From 5d72b382fb1473917a57270e412dcd7b23fcf430 Mon Sep 17 00:00:00 2001 From: Vedha Viyash <49812166+vedhav@users.noreply.github.com> Date: Thu, 12 Dec 2024 20:03:08 +0530 Subject: [PATCH] add setup-r-dependencies (#233) Related to https://github.com/insightsengineering/nestdevs-tasks/issues/65 Switch to setup-r-dependencies. Added `hermes` for lookup-refs. --- .github/workflows/check.yaml | 3 +++ .github/workflows/docs.yaml | 1 + .github/workflows/release.yaml | 4 ++++ man/HermesData-class.Rd | 6 +++--- man/cbind.Rd | 4 ++-- man/expression_set.Rd | 4 ++-- man/hermes_data.Rd | 4 ++-- man/isEmpty.Rd | 2 +- man/rbind.Rd | 4 ++-- man/rename.Rd | 4 ++-- man/show.Rd | 2 +- man/summarized_experiment.Rd | 4 ++-- man/validate.Rd | 2 +- 13 files changed, 26 insertions(+), 18 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index c7857745..61831a82 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -27,6 +27,7 @@ jobs: with: additional-env-vars: | NOT_CRAN=true + deps-installation-method: setup-r-dependencies bioccheck: name: BiocCheck 🩺 uses: insightsengineering/r.pkg.template/.github/workflows/bioccheck.yaml@main @@ -42,6 +43,7 @@ jobs: with: additional-env-vars: | NOT_CRAN=true + deps-installation-method: setup-r-dependencies linter: if: github.event_name != 'push' name: SuperLinter πŸ¦Έβ€β™€οΈ @@ -53,6 +55,7 @@ jobs: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} with: auto-update: true + deps-installation-method: setup-r-dependencies gitleaks: name: gitleaks πŸ’§ uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml index 9b7a7e54..281dff41 100644 --- a/.github/workflows/docs.yaml +++ b/.github/workflows/docs.yaml @@ -41,3 +41,4 @@ jobs: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} with: default-landing-page: latest-tag + deps-installation-method: setup-r-dependencies diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml index cf7732ab..6a4a5b8c 100644 --- a/.github/workflows/release.yaml +++ b/.github/workflows/release.yaml @@ -17,6 +17,7 @@ jobs: with: skip-r-cmd-check: true skip-r-cmd-install: true + deps-installation-method: setup-r-dependencies docs: name: Pkgdown Docs πŸ“š needs: release @@ -25,12 +26,15 @@ jobs: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} with: default-landing-page: latest-tag + deps-installation-method: setup-r-dependencies validation: name: R Package Validation report πŸ“ƒ needs: release uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main secrets: REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }} + with: + deps-installation-method: setup-r-dependencies release: name: Create release πŸŽ‰ uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main diff --git a/man/HermesData-class.Rd b/man/HermesData-class.Rd index f13854de..53ab50cb 100644 --- a/man/HermesData-class.Rd +++ b/man/HermesData-class.Rd @@ -25,7 +25,7 @@ If this is a \code{RangedSummarizedExperiment}, then the result will be \item{counts}{(\code{matrix})\cr counts to create the \code{\link{HermesData}} object from.} \item{...}{additional arguments, e.g. \code{rowData}, \code{colData}, etc. passed to -\code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment()}} internally. Note that if \code{rowRanges} +\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment()}} internally. Note that if \code{rowRanges} is passed instead of \code{rowData}, then the result will be a \code{\link{RangedHermesData}} object.} } \value{ @@ -34,7 +34,7 @@ An object of class \code{\link{AnyHermesData}} (\code{\link{HermesData}} or \cod \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -The \code{\link{HermesData}} class is an extension of \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} +The \code{\link{HermesData}} class is an extension of \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} with additional validation criteria. } \details{ @@ -66,7 +66,7 @@ same time with the \code{\link{AnyHermesData}} signature. A \code{\link[Biobase:class.ExpressionSet]{Biobase::ExpressionSet}} object can be imported by using the \code{\link[SummarizedExperiment:makeSummarizedExperimentFromExpressionSet]{SummarizedExperiment::makeSummarizedExperimentFromExpressionSet()}} function to -first convert it to a \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object before +first convert it to a \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object before converting it again into a \code{\link{HermesData}} object. } \section{Slots}{ diff --git a/man/cbind.Rd b/man/cbind.Rd index 2de35ed6..2b9df9d5 100644 --- a/man/cbind.Rd +++ b/man/cbind.Rd @@ -19,9 +19,9 @@ samples (columns in assays). \itemize{ \item Note that this just inherits \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::cbind,SummarizedExperiment-method()}}. When binding a -\code{\link{AnyHermesData}} object with a \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} +\code{\link{AnyHermesData}} object with a \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object, then the result will be a -\code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object (the more general +\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object (the more general class). \item Note that the combined object needs to have unique sample IDs (column names). } diff --git a/man/expression_set.Rd b/man/expression_set.Rd index 5b4fb894..a9cfc359 100644 --- a/man/expression_set.Rd +++ b/man/expression_set.Rd @@ -23,9 +23,9 @@ object into a \code{\link{HermesData}} object. \seealso{ \itemize{ \item \code{\link[SummarizedExperiment:makeSummarizedExperimentFromExpressionSet]{SummarizedExperiment::makeSummarizedExperimentFromExpressionSet()}} to