From eabfa41a2afb554a89b2d06375f8fd28fe9266df Mon Sep 17 00:00:00 2001 From: m7pr Date: Fri, 30 Jun 2023 15:53:49 +0200 Subject: [PATCH 1/4] reduce the content of WORDLIST --- NEWS.md | 4 ++-- R/adtteSpec.R | 14 +++++++------- R/argument_convention.R | 6 +++--- R/checkmate.R | 4 ++-- R/km.R | 6 +++--- README.md | 10 +++++----- inst/WORDLIST | 9 --------- man/adtteSpecInput.Rd | 4 ++-- man/adtteSpecServer.Rd | 12 ++++++------ man/assert_adtte_vars.Rd | 4 ++-- man/assertion_arguments.Rd | 2 +- man/check_tag.Rd | 2 +- man/h_km_mae_to_adtte.Rd | 2 +- man/module_arguments.Rd | 4 ++-- man/tm_g_forest_tte.Rd | 4 ++-- man/tm_g_km.Rd | 10 +++++----- tests/testthat/setup-skip_if_too_deep.R | 2 +- 17 files changed, 45 insertions(+), 54 deletions(-) diff --git a/NEWS.md b/NEWS.md index 87dda4a7..8e089934 100644 --- a/NEWS.md +++ b/NEWS.md @@ -21,7 +21,7 @@ * Rewrote modules to use `moduleServer` and updated call to `plot_with_settings_srv` after changes in `teal.devel`. * Replaced calls to `teal::root_modules` with `teal::modules` following deprecation of `teal::root_modules`. * Added basic logging to the modules. -* Fixed the `geneSpecInput` so that the hermes app doesn't fail anymore (on chrome) on an experiment with no genes. +* Fixed the `geneSpecInput` so that the `hermes` app doesn't fail anymore (on chrome) on an experiment with no genes. # teal.modules.hermes 0.1.1 @@ -43,7 +43,7 @@ * `tm_g_barplot` is a barplot module for RNA-seq gene expression analysis. * `tm_g_boxplot` is a boxplot module for RNA-seq gene expression analysis. * `tm_g_forest_tte` is a survival forest plot module to analyze RNA-seq gene expression data together with survival data. -* `tm_g_km` is a Kaplan-Meier plot module to analyze RNA-seq gene expression data together with survival data. +* `tm_g_km` is a `Kaplan-Meier` plot module to analyze RNA-seq gene expression data together with survival data. * `tm_g_pca` is a principal components analysis plot module for RNA-seq gene expression analysis. * `tm_g_quality` is a quality control module for RNA-seq gene expression data. * `tm_g_scatterplot` is a scatterplot module for RNA-seq gene expression analysis. diff --git a/R/adtteSpec.R b/R/adtteSpec.R index 3856672f..d0fe8dc8 100644 --- a/R/adtteSpec.R +++ b/R/adtteSpec.R @@ -1,4 +1,4 @@ -#' Data Preprocessing for ADTTE Module +#' Data Preprocessing for `ADTTE` Module #' #' @description `r lifecycle::badge("experimental")` #' @@ -88,11 +88,11 @@ h_km_mae_to_adtte <- function(adtte, ) } -#' Module Input for ADTTE Specification +#' Module Input for `ADTTE` Specification #' #' @description `r lifecycle::badge("experimental")` #' -#' This defines the input for the ADTTE specification. +#' This defines the input for the `ADTTE` specification. #' #' @inheritParams module_arguments #' @param label_paramcd (`string`)\cr label for the endpoint (`PARAMCD`) selection. @@ -114,12 +114,12 @@ adtteSpecInput <- function(inputId, # nolint ) } -#' Module Server for ADTTE Specification +#' Module Server for `ADTTE` Specification #' #' @description `r lifecycle::badge("experimental")` #' -#' This defines the server part for the ADTTE specification. The resulting data -#' set `binned_adtte_subset` contains the subset of ADTTE selected by the time-to-event +#' This defines the server part for the `ADTTE` specification. The resulting data +#' set `binned_adtte_subset` contains the subset of `ADTTE` selected by the time-to-event #' endpoint, joined together with the gene information extracted from specified assay #' and experiment, as numeric and factor columns. The factor column is created by binning #' the numeric column according to the quantile cutoffs specified in `probs`. @@ -133,7 +133,7 @@ adtteSpecInput <- function(inputId, # nolint #' into. #' #' @return List with the following elements: -#' - `binned_adtte_subset`: reactive containing the joined ADTTE and gene data. +#' - `binned_adtte_subset`: reactive containing the joined `ADTTE` and gene data. #' - `gene_col`: reactive containing the string with the column name of the original #' numeric gene variable. #' - `gene_factor`: string with the variable name for the binned gene data. diff --git a/R/argument_convention.R b/R/argument_convention.R index 06f44ee9..ad264677 100644 --- a/R/argument_convention.R +++ b/R/argument_convention.R @@ -13,9 +13,9 @@ #' @param inputId (`string`)\cr #' the ID used to call the module input. #' @param adtte_name (`string`)\cr -#' name of the ADTTE dataset. +#' name of the `ADTTE` dataset. #' @param adtte_vars (named `list` of `string`)\cr -#' names of the variables to use in the ADTTE dataset. It should comprise elements: +#' names of the variables to use in the `ADTTE` dataset. It should comprise elements: #' - `aval`: the numeric time-to-event variable. #' - `avalu`: the variable holding the unit of `aval`. #' - `is_event`: the logical event variable. It needs to be `TRUE` @@ -63,7 +63,7 @@ NULL #' @param add (`AssertCollection` or `NULL`)\cr collection to store #' assertion messages, see