Package 'verdepcheck'

Executes rcmdcheck::rcmdcheck() on a local package using libpath from the installation plan.

Description

Executes rcmdcheck::rcmdcheck() on a local package using libpath from the installation plan.

Usage

check_ip(ip, path, build_args = character(), check_args = character(), ...)

Arguments

ip	(pkg_installation_plan) object to execute
path	(string) path to the package sources
build_args	(string) value passed as build_args argument into rcmdcheck::rcmdcheck()
check_args	(string) value passed as args argument into rcmdcheck::rcmdcheck()
...	other arguments passed to rcmdcheck::rcmdcheck()

Value

An S3 object (list) with fields errors, warnings and notes. These are all character vectors containing the output for the failed check.

See Also

rcmdcheck::rcmdcheck() for other configuration possibilities

---

Solve installation plan ignoring entries with "@*release" remote refs for detected conflicts.

Description

Solve installation plan ignoring entries with "@*release" remote refs for detected conflicts.

Usage

download_ip(ip)

Arguments

ip	(pkg_installation_plan) object to execute

Value

pkg_installation_plan object invisibly

---

Executes installation plan and rcmdcheck::rcmdcheck() in "try mode" to always return.

Description

Executes installation plan and rcmdcheck::rcmdcheck() in "try mode" to always return.

Usage

execute_ip(ip, path, build_args, check_args, ...)

Arguments

ip	(pkg_installation_plan) object to execute
path	(string) path to the package sources
build_args	(string) value passed as build_args argument into rcmdcheck::rcmdcheck()
check_args	(string) value passed as args argument into rcmdcheck::rcmdcheck()
...	other arguments passed to rcmdcheck::rcmdcheck()

Value

a named list with two elements:

• "ip" - installation plan object

• "check" - returned value from rcmdcheck::rcmdcheck()

---

Get available date for the package.

Description

Oftentimes, the release date of the package does not correspond to the date when the package is available in the PPM. Usually it takes one day for the PPM to sync with the CRAN. This function will return the date when the package is available in the PPM.

Usage

get_avail_date(remote_ref, start = get_release_date(remote_ref))

## S3 method for class 'remote_ref_cran'
get_avail_date(remote_ref, start = get_release_date(remote_ref))

## S3 method for class 'remote_ref_standard'
get_avail_date(remote_ref, start = get_release_date(remote_ref))

## S3 method for class 'remote_ref'
get_avail_date(remote_ref, start = get_release_date(remote_ref))

Arguments

remote_ref	(remote_ref) object created with pkgdepends::parse_pkg_ref()
start	(Date) optional, the date when the package was released

Value

Date. This can be safely used as a snapshot date for the PPM.

Examples

get_avail_date(pkgdepends::parse_pkg_ref("cran::dplyr"))
get_avail_date(pkgdepends::parse_pkg_ref("cran::[email protected]"))


get_avail_date(pkgdepends::parse_pkg_ref("dplyr"))
get_avail_date(pkgdepends::parse_pkg_ref("[email protected]"))


get_avail_date(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))
get_avail_date(pkgdepends::parse_pkg_ref("tidyverse/[email protected]"))

---

Get reference to the maximal version of the package.

Description

Get reference to the maximal version of the package.

Usage

get_ref_max(remote_ref)

Arguments

remote_ref

(remote_ref) object created with pkgdepends::parse_pkg_ref()

Value

(remote_ref) object with the package reference

Examples

get_ref_max(pkgdepends::parse_pkg_ref("dplyr"))
get_ref_max(pkgdepends::parse_pkg_ref("cran::dplyr"))
get_ref_max(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
get_ref_max(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))

---

Get reference to the minimal version of the package.

Description

Get reference to the minimal version of the package.

• for standard and CRAN-type of remote - this would use pkgcache::cran_archive_list() to obtain historical data.

• for GitHub type of remote - this would use gh::gh_gql() to get list of all releases or tags and then gh::gh() to download DESCRIPTION file and then read package version.

Usage

get_ref_min(remote_ref, op = "", op_ver = "")

## S3 method for class 'remote_ref'
get_ref_min(remote_ref, op = "", op_ver = "")

## S3 method for class 'remote_ref_cran'
get_ref_min(remote_ref, op = "", op_ver = "")

## S3 method for class 'remote_ref_standard'
get_ref_min(remote_ref, op = "", op_ver = "")

## S3 method for class 'remote_ref_github'
get_ref_min(remote_ref, op = "", op_ver = "")

Arguments

remote_ref	(remote_ref) object created with pkgdepends::parse_pkg_ref()
op	(character(1)) optional, version condition comparison operator (e.g. ">", ">=")
op_ver	(character(1)) optional, version number against which op argument is applied

Value

(remote_ref) object with the package reference

See Also

get_ref_min_incl_cran()

Examples

get_ref_min(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))

get_ref_min(pkgdepends::parse_pkg_ref("cran::dplyr"))


get_ref_min(pkgdepends::parse_pkg_ref("dplyr"))


get_ref_min(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))

---

Get reference to the minimal version of the package including also check in CRAN repository.

