)

## End(Not run)
## Not run: 
pacs::pac_deps("stats", base = TRUE)$Package
pacs::pac_deps("memoise")$Package
pacs::pac_deps("memoise", description_v = FALSE)
# raw dependencies from DESCRIPTION file
pacs::pac_deps("memoise", description_v = TRUE, recursive = FALSE)
# raw dependencies from DESCRIPTION file - last release
pacs::pac_deps("memoise", description_v = TRUE, local = FALSE, recursive = FALSE)

## End(Not run)

Package dependencies - developer perspective

Description

A higher-level function, build from pacs::pacs_deps. Package dependencies installed when e.g. ⁠R CMD check⁠ a package. ⁠"Depends", "Imports", "LinkingTo", "Suggests"⁠ fields from the DESCRIPTION file and their recursive dependencies taken from ⁠"Depends", "Imports", "LinkingTo"⁠ fields. Dependencies are taken remotely for the newest version.

Usage

pac_deps_dev(
  pac,
  base = FALSE,
  local = FALSE,
  attr = TRUE,
  repos = pacs::biocran_repos()
)
pac_deps_dev(
  pac,
  base = FALSE,
  local = FALSE,
  attr = TRUE,
  repos = pacs::biocran_repos()
)

Arguments

`pac`	`character` a package name.
`base`	`logical` if to add base packages too. If `TRUE` then `pacs::pacs_base()` are taken into account. Default: `FALSE`
`local`	`logical` if to use local repository (or newest remote packages). Default: `FALSE`
`attr`	`logical` if a package and its version should be added as an attribute of data.frame or for FALSE as an additional record. Default: TRUE
`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 packages and their versions. Versions are taken from installed.packages or newest released.

Examples

## Not run: 
pacs::pac_deps_dev("dplyr")
pacs::pac_deps_dev("pacs")
# with the main package in the list
pacs::pac_deps_dev("pacs", attr = FALSE)

## End(Not run)
## Not run: 
pacs::pac_deps_dev("dplyr")
pacs::pac_deps_dev("pacs")
# with the main package in the list
pacs::pac_deps_dev("pacs", attr = FALSE)

## End(Not run)

Package direct dependencies and number of dependencies for each of them

Description

A higher-level function, build from pacs::pacs_deps and tools::package_dependencies. A tool to identify a main sources of dependencies, which direct dependencies are the heaviest one.

Usage

pac_deps_heavy(
  pac,
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  base = FALSE,
  local = FALSE,
  repos = pacs::biocran_repos()
)
pac_deps_heavy(
  pac,
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  base = FALSE,
  local = FALSE,
  repos = pacs::biocran_repos()
)

Arguments

`pac`	`character` a package name.
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`base`	`logical` if to add base packages too. If `TRUE` then `pacs::pacs_base()` are taken into account. Default: `FALSE`
`local`	`logical` if to use local repository (or newest remote packages). Default: `FALSE`
`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 three columns c("Package", "NrDeps", "NrUniqueDeps"): package name, number of dependencies and number of unique dependencies (not shared by other direct dependencies).

Note

Please take into account that the sum of the dependencies is not equal to the number of dependencies of the main package, because some dependencies are overlapping.

Examples

## Not run: 
pacs::pac_deps_heavy("caret")
pacs::pac_deps_heavy("dplyr")

## End(Not run)
## Not run: 
pacs::pac_deps_heavy("caret")
pacs::pac_deps_heavy("dplyr")

## End(Not run)

R CRAN package dependencies for a certain version or time point

Description

Package dependencies from DESCRIPTION files retrieved recursively for certain version or time point.

Usage

pac_deps_timemachine(
  pac,
  version = NULL,
  at = NULL,
  fields = c("Depends", "Imports", "LinkingTo"),
  recursive = TRUE
)
pac_deps_timemachine(
  pac,
  version = NULL,
  at = NULL,
  fields = c("Depends", "Imports", "LinkingTo"),
  recursive = TRUE
)

Arguments

`pac`	`character` a package name.
`version`	`character` version of a package. Default: `NULL`
`at`	`Date` from which to take the version. Default: `NULL`
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`recursive`	`logical` if to assess the dependencies recursively. Default: TRUE

Value

⁠named vector⁠ package dependencies and their versions at the release date of main package plus one day.

