diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml index 8505458..b1d2f16 100644 --- a/.github/workflows/R-CMD-check.yml +++ b/.github/workflows/R-CMD-check.yml @@ -1,8 +1,6 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: - push: - branches: main pull_request: branches: main diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index cbee7ac..003657f 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -1,10 +1,11 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: - push: - branches: main pull_request: - branches: main + types: + - closed + branches: + - main name: test-coverage diff --git a/NEWS.md b/NEWS.md index 4b3b6df..9573256 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ # goldfish 1.6.9 +* Solving missing package anchors in the documentation. * Update deprecated functions in the vignettes from `manynet`. * Solve issue on `Makevars.in` file that produced a note when check as CRAN. diff --git a/R/functions_data.R b/R/functions_data.R index f30967f..511fcf4 100644 --- a/R/functions_data.R +++ b/R/functions_data.R @@ -305,8 +305,8 @@ as.matrix.network.goldfish <- function(x, ..., time = -Inf, startTime = -Inf) { #' object by using the [linkEvents()]. #' A new call of `linkEvents()` is required for each attribute that is dynamic. #' -#' Objects of class [tbl_df] from the tibble package frequently use in the -#' tidyverse ecosystem and objects of class `data.table` will produce +#' Objects of class [tibble::tbl_df] from the tibble package frequently use in the +#' tidyverse ecosystem and objects from the \pkg{data.table} package will produce #' errors in later steps for goldfish. #' Current implementation of goldfish relies on the subsetting behavior of #' data frames objects. The previous mentioned objects classes change this diff --git a/R/functions_diagnostics.R b/R/functions_diagnostics.R index f3cba83..ea0b278 100644 --- a/R/functions_diagnostics.R +++ b/R/functions_diagnostics.R @@ -155,10 +155,10 @@ examineOutliers <- function(x, #' For a detail description see \code{\link[changepoint]{cpt.mean}} or #' \code{\link[changepoint]{cpt.var}}. The default value is \code{"PELT"}. #' @param ... additional arguments to be passed to the functions in the -#' \code{\link{changepoint}} package. +#' \pkg{changepoint} package. #' @section Change point: #' The parameter \code{moment} controls which method from the package -#' \code{\link{changepoint}} is used: +#' \pkg{changepoint} is used: #' \describe{ #' \item{\code{"mean"}}{It uses the \code{\link[changepoint]{cpt.mean}} #' function to investigate optimal positioning and (potentially) number diff --git a/cran-comments.md b/cran-comments.md index 0fdd568..2bc166c 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,13 +1,15 @@ ## Test environments * local R installation, Windows 10 x64 19405, R 4.3.1 -* Mac OS Monterey 12.7.3 (on Github), R 4.3.3 -* Microsoft Windows Server 2022 10.0.20348 (on Github), R 4.3.3 -* Ubuntu 20.04.6 (on Github), R 4.3.3 +* Mac OS Darwin 14.6.1 (on Github), R 4.4.1 +* Microsoft Windows Server 2022 10.0.20348 (on Github), R 4.4.1 +* Ubuntu 22.04.4 (on Github), R 4.4.1 ## R CMD check results 0 errors | 0 warnings | 1 note * This is a new release. -* `checkEvents()` method addresses S3 generic/method consistency. \ No newline at end of file +* Solving missing package anchors in the documentation. +* Update deprecated functions in the vignettes from `manynet`. +* Solve issue on `Makevars.in` file that produced a note when check as CRAN. diff --git a/man/defineNodes.Rd b/man/defineNodes.Rd index 9a0ebd5..68f6f93 100644 --- a/man/defineNodes.Rd +++ b/man/defineNodes.Rd @@ -50,8 +50,8 @@ can be linked to a dynamic event-list data frames in the initial state object by using the \code{\link[=linkEvents]{linkEvents()}}. A new call of \code{linkEvents()} is required for each attribute that is dynamic. -Objects of class \link{tbl_df} from the tibble package frequently use in the -tidyverse ecosystem and objects of class \code{data.table} will produce +Objects of class \link[tibble:tbl_df-class]{tibble::tbl_df} from the tibble package frequently use in the +tidyverse ecosystem and objects from the \pkg{data.table} package will produce errors in later steps for goldfish. Current implementation of goldfish relies on the subsetting behavior of data frames objects. The previous mentioned objects classes change this diff --git a/man/examine.Rd b/man/examine.Rd index 5dc5f13..00df6cb 100644 --- a/man/examine.Rd +++ b/man/examine.Rd @@ -41,7 +41,7 @@ By default it is half the width of the event sequence.} See section \emph{Change point} for details.} \item{...}{additional arguments to be passed to the functions in the -\code{\link{changepoint}} package.} +\pkg{changepoint} package.} } \value{ \code{NULL} if neither outliers nor change points are identified. @@ -64,7 +64,7 @@ with labels indicating the sender and recipient. \section{Change point}{ The parameter \code{moment} controls which method from the package -\code{\link{changepoint}} is used: +\pkg{changepoint} is used: \describe{ \item{\code{"mean"}}{It uses the \code{\link[changepoint]{cpt.mean}} function to investigate optimal positioning and (potentially) number