diff --git a/DESCRIPTION b/DESCRIPTION index 375726d..8583318 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,70 +1,58 @@ Package: val.meter -Title: - validation-ready package quantification supporting regulatory use of R +Title:validation-ready package quantification supporting regulatory use + of R Version: 0.0.0.9000 -Authors@R: - c( - person( - "Doug", "Kelkhoff", - email = "doug.kelkhoff@gmail.com", - role = c("aut", "cre") - ), - person( - "Aaron", "Clark", - email = "clark.aaronchris@gmail.com", - role = c("ctb") - ), - person( - "R Validation Hub", - email = "r-val-hub-maintainers@lists.r-consortium.org", - comment = c("website" = "https://www.pharmar.org"), - role = c("cph") - ) - ) -Description: - Measures packages for common best practices, adoption and code execution. - Built with regulated industries in mind, supporting the surveying of - packages and aggregating findings into a portable format to support - activities like selecting mature packages and reporting on risk-based - software decision-making. +Authors@R: c( + person("Doug", "Kelkhoff", , "doug.kelkhoff@gmail.com", role = c("aut", "cre")), + person("Aaron", "Clark", , "clark.aaronchris@gmail.com", role = "ctb"), + person("Lluís", "Revilla Sancho", , "lluis.revilla@gmail.com", role = "ctb", + comment = c(ORCID = "0000-0001-9747-2570")), + person("R Validation Hub", , , "r-val-hub-maintainers@lists.r-consortium.org", role = "cph", + comment = c(website = "https://www.pharmar.org")) + ) +Description:Measures packages for common best practices, adoption and + code execution. Built with regulated industries in mind, supporting + the surveying of packages and aggregating findings into a portable + format to support activities like selecting mature packages and + reporting on risk-based software decision-making. License: MIT + file LICENSE -URL: - https://pharmar.github.io/val.meter, - https://github.com/pharmar/val.meter, - https://pharmar.org/ -BugReports: - https://github.com/pharmaR/val.meter/issues +URL: https://pharmar.github.io/val.meter, + https://github.com/pharmar/val.meter, https://pharmar.org/ +BugReports:https://github.com/pharmaR/val.meter/issues +Depends: + R (>= 3.5) Imports: cli, desc, evaluate, + httr2, + jsonlite, options, S7, + stats, tools, utils, - stats, - jsonlite, - httr2, xml2 Suggests: covr, - rcmdcheck, htmltools, igraph, knitr, + rcmdcheck, rmarkdown, rosv, testthat (>= 3.0.0), withr -Config/Needs/vignettes: - knitr, - rmarkdown, - rosv, - testthat (>= 3.0.0) -Config/Needs/readme: - asciicast -Config/Needs/data: - tidytext +VignetteBuilder: + knitr +Config/Needs/data:tidytext +Config/Needs/readme:asciicast +Config/Needs/vignettes:knitr, rmarkdown, rosv, testthat (>= 3.0.0) +Config/roxygen2/version: 8.1.0 +Config/testthat/edition: 3 +Encoding: UTF-8 +LazyData: true +Roxygen: list(markdown = TRUE) Collate: 'utils_enum_vector.R' 'class_tags.R' @@ -108,11 +96,3 @@ Collate: 'utils_rstudio.R' 'utils_tmp.R' 'zzz.R' -Encoding: UTF-8 -Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 -Depends: - R (>= 3.5) -LazyData: true -VignetteBuilder: knitr -Config/testthat/edition: 3 diff --git a/NAMESPACE b/NAMESPACE index 9bf65a3..60a5ab0 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -50,26 +50,36 @@ import(cli) import(options) importFrom(desc,desc) importFrom(evaluate,replay) -importFrom(httr2,req_perform) -importFrom(httr2,request) -importFrom(httr2,resp_body_html) +importFrom(httr2, + req_perform, + request, + resp_body_html +) importFrom(jsonlite,read_json) -importFrom(stats,rbinom) -importFrom(stats,rpois) -importFrom(stats,runif) -importFrom(tools,dependsOnPkgs) -importFrom(tools,file_ext) -importFrom(tools,getVignetteInfo) -importFrom(tools,toRd) -importFrom(utils,.DollarNames) -importFrom(utils,available.packages) -importFrom(utils,capture.output) -importFrom(utils,download.file) -importFrom(utils,download.packages) -importFrom(utils,getCRANmirrors) -importFrom(utils,head) -importFrom(utils,install.packages) -importFrom(utils,packageName) -importFrom(utils,packageVersion) -importFrom(xml2,xml_attrs) -importFrom(xml2,xml_find_all) +importFrom(stats, + rbinom, + rpois, + runif +) +importFrom(tools, + dependsOnPkgs, + file_ext, + getVignetteInfo, + toRd +) +importFrom(utils, + .DollarNames, + available.packages, + capture.output, + download.file, + download.packages, + getCRANmirrors, + head, + install.packages, + packageName, + packageVersion +) +importFrom(xml2, + xml_attrs, + xml_find_all +) diff --git a/R/data_desc.R b/R/data_desc.R index 874c175..34c6556 100644 --- a/R/data_desc.R +++ b/R/data_desc.R @@ -1,10 +1,12 @@ #' @include impl_data.R +source_code_or_install <- new_union(source_code_resource, install_resource) + #' @importFrom desc desc impl_data( "desc", class = c("description", "R6"), - for_resource = new_union(source_code_resource, install_resource), + for_resource = source_code_or_install, function(pkg, resource, field, ...) { desc::desc(resource@path) } @@ -14,7 +16,7 @@ impl_data( "name", title = "Package name", class = class_character, - for_resource = new_union(source_code_resource, install_resource), + for_resource = source_code_or_install, function(pkg, resource, field, ...) { pkg$desc$get_field("Package") } @@ -31,7 +33,7 @@ impl_data( impl_data( "version", class = class_character, - for_resource = new_union(source_code_resource, install_resource), + for_resource = source_code_or_install, function(pkg, resource, field, ...) { pkg$desc$get_field("Version") } @@ -48,7 +50,7 @@ impl_data( impl_data( "md5", class = class_character, - for_resource = new_union(source_code_resource, install_resource), + for_resource = source_code_or_install, function(pkg, resource, field, ...) { pkg$desc$get_field("MD5sum") } diff --git a/R/data_has_current_news.R b/R/data_has_current_news.R index 8b47c77..5922836 100644 --- a/R/data_has_current_news.R +++ b/R/data_has_current_news.R @@ -50,7 +50,7 @@ impl_data( #' @importFrom tools file_ext impl_data( "has_current_news", - for_resource = new_union(install_resource, source_code_resource), + for_resource = source_code_or_install, overwrite = TRUE, function(pkg, resource, field, ...) { files <- resource@path |> diff --git a/R/generic_pkg_data_derive.R b/R/generic_pkg_data_derive.R index 8356be9..8065d1e 100644 --- a/R/generic_pkg_data_derive.R +++ b/R/generic_pkg_data_derive.R @@ -99,7 +99,7 @@ method( #' @noRd method( pkg_data_derive, - list(class_pkg, new_union(NULL, class_missing), class_any) + list(class_pkg, class_missing | new_S3_class("NULL"), class_any) ) <- function(pkg, resource, field, ...) { pkg_data_derive(pkg = pkg, resource = pkg@resource, field = field, ...) diff --git a/man/class_metric_data_frame.Rd b/man/class_metric_data_frame.Rd index 7d1dea1..83ba194 100644 --- a/man/class_metric_data_frame.Rd +++ b/man/class_metric_data_frame.Rd @@ -7,7 +7,7 @@ class_metric_data_frame(.data = list(), row.names = NULL) } \arguments{ -\item{.data, row.names}{See \code{\link[S7:base_s3_classes]{S7::class_data.frame}}} +\item{.data, row.names}{See \code{\link[S7:class_data.frame]{S7::class_data.frame}}} } \description{ A \code{\link{data.frame}}, for all intents and purposes, with column names diff --git a/man/class_package_matrix.Rd b/man/class_package_matrix.Rd index 352d93b..e32539c 100644 --- a/man/class_package_matrix.Rd +++ b/man/class_package_matrix.Rd @@ -7,7 +7,7 @@ class_package_matrix(.data = character(0)) } \arguments{ -\item{.data}{See \code{\link[S7:base_classes]{S7::class_character}}} +\item{.data}{See \code{\link[S7:class_character]{S7::class_character}}} } \description{ A matrix produced by \code{available.packages} diff --git a/man/cran_repo_resource.Rd b/man/cran_repo_resource.Rd index 9b33b7a..14ce3fa 100644 --- a/man/cran_repo_resource.Rd +++ b/man/cran_repo_resource.Rd @@ -35,24 +35,24 @@ is to be sourced.} } \description{ A reference to a listing in CRAN. CRAN Resources must be from one of the -repositories listed in \code{\link[utils:chooseCRANmirror]{utils::getCRANmirrors()}}. To assert that a new url +repositories listed in \code{\link[utils:getCRANmirrors]{utils::getCRANmirrors()}}. To assert that a new url is also a CRAN mirror, please follow instructions in -\code{\link[utils:chooseCRANmirror]{utils::getCRANmirrors()}}. +\code{\link[utils:getCRANmirrors]{utils::getCRANmirrors()}}. } \seealso{ -Other resources: -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/errors.Rd b/man/errors.Rd index 09cd65c..29a22de 100644 --- a/man/errors.Rd +++ b/man/errors.Rd @@ -1,6 +1,5 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/utils_err.R -\docType{data} \name{errors} \alias{errors} \alias{.state} @@ -11,11 +10,6 @@ \alias{new_err} \alias{err} \title{Package data derivation error handling} -\format{ -An object of class \code{environment} of length 2. - -An object of class \code{list} of length 6. -} \usage{ .state @@ -97,5 +91,4 @@ be derived because it is not implemented for this resource.