Note

Longer lived version is taken if 2 is available at the same date (switch time).

Examples

## Not run: 
pacs::pac_deps_timemachine("memoise", "0.2.1")
pacs::pac_deps_timemachine("memoise", at = as.Date("2019-01-01"))
pacs::pac_deps_timemachine("dplyr", at = as.Date("2015-01-01"))

## End(Not run)
## Not run: 
pacs::pac_deps_timemachine("memoise", "0.2.1")
pacs::pac_deps_timemachine("memoise", at = as.Date("2019-01-01"))
pacs::pac_deps_timemachine("dplyr", at = as.Date("2015-01-01"))

## End(Not run)

Package dependencies - user perspective

Description

A higher-level function, build from pacs::pacs_deps. Package dependencies installed when run installed.packages. ⁠"Depends", "Imports", "LinkingTo"⁠ fields from the DESCRIPTION file and their recursive dependencies taken from the same fields. Dependencies are taken remotely for the newest version.

Usage

pac_deps_user(
  pac,
  base = FALSE,
  local = FALSE,
  attr = TRUE,
  repos = pacs::biocran_repos()
)
pac_deps_user(
  pac,
  base = FALSE,
  local = FALSE,
  attr = TRUE,
  repos = pacs::biocran_repos()
)

Arguments

`pac`	`character` a package name.
`base`	`logical` if to add base packages too. If `TRUE` then `pacs::pacs_base()` are taken into account. Default: `FALSE`
`local`	`logical` if to use local repository (or newest remote packages). Default: `FALSE`
`attr`	`logical` if a package and its version should be added as an attribute of data.frame or for FALSE as an additional record. Default: TRUE
`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 packages and their versions. Versions are taken from installed.packages or newest released.

Examples

## Not run: 
pacs::pac_deps_user("dplyr")
pacs::pac_deps_user("pacs")
# with the main package in the list
pacs::pac_deps_user("pacs", attr = FALSE)

## End(Not run)
## Not run: 
pacs::pac_deps_user("dplyr")
pacs::pac_deps_user("pacs")
# with the main package in the list
pacs::pac_deps_user("pacs", attr = FALSE)

## End(Not run)

package DESCRIPTION file

Description

CRAN package DESCRIPTION file taken locally or remotely from GITHUB CRAN mirror or CRAN website. By default works for the newest package version.

Usage

pac_description(
  pac,
  version = NULL,
  at = NULL,
  local = FALSE,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)
pac_description(
  pac,
  version = NULL,
  at = NULL,
  local = FALSE,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)

Arguments

`pac`	`character` a package name.
`version`	`character` version of a package. Default: `NULL`
`at`	`Date` from which to take the version. Default: `NULL`
`local`	`logical` if to use local repository (or newest remote packages). Default: `FALSE`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`repos`	`character` vector repositories URLs to use. Used only for the validation. Default `⁠https://cran.rstudio.com/⁠`

Value

list with names proper for DESCRIPTION file fields.

Note

Results are cached for 30 minutes with memoise package.

Examples

## Not run: 
pacs::pac_description("dplyr", version = "0.8.0")
pacs::pac_description("dplyr", at = as.Date("2019-02-01"))

## End(Not run)
## Not run: 
pacs::pac_description("dplyr", version = "0.8.0")
pacs::pac_description("dplyr", at = as.Date("2019-02-01"))

## End(Not run)

CRAN package health state at a specific Date or for a specific version

Description

a package health for a certain version or at a specific Date. By default works for the newest package version. A healthy package was published for more than x days, where default is 14 days. CRAN team gives around one/two week to resolved a package which gave errors under the check page. The newest release is checked for any warnings/errors on the R CRAN package check page.