Description

Get reference to the minimal version of the package including also check in CRAN repository.

Usage

get_ref_min_incl_cran(remote_ref, op = "", op_ver = "")

## S3 method for class 'remote_ref'
get_ref_min_incl_cran(remote_ref, op = "", op_ver = "")

## S3 method for class 'remote_ref_github'
get_ref_min_incl_cran(remote_ref, op = "", op_ver = "")

Arguments

remote_ref	(remote_ref) object created with pkgdepends::parse_pkg_ref()
op	(character(1)) optional, version condition comparison operator (e.g. ">", ">=")
op_ver	(character(1)) optional, version number against which op argument is applied

Value

(remote_ref) object with the package reference

See Also

get_ref_min_incl_cran()

Examples

verdepcheck:::get_ref_min_incl_cran(pkgdepends::parse_pkg_ref("dplyr"))

verdepcheck:::get_ref_min_incl_cran(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))

verdepcheck:::get_ref_min_incl_cran(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))

---

Get reference to the release version of the package.

Description

Get reference to the release version of the package.

Usage

get_ref_release(remote_ref)

Arguments

remote_ref

(remote_ref) object created with pkgdepends::parse_pkg_ref()

Value

(remote_ref) object with the package reference

Examples

get_ref_release(pkgdepends::parse_pkg_ref("dplyr"))
get_ref_release(pkgdepends::parse_pkg_ref("cran::dplyr"))
get_ref_release(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
get_ref_release(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))

---

Get release date.

Description

Get release date.

Usage

get_release_date(remote_ref)

## S3 method for class 'remote_ref_github'
get_release_date(remote_ref)

## S3 method for class 'remote_ref_cran'
get_release_date(remote_ref)

## S3 method for class 'remote_ref_standard'
get_release_date(remote_ref)

## S3 method for class 'remote_ref_bioc'
get_release_date(remote_ref)

## S3 method for class 'remote_ref'
get_release_date(remote_ref)

Arguments

remote_ref

(remote_ref) object created with pkgdepends::parse_pkg_ref()

Value

Date

Examples

get_release_date(pkgdepends::parse_pkg_ref("tidyverse/[email protected]"))


get_release_date(pkgdepends::parse_pkg_ref("cran::dplyr"))
get_release_date(pkgdepends::parse_pkg_ref("cran::[email protected]"))


get_release_date(pkgdepends::parse_pkg_ref("dplyr"))


get_release_date(pkgdepends::parse_pkg_ref("MultiAssayExperiment"))

---

Get package version.

Description

Get package version.

Usage

get_version(remote_ref)

## S3 method for class 'remote_ref'
get_version(remote_ref)

Arguments

remote_ref

(remote_ref) object created with pkgdepends::parse_pkg_ref()

Value

Package version created with package_version.

Examples

get_version(pkgdepends::parse_pkg_ref("dplyr"))
get_version(pkgdepends::parse_pkg_ref("tidyverse/dplyr"))
get_version(pkgdepends::parse_pkg_ref("tidyverse/[email protected]"))
get_version(pkgdepends::parse_pkg_ref("bioc::MultiAssayExperiment"))

---

Executes installation plan.

Description

This function would executes the following:

• solves package dependencies

• downloads all package dependencies

• installs system requirements

• installs all package dependencies

Usage

install_ip(ip)

Arguments

ip	(pkg_installation_plan) object to execute

Value

pkg_installation_plan object invisibly

---

Execute ⁠R CMD CHECK⁠ on a local package with all dependencies pre-installed using various strategies.

Description

Execute ⁠R CMD CHECK⁠ on a local package with all dependencies pre-installed using various strategies.

Usage

max_deps_check(
  path,
  extra_deps = character(),
  config = list(),
  build_args = character(),
  check_args = character(),
  ...
)

release_deps_check(
  path,
  extra_deps = character(),
  config = list(),
  build_args = character(),
  check_args = character(),
  ...
)

min_cohort_deps_check(
  path,
  extra_deps = character(),
  config = list(),
  build_args = character(),
  check_args = character(),
  ...
)

min_isolated_deps_check(
  path,
  extra_deps = character(),
  config = list(),
  build_args = character(),
  check_args = character(),
  ...
)

Arguments

path	(string) path to the package sources
extra_deps	(character(1)) Extra dependencies specified similarly as in the DESCRIPTION file, i.e. "<package name> (<operator> <version>)" where both ⁠<operator>⁠ and ⁠<version>⁠ are optional. Multiple entries are possible separated by ";".
config	(list) configuration options. See pkgdepends::pkg_config for details. "dependencies" and "library" elements are overwritten by package level defaults.
build_args	(string) value passed as build_args argument into rcmdcheck::rcmdcheck()
check_args	(string) value passed as args argument into rcmdcheck::rcmdcheck()
...	other arguments passed to rcmdcheck::rcmdcheck()

Value

a named list with two elements:

• "ip" - installation plan object

• "check" - returned value from rcmdcheck::rcmdcheck()

strategies

Currently implemented strategies:

• max - use the greatest version of dependent packages. Please note that using development version is not guaranteed to be stable. See get_ref_max for details.