} packag error type for communication.} }} -\keyword{datasets} \keyword{internal} diff --git a/man/format_output.Rd b/man/format_output.Rd index 437a623..2d45794 100644 --- a/man/format_output.Rd +++ b/man/format_output.Rd @@ -27,10 +27,10 @@ directly.} \item{envir}{An environment in which expression \code{x} should be evaluated.} } \description{ -Captures output and formats it according to \code{style}. Uses the \link[evaluate:evaluate]{evaluate::evaluate} +Captures output and formats it according to \code{style}. Uses the \link[evaluate:evaluate]{evaluate} package to capture output to be more resilient to other processes sinking output, causing issues with \code{capture.output} -- notably when used with -\link[knitr:knitr-package]{knitr::knitr}. +\link[knitr:knitr]{knitr}. } \examples{ format_output( diff --git a/man/git_resource.Rd b/man/git_resource.Rd index e2ec418..a8c7d67 100644 --- a/man/git_resource.Rd +++ b/man/git_resource.Rd @@ -36,19 +36,19 @@ acquiring resources.} A reference to a listing in an R package git source code repository. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/http_resource.Rd b/man/http_resource.Rd index e9ef283..b8eeaed 100644 --- a/man/http_resource.Rd +++ b/man/http_resource.Rd @@ -37,19 +37,19 @@ A web-based reference to an R package file. Most often this will be used to resolve an http url into a source code archive. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/install_resource.Rd b/man/install_resource.Rd index 7ddfb51..cbaf23b 100644 --- a/man/install_resource.Rd +++ b/man/install_resource.Rd @@ -37,19 +37,19 @@ resource.} An installed version of a package, as would be found in a package library. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/local_resource.Rd b/man/local_resource.Rd index a001ca1..0e495a6 100644 --- a/man/local_resource.Rd +++ b/man/local_resource.Rd @@ -38,19 +38,19 @@ This abstract class represents any type of package resource that is derived from files locally on the filesystem. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/local_source_resource.Rd b/man/local_source_resource.Rd index 7738754..105ded5 100644 --- a/man/local_source_resource.Rd +++ b/man/local_source_resource.Rd @@ -44,19 +44,19 @@ code contains all tests and files which may be ignored as part of the build process, yet may be informative for metric assessment. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/mock_resource.Rd b/man/mock_resource.Rd index 778b119..6c6bb05 100644 --- a/man/mock_resource.Rd +++ b/man/mock_resource.Rd @@ -37,19 +37,19 @@ resource is needed is when adding your own data implementations and adding a custom data simulation method. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/multi_resource.Rd b/man/multi_resource.Rd index d43dc80..b83162e 100644 --- a/man/multi_resource.Rd +++ b/man/multi_resource.Rd @@ -48,19 +48,19 @@ to derive package data. The package only raises an error when no resource can successfully derive the expected data. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/pkg_data_derive.Rd b/man/pkg_data_derive.Rd index 5a1e69d..31ab2f5 100644 --- a/man/pkg_data_derive.Rd +++ b/man/pkg_data_derive.Rd @@ -34,7 +34,7 @@ This function is used internally when accessing a \code{\link{pkg}} object using \code{[[} and \code{[}. } \seealso{ -Other generics: -\code{\link{pkg_data_info}()} +Other generics: +\code{\link[=pkg_data_info]{pkg_data_info()}} } \concept{generics} diff --git a/man/pkg_data_info.Rd b/man/pkg_data_info.Rd index d377241..0606bc7 100644 --- a/man/pkg_data_info.Rd +++ b/man/pkg_data_info.Rd @@ -21,7 +21,7 @@ retrieving package data info.} Retrieve metadata about a data field. } \seealso{ -Other generics: -\code{\link{pkg_data_derive}()} +Other generics: +\code{\link[=pkg_data_derive]{pkg_data_derive()}} } \concept{generics} diff --git a/man/remote_resource.Rd b/man/remote_resource.Rd index b1af097..cd5faa6 100644 --- a/man/remote_resource.Rd +++ b/man/remote_resource.Rd @@ -33,19 +33,19 @@ acquiring resources.} Abstract Class for Remote Package Resources } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/repo_resource.Rd b/man/repo_resource.Rd index b0c4498..2d4fa27 100644 --- a/man/repo_resource.Rd +++ b/man/repo_resource.Rd @@ -37,19 +37,19 @@ is to be sourced.