Usage

pac_health(
  pac,
  version = NULL,
  at = NULL,
  limit = 14,
  scope = c("ERROR", "FAIL"),
  flavors = NULL,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/",
  source = c("cran", "crandb")
)
pac_health(
  pac,
  version = NULL,
  at = NULL,
  limit = 14,
  scope = c("ERROR", "FAIL"),
  flavors = NULL,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/",
  source = c("cran", "crandb")
)

Arguments

`pac`	`character` a package name.
`version`	`character` version of a package. Default: `NULL`
`at`	`Date` from which to take the version. Default: `NULL`
`limit`	`numeric` at least days to treat as healthy, ">=limit". Default: 14
`scope`	`character` vector scope of the check, accepted values c("ERROR", "FAIL", "WARN", "NOTE"). Default: `c("ERROR", "FAIL")`
`flavors`	`character` vector of CRAN server names to consider, possible names could be get with `pacs::cran_flavors()$Flavor`. The `pacs::match_flavors()` function could be used to get CRAN server names matched for your local `OS`. By default all CRAN machines are considered `NULL` value. Default: `NULL`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`repos`	character vector repositories URLs to use. Default `⁠https://cran.rstudio.com/⁠`
`source`	`character` one of `c("cran", "crandb")`. Using the `⁠MEATCRAN CRANDB⁠` or the direct web page download from CRAN. When `"crandb"` is set then `options(pacs.crandb_ntry = 3)` and `options(pacs.crandb_nsleep = 0.001)` can be used to control the fetch. `"pacs.crandb_ntry"` can be used to set the maximum number of try outs, by default 3. `"pacs.crandb_nsleep"` can be used to set the sleep duration between fetch try outs, by default 0.001. Default: `"cran"`

Value

logical if a package is healthy.

Note

Results are cached for 30 minutes with memoise package. 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/⁠. For source = "cran"the function will scrap two CRAN URLS. Works only with CRAN packages. Please as a courtesy to the R CRAN, don't overload their servers by constantly using this function.

Examples

## Not run: 
pacs::pac_health("memoise")
pacs::pac_health("dplyr", version = "0.8.0", limit = 14)
pacs::pac_health("dplyr", at = as.Date("2019-02-14"))
pacs::pac_health("dplyr", limit = 14, scope = c("ERROR", "FAIL"))

## End(Not run)
## Not run: 
pacs::pac_health("memoise")
pacs::pac_health("dplyr", version = "0.8.0", limit = 14)
pacs::pac_health("dplyr", at = as.Date("2019-02-14"))
pacs::pac_health("dplyr", limit = 14, scope = c("ERROR", "FAIL"))

## End(Not run)

Checking if a package is in repositories

Description

using utils::available.packages to check if package is in repositories.

Usage

pac_isin(pac, repos = biocran_repos())
pac_isin(pac, repos = biocran_repos())

Arguments

`pac`	`character` a package name.
`repos`	character vector base URLs of the repositories to use. By default checking CRAN and newest Bioconductor per R version. Default `pacs::biocran_repos()`

Value

logical if a package is inside repositories.

Note

Results are cached for 30 minutes with memoise package.

Examples

## Not run: 
pac_isin("dplyr")
pac_isin("dplyr", repos = "https://cran.rstudio.com/")
pac_isin("dplyr", repos = biocran_repos()[grep("Bio", names(biocran_repos()))])

## End(Not run)
## Not run: 
pac_isin("dplyr")
pac_isin("dplyr", repos = "https://cran.rstudio.com/")
pac_isin("dplyr", repos = biocran_repos()[grep("Bio", names(biocran_repos()))])

## End(Not run)

Checking if a package version is the most recent one

Description

checking if a package version is the most recent one, by default the installed version is compared.

Usage

pac_islast(pac, version = NULL, lib.loc = .libPaths(), repos = biocran_repos())
pac_islast(pac, version = NULL, lib.loc = .libPaths(), repos = biocran_repos())

Arguments

`pac`	`character` a package name.
`version`	`character` version of a package. Default: `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

logical if a package is inside repositories.

Note

Results are cached for 30 minutes with memoise package.