convert into a -\code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}}. +\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}}. \item \code{\link{summarized_experiment}} which contains similar data already as a -\code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}}. +\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}}. } } \keyword{datasets} diff --git a/man/hermes_data.Rd b/man/hermes_data.Rd index 33529262..3bde6b30 100644 --- a/man/hermes_data.Rd +++ b/man/hermes_data.Rd @@ -17,12 +17,12 @@ hermes_data \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} -This example \code{\link{HermesData}} is created from the underlying \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} +This example \code{\link{HermesData}} is created from the underlying \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object by renaming descriptors to align with standard specification. It already contains the required columns in \code{rowData} and \code{colData}. } \seealso{ -\code{\link{summarized_experiment}} for the underlying \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} +\code{\link{summarized_experiment}} for the underlying \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object. } \keyword{datasets} diff --git a/man/isEmpty.Rd b/man/isEmpty.Rd index ab11dc35..3414fdc5 100644 --- a/man/isEmpty.Rd +++ b/man/isEmpty.Rd @@ -16,7 +16,7 @@ Flag whether the \code{object} is empty. \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -This method checks whether a \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object is empty. +This method checks whether a \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object is empty. } \examples{ isEmpty(summarized_experiment) diff --git a/man/rbind.Rd b/man/rbind.Rd index faa61017..f84e93af 100644 --- a/man/rbind.Rd +++ b/man/rbind.Rd @@ -19,9 +19,9 @@ features of interest (rows in assays). \itemize{ \item Note that this just inherits \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::rbind,SummarizedExperiment-method()}}. When binding a -\code{\link{AnyHermesData}} object with a \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} +\code{\link{AnyHermesData}} object with a \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object, then the result will be a -\code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object (the more general +\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object (the more general class). \item Note that we need to have unique gene IDs (row names) and the same prefix across the combined object. diff --git a/man/rename.Rd b/man/rename.Rd index d5c598af..cc15e777 100644 --- a/man/rename.Rd +++ b/man/rename.Rd @@ -31,13 +31,13 @@ to new (left-hand side names) assay names.} \item{...}{additional arguments (not used here).} } \value{ -The \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object with renamed contents. +The \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} object with renamed contents. } \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} This method renames columns of the \code{rowData} and \code{colData}, as well as assays, of -\code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} objects. This increases the flexibility +\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} objects. This increases the flexibility since renaming can be done before conversion to a \code{\link{HermesData}} object. } \examples{ diff --git a/man/show.Rd b/man/show.Rd index 2cb737e4..dc937781 100644 --- a/man/show.Rd +++ b/man/show.Rd @@ -25,7 +25,7 @@ A show method that displays high-level information of \code{\link{AnyHermesData} \note{ The same method is used for both \code{\link{HermesData}} and \code{\link{RangedHermesData}} objects. We need to define this separately to have this method used instead of -the one inherited from \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}}. +the one inherited from \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}}. } \examples{ object <- hermes_data diff --git a/man/summarized_experiment.Rd b/man/summarized_experiment.Rd index bef8eb4f..3ba11d15 100644 --- a/man/summarized_experiment.Rd +++ b/man/summarized_experiment.Rd @@ -5,7 +5,7 @@ \alias{summarized_experiment} \title{Example \code{SummarizedExperiment} Data} \format{ -A \link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment} object with 20 samples covering +A \link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment} object with 20 samples covering 5085 features (\code{Entrez} gene IDs). } \source{ @@ -17,7 +17,7 @@ summarized_experiment \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#stable}{\figure{lifecycle-stable.svg}{options: alt='[Stable]'}}}{\strong{[Stable]}} -This example \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} can be used to create a +This example \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} can be used to create a \code{\link{HermesData}} object. It already contains the required columns in \code{rowData} and \code{colData}. } \seealso{ diff --git a/man/validate.Rd b/man/validate.Rd index 909a5d20..18a886fb 100644 --- a/man/validate.Rd +++ b/man/validate.Rd @@ -35,7 +35,7 @@ case validation passes. } \description{ These functions are used internally only and therefore not exported. They work on -\code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} objects, and \code{\link{AnyHermesData}} objects are +\code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment::SummarizedExperiment}} objects, and \code{\link{AnyHermesData}} objects are defined by successfully passing these validation checks. } \section{Functions}{