• release - use the released version of dependent packages. It will try use CRAN if possible else if GitHub release is available then use it else fail. See get_ref_release for details.

• min_cohort - find maximum date of directly dependent packages release dates and use that as PPM snapshot date for dependency resolve.

• min_isolated - for each direct dependency: find its release date and use it as PPM snapshot for resolving itself. Next, combine all the individual resolutions and resolve it altogether again.

Both "min" strategies relies on PPM snapshot in order to limit the versions of indirect dependencies so that dependency resolution ends with a package released no earlier than any of its dependency. However, that's not always true for min_isolated strategy - done on purpose.

Please note that only min_cohort and min_isolated strategies are "stable". The rest are basing on dynamic references therefore it results might be different without changes in tested package. The most straightforward example is max strategy in which the environment will be different after any push of any of the dependencies.

See Also

deps_installation_proposal

Examples

x <- max_deps_check(".")
x$ip
x$check


x <- release_deps_check(".")
x$ip
x$check


x <- min_cohort_deps_check(".")
x$ip
x$check


x <- min_isolated_deps_check(".")
x$ip
x$check

---

Create installation proposal using various dependency strategies

Description

These functionalities would read local package DESCRIPTION file, derive dependencies from "Config/Needs/verdepcheck" and create an installation proposal using various strategies for package versions as described below.

Usage

new_max_deps_installation_proposal(
  path,
  extra_deps = character(0L),
  config = list()
)

new_release_deps_installation_proposal(
  path,
  extra_deps = character(0L),
  config = list()
)

new_min_cohort_deps_installation_proposal(
  path,
  extra_deps = character(0L),
  config = list()
)

new_min_isolated_deps_installation_proposal(
  path,
  extra_deps = character(0L),
  config = list()
)

Arguments

path	(string) path to the package sources
extra_deps	(character(1)) Extra dependencies specified similarly as in the DESCRIPTION file, i.e. "<package name> (<operator> <version>)" where both ⁠<operator>⁠ and ⁠<version>⁠ are optional. Multiple entries are possible separated by ";".
config	(list) configuration options. See pkgdepends::pkg_config for details. "dependencies" and "library" elements are overwritten by package level defaults.

Value

pkg_installation_plan object

strategies

Currently implemented strategies:

• max - use the greatest version of dependent packages. Please note that using development version is not guaranteed to be stable. See get_ref_max for details.

• release - use the released version of dependent packages. It will try use CRAN if possible else if GitHub release is available then use it else fail. See get_ref_release for details.

• min_cohort - find maximum date of directly dependent packages release dates and use that as PPM snapshot date for dependency resolve.

• min_isolated - for each direct dependency: find its release date and use it as PPM snapshot for resolving itself. Next, combine all the individual resolutions and resolve it altogether again.

Both "min" strategies relies on PPM snapshot in order to limit the versions of indirect dependencies so that dependency resolution ends with a package released no earlier than any of its dependency. However, that's not always true for min_isolated strategy - done on purpose.

Please note that only min_cohort and min_isolated strategies are "stable". The rest are basing on dynamic references therefore it results might be different without changes in tested package. The most straightforward example is max strategy in which the environment will be different after any push of any of the dependencies.

configuration

verdepcheck will look into "Config/Needs/verdepcheck" field of the DESCRIPTION file for dependent packages references. See pkgdepends::pkg_refs for details and this package DESCRIPTION file for an example. Please note that some features are enabled only for package references from GitHub. If you specify additional details (i.e. tag, commit, PR or ⁠@*release⁠) in the reference then it wouldn't be changed. Therefore, in order to make full use of various strategies, it is recommended to specify general reference in form of ⁠[<package>=][github::]<username>/<repository>[/<subdir>]⁠ - i.e. without ⁠[<detail>]⁠ part. Please see also pkgdepends::pkg_config and pak::pak-config for other configuration possibilities.

See Also

pkgdepends::pkg_installation_proposal

Examples

x <- new_max_deps_installation_proposal(".")
x$solve()
x$get_solution()


x <- new_release_deps_installation_proposal(".")
x$solve()
x$get_solution()


x <- new_min_cohort_deps_installation_proposal(".")
solve_ip(x)
x$get_solution()


x <- new_min_isolated_deps_installation_proposal(".")
solve_ip(x)
x$get_solution()

---

Try to solve using standard method. If error - use resolve_ignoring_release_remote.

Description

Try to solve using standard method. If error - use resolve_ignoring_release_remote.

Usage

solve_ip(ip)

Arguments

ip	(pkg_installation_plan) object to execute

Value

pkg_installation_plan object invisibly

---