Examples

## Not run: 
pac_islast("memoise")
pac_islast("dplyr", version = "1.0.0")
pac_islast("S4Vectors")
pac_islast("S4Vectors", version = pac_last("S4Vectors"))

## End(Not run)
## Not run: 
pac_islast("memoise")
pac_islast("dplyr", version = "1.0.0")
pac_islast("S4Vectors")
pac_islast("S4Vectors", version = pac_last("S4Vectors"))

## End(Not run)

Getting the most recent package version

Description

using utils::available.packages to get the newest package version.

Usage

pac_last(pac, repos = biocran_repos())
pac_last(pac, repos = biocran_repos())

Arguments

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

Value

character most recent package version.

Note

Results are cached for 30 minutes with memoise package. For Bioconductor the newest one per R version.

Examples

## Not run: 
pac_last("dplyr")
pac_last("S4Vectors")

## End(Not run)
## Not run: 
pac_last("dplyr")
pac_last("S4Vectors")

## End(Not run)

Package version life duration at specific Date or for a specific version

Description

a package life duration for a certain version or at a specific Date. By default works for the newest package version.

Usage

pac_lifeduration(
  pac,
  version = NULL,
  at = NULL,
  lib.loc = .libPaths(),
  repos = biocran_repos(),
  source = c("cran", "crandb")
)
pac_lifeduration(
  pac,
  version = NULL,
  at = NULL,
  lib.loc = .libPaths(),
  repos = biocran_repos(),
  source = c("cran", "crandb")
)

Arguments

`pac`	`character` a package name.
`version`	`character` version of a package. Default: `NULL`
`at`	`Date` from which to take the version. Default: `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()`
`source`	`character` one of `c("cran", "crandb")`. Using the `⁠MEATCRAN CRANDB⁠` or the direct web page download from CRAN. When `"crandb"` is set then `options(pacs.crandb_ntry = 3)` and `options(pacs.crandb_nsleep = 0.001)` can be used to control the fetch. `"pacs.crandb_ntry"` can be used to set the maximum number of try outs, by default 3. `"pacs.crandb_nsleep"` can be used to set the sleep duration between fetch try outs, by default 0.001. Default: `"cran"`

Value

difftime, number of days package version was the newest one.

Note

Examples

## Not run: 
pacs::pac_lifeduration("memoise")
pacs::pac_lifeduration("memoise", source = "cran")
pacs::pac_lifeduration("dplyr", version = "0.8.0")
pacs::pac_lifeduration("dplyr", at = as.Date("2019-02-14"))
# For Bioconductor packages it will work only for the newest per R version and installed ones.
pacs::pac_lifeduration("S4Vectors")

## End(Not run)
## Not run: 
pacs::pac_lifeduration("memoise")
pacs::pac_lifeduration("memoise", source = "cran")
pacs::pac_lifeduration("dplyr", version = "0.8.0")
pacs::pac_lifeduration("dplyr", at = as.Date("2019-02-14"))
# For Bioconductor packages it will work only for the newest per R version and installed ones.
pacs::pac_lifeduration("S4Vectors")

## End(Not run)

package NAMESPACE file

Description

CRAN package NAMESPACE file taken locally or remotely from GITHUB CRAN mirror or CRAN website. By default works for the newest package version.

Usage

pac_namespace(
  pac,
  version = NULL,
  at = NULL,
  local = FALSE,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)
pac_namespace(
  pac,
  version = NULL,
  at = NULL,
  local = FALSE,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)

Arguments

`pac`	`character` a package name.
`version`	`character` version of a package. Default: `NULL`
`at`	`Date` from which to take the version. Default: `NULL`
`local`	`logical` if to use local repository (or newest remote packages). Default: `FALSE`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`repos`	`character` vector repositories URLs to use. Used only for the validation. Default `⁠https://cran.rstudio.com/⁠`

Value

list with names proper for NAMESPACE file, the same as format as returned by base::parseNamespaceFile.

Note

Results are cached for 30 minutes with memoise package. This function is mainly built under source code from base::parseNamespaceFile.