} A reference to a listing in an R package repository. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/resource.Rd b/man/resource.Rd index 0646f87..41617d3 100644 --- a/man/resource.Rd +++ b/man/resource.Rd @@ -44,19 +44,19 @@ a reference may populate a local directory with the source code of the package. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/source_archive_resource.Rd b/man/source_archive_resource.Rd index c67dd86..4ea665b 100644 --- a/man/source_archive_resource.Rd +++ b/man/source_archive_resource.Rd @@ -37,19 +37,19 @@ resource.} The extracted source code from a package's build archive. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_code_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/source_code_resource.Rd b/man/source_code_resource.Rd index 5db0244..7b2968f 100644 --- a/man/source_code_resource.Rd +++ b/man/source_code_resource.Rd @@ -37,19 +37,19 @@ resource.} A union of all package resource classes that have local source code. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{unknown_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=unknown_resource]{unknown_resource()}} } \concept{resources} diff --git a/man/unknown_resource.Rd b/man/unknown_resource.Rd index 3284f06..f402e4e 100644 --- a/man/unknown_resource.Rd +++ b/man/unknown_resource.Rd @@ -34,20 +34,20 @@ Used as a placeholder when the exact source of metrics is unknown. Most, commonly when a package object is reconstructed from a \code{PACKAGES} file. } \seealso{ -Other resources: -\code{\link{cran_repo_resource}()}, -\code{\link{git_resource}()}, -\code{\link{http_resource}()}, -\code{\link{install_resource}()}, -\code{\link{local_resource}()}, -\code{\link{local_source_resource}()}, -\code{\link{mock_resource}()}, -\code{\link{multi_resource}()}, -\code{\link{remote_resource}()}, -\code{\link{repo_resource}()}, -\code{\link{resource}()}, -\code{\link{source_archive_resource}()}, -\code{\link{source_code_resource}()} +Other resources: +\code{\link[=cran_repo_resource]{cran_repo_resource()}}, +\code{\link[=git_resource]{git_resource()}}, +\code{\link[=http_resource]{http_resource()}}, +\code{\link[=install_resource]{install_resource()}}, +\code{\link[=local_resource]{local_resource()}}, +\code{\link[=local_source_resource]{local_source_resource()}}, +\code{\link[=mock_resource]{mock_resource()}}, +\code{\link[=multi_resource]{multi_resource()}}, +\code{\link[=remote_resource]{remote_resource()}}, +\code{\link[=repo_resource]{repo_resource()}}, +\code{\link[=resource]{resource()}}, +\code{\link[=source_archive_resource]{source_archive_resource()}}, +\code{\link[=source_code_resource]{source_code_resource()}} } \concept{resources} \keyword{internal} diff --git a/man/val.meter-package.Rd b/man/val.meter-package.Rd index 51450d6..d726f9a 100644 --- a/man/val.meter-package.Rd +++ b/man/val.meter-package.Rd @@ -21,10 +21,16 @@ Useful links: \author{ \strong{Maintainer}: Doug Kelkhoff \email{doug.kelkhoff@gmail.com} +Authors: +\itemize{ + \item Doug Kelkhoff \email{doug.kelkhoff@gmail.com} +} + Other contributors: \itemize{ \item Aaron Clark \email{clark.aaronchris@gmail.com} [contributor] - \item R Validation Hub \email{r-val-hub-maintainers@lists.r-consortium.org} (https://www.pharmar.org) [copyright holder] + \item Lluís Revilla Sancho \email{lluis.revilla@gmail.com} (\href{https://orcid.org/0000-0001-9747-2570}{ORCID}) [contributor] + \item R Validation Hub \email{r-val-hub-maintainers@lists.r-consortium.org} (website: https://www.pharmar.org) [copyright holder] } } diff --git a/vignettes/adding-metric.Rmd b/vignettes/adding-metric.Rmd index 0c0c699..376a2af 100644 --- a/vignettes/adding-metric.Rmd +++ b/vignettes/adding-metric.Rmd @@ -203,7 +203,7 @@ Let's implement a rigorous metric, which will surface vulnerabilities using the vulnerabilities (OSV) database. In our case, we can use a known example to see how vulnerabilities might be reported: -```{r} +```{r, eval = requireNamespace("rosv", quietly = TRUE)} rosv::osv_query( "haven", version = "0.1.1", @@ -236,7 +236,7 @@ are the same as those coming from `CRAN`. There are tens of thousands of packages on `CRAN` and we don't want to accidentally report that a package has no vulnerabilities just because it shares a name with one of them. -```{r} +```{r, eval = requireNamespace("rosv", quietly = TRUE)} impl_data( "rosv_vulnerability_df",