Examples

## Not run: 
pacs::pac_namespace("dplyr", version = "0.8.0")
pacs::pac_namespace("dplyr", at = as.Date("2019-02-01"))
pacs::pac_namespace("memoise", local = TRUE)

## End(Not run)
## Not run: 
pacs::pac_namespace("dplyr", version = "0.8.0")
pacs::pac_namespace("dplyr", at = as.Date("2019-02-01"))
pacs::pac_namespace("memoise", local = TRUE)

## End(Not run)

Get NEWS for a package

Description

Get NEWS for a package from CRAN or local

Usage

pac_news(
  pac,
  version = NULL,
  at = NULL,
  local = FALSE,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)
pac_news(
  pac,
  version = NULL,
  at = NULL,
  local = FALSE,
  lib.loc = .libPaths(),
  repos = "https://cran.rstudio.com/"
)

Arguments

`pac`	`character` a package name.
`version`	`character` version of a package. Default: `NULL`
`at`	`Date` from which to take the version. Default: `NULL`
`local`	`logical` if to use local repository (or newest remote packages). Default: `FALSE`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`repos`	`character` vector repositories URLs to use. Used only for the validation. Default `⁠https://cran.rstudio.com/⁠`

Value

character with NEWS content.

Note

Results are cached for 30 minutes with memoise package.

Examples

## Not run: 
pacs::pac_news("dplyr", version = "0.8.0")
pacs::pac_news("dplyr", at = as.Date("2019-02-01"))

## End(Not run)
## Not run: 
pacs::pac_news("dplyr", version = "0.8.0")
pacs::pac_news("dplyr", at = as.Date("2019-02-01"))

## End(Not run)

Size of the package

Description

Size of package.

Usage

pac_size(pac, lib.loc = .libPaths())
pac_size(pac, lib.loc = .libPaths())

Arguments

`pac`	`character` a package name.
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`

Value

numeric size in bytes, to get MB ten divide by 10**6.

Examples

## Not run: 
cat(pacs::pac_size("stats") / 10**6, "MB")

## End(Not run)
## Not run: 
cat(pacs::pac_size("stats") / 10**6, "MB")

## End(Not run)

Package metadata for all releases

Description

Using CRAN website to get a package metadata used at a specific Date or a Date interval or for specific version.

Usage

pac_timemachine(
  pac,
  at = NULL,
  from = NULL,
  to = NULL,
  version = NULL,
  source = c("cran", "crandb")
)
pac_timemachine(
  pac,
  at = NULL,
  from = NULL,
  to = NULL,
  version = NULL,
  source = c("cran", "crandb")
)

Arguments

`pac`	`character` a package name.
`at`	`Date` from which to take the version. Default: `NULL`
`from`	`Date` the lower limit. Default: `NULL`
`to`	`Date` the upper limit. Default: `NULL`
`version`	`character` version of a package. Default: `NULL`
`source`	`character` one of `c("cran", "crandb")`. Using the `⁠MEATCRAN CRANDB⁠` or the direct web page download from CRAN. When `"crandb"` is set then `options(pacs.crandb_ntry = 3)` and `options(pacs.crandb_nsleep = 0.001)` can be used to control the fetch. `"pacs.crandb_ntry"` can be used to set the maximum number of try outs, by default 3. `"pacs.crandb_nsleep"` can be used to set the sleep duration between fetch try outs, by default 0.001. Default: `"cran"`

Value

data.frame with 7 columns

Package: character package name.
Version: character package version.
Released: character release Date
Archived: character archived Date.
LifeDuration: difftime number of days the version was the newest one.
URL: character the suffix of the base URL to tar.gz file. The base part of URL in the result is ⁠https://cran.r-project.org/src/contrib/⁠.
Size: character size of the tar.gz file.

Note

Examples

## Not run: 
pacs::pac_timemachine("dplyr")
pacs::pac_timemachine("dplyr", at = as.Date("2017-02-02"))
pacs::pac_timemachine("dplyr", from = as.Date("2017-02-02"), to = as.Date("2018-04-02"))
pacs::pac_timemachine("dplyr", at = Sys.Date())
pacs::pac_timemachine("tidyr", from = as.Date("2020-06-01"), to = Sys.Date())

## End(Not run)
## Not run: 
pacs::pac_timemachine("dplyr")
pacs::pac_timemachine("dplyr", at = as.Date("2017-02-02"))
pacs::pac_timemachine("dplyr", from = as.Date("2017-02-02"), to = as.Date("2018-04-02"))
pacs::pac_timemachine("dplyr", at = Sys.Date())
pacs::pac_timemachine("tidyr", from = as.Date("2020-06-01"), to = Sys.Date())

## End(Not run)

True size of the package

Description

True size of the package as it takes into account its all dependencies, recursively.

Usage

pac_true_size(
  pac,
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  exclude_joint = 0L
)
pac_true_size(
  pac,
  fields = c("Depends", "Imports", "LinkingTo"),
  lib.loc = .libPaths(),
  exclude_joint = 0L
)

Arguments

`pac`	`character` a package name.
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`exclude_joint`	`integer` exclude packages which are dependencies of at least N other packages, not count main package dependencies. Default: `0`

Value

numeric size in bytes, to get MB then divide by 10**6.

Note

R base packages are not counted. The default value of fields should be suited for almost all scenarios.

Examples

## Not run: 
# size in MB, with all its dependencies
pacs::pac_true_size("memoise") / 10**6

## End(Not run)
## Not run: 
# size in MB, with all its dependencies
pacs::pac_true_size("memoise") / 10**6

## End(Not run)

Validate a specific local package

Description

Checking if installed package dependencies have correct versions taking into account their DESCRIPTION files requirements. Moreover identifying which packages are newest releases. Optionally we could add life duration and CRAN check page status for each dependency.

Usage

pac_validate(
  pac,
  lib.loc = .libPaths(),
  fields = c("Depends", "Imports", "LinkingTo"),
  lifeduration = FALSE,
  checkred = list(scope = character(0), flavors = NULL),
  repos = biocran_repos()
)
pac_validate(
  pac,
  lib.loc = .libPaths(),
  fields = c("Depends", "Imports", "LinkingTo"),
  lifeduration = FALSE,
  checkred = list(scope = character(0), flavors = NULL),
  repos = biocran_repos()
)

Arguments

`pac`	`character` a package name.
`lib.loc`	`character` vector of search paths with local packages. Default: `.libPaths()`
`fields`	`character` vector listing the types of dependencies, a subset of `c("Depends", "Imports", "LinkingTo", "Suggests", "Enhances")`. Character string "all" is shorthand for that vector, character string "most" for the same vector without "Enhances", character string "strong" (default) for the first three elements of that vector. Default: `c("Depends", "Imports", "LinkingTo")`
`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)`
`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 5/7/8/9 columns.

Package: character a package name.
Version.expected.min: character expected by DESCRIPTION files minimal version. "" means not specified so the newest version.
Version.have: character installed package version.
version_status: 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.
direct: logical if the package is in the first dependency layer, direct dependencies from DESCRIPTION file.
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. When turn on the lifeduration option, calculations might be time consuming when there is more than 500 packages. Please as a courtesy to the R CRAN, don't overload their server by constantly using this function with lifeduration or checkred turned on. Results are cached with memoise package, memory cache. 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: 
pacs::pac_validate("memoise")
pacs::pac_validate(
  "memoise",
  lifeduration = TRUE,
  checkred = list(scope = c("ERROR", "FAIL"), flavors = NULL)
)
pacs::pac_validate(
  "memoise",
  lifeduration = TRUE,
  checkred = list(scope = c("ERROR", "FAIL"), flavors = pacs::match_flavors())
)

## End(Not run)
## Not run: 
pacs::pac_validate("memoise")
pacs::pac_validate(
  "memoise",
  lifeduration = TRUE,
  checkred = list(scope = c("ERROR", "FAIL"), flavors = NULL)
)
pacs::pac_validate(
  "memoise",
  lifeduration = TRUE,
  checkred = list(scope = c("ERROR", "FAIL"), flavors = pacs::match_flavors())
)

## End(Not run)

Get base R packages

Description

get base packages, all or only startup.

Usage

pacs_base(startup = FALSE)
pacs_base(startup = FALSE)

Arguments

startup

logical include only startup packages. Default: FALSE

Value

character vector

Examples

## Not run: 
pacs_base()
pacs_base(startup = TRUE)

## End(Not run)
## Not run: 
pacs_base()
pacs_base(startup = TRUE)

## End(Not run)

Packages life duration for a specific version

Description

packages life duration for certain versions.

Usage

pacs_lifeduration(
  pacs,
  versions,
  source = c("crandb", "loop_crandb", "loop_cran"),
  lib.loc = .libPaths(),
  repos = biocran_repos()
)
pacs_lifeduration(
  pacs,
  versions,
  source = c("crandb", "loop_crandb", "loop_cran"),
  lib.loc = .libPaths(),
  repos = biocran_repos()
)

Arguments

`pacs`	`character` vector of packages names.
`versions`	`character` vector of packages versions.
`source`	character one of `c("crandb", "loop_crandb", "loop_cran")`. The `"crandb"` works if less than `getOption("pacs.crandb_limit")` (currently 500) packages are looked for. When `crandb` linked source is used then `options(pacs.crandb_ntry = 3)` and `options(pacs.crandb_nsleep = 0.001)` can be used to control the fetch. `"pacs.crandb_ntry"` can be used to set the maximum number of try outs, by default 3. `"pacs.crandb_nsleep"` can be used to set the sleep duration between fetch try outs, by default 0.001. Default: `"crandb"`
`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 two columns package name and life duration.

Note

Results are cached for 30 minutes with memoise package. 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/⁠. For source = "loop_cran"the function will scrap two CRAN URLS. Works only with CRAN packages. Please as a courtesy to the R CRAN, don't overload their servers by constantly using this function.

Examples

## Not run: 
pacs::pacs_lifeduration(c("dplyr", "tidyr"), c("1.0.0", "1.2.0"))
pacs::pacs_lifeduration(c("dplyr", "tidyr"), c("1.0.0", "1.2.0"), source = "loop_cran")
# last versions
pacs::pacs_lifeduration(c("dplyr", "tidyr"), sapply(c("dplyr", "tidyr"), pacs::pac_last))

## End(Not run)
## Not run: 
pacs::pacs_lifeduration(c("dplyr", "tidyr"), c("1.0.0", "1.2.0"))
pacs::pacs_lifeduration(c("dplyr", "tidyr"), c("1.0.0", "1.2.0"), source = "loop_cran")
# last versions
pacs::pacs_lifeduration(c("dplyr", "tidyr"), sapply(c("dplyr", "tidyr"), pacs::pac_last))

## End(Not run)

Package 'pacs'

Help Index

The shiny app dependencies

Description

Usage

Arguments

Value

Note

Examples

Size of the shiny app

Description

Usage

Arguments

Value

Note

Examples

Retrieving all Bioconductor releases

Description

Usage

Value

Note

Examples

CRAN and Bioconductor repositories

Description

Usage

Arguments

Value

Note

Examples

Retrieving all R CRAN packages check pages statuses.

Description

Usage

Value

Note

Examples

Maximum version across the vector

Description

Usage

Arguments

Value

Examples

Minimum version across the vector

Description

Usage

Arguments

Value

Examples

Retrieving all R CRAN servers flavors

Description

Usage

Value

Note

Examples

Size of the package

Description

Usage

Arguments

Value

Examples

Validate the local library

Description

Usage

Arguments

Value

Note

Examples

Validate a specific renv lock file

Description

Usage

Arguments

Value

Note

Examples

Get all matched CRAN servers to the local OS

Description

Usage

Value

Note

Examples

Retrieving the R CRAN package check page

Get all matched CRAN servers to the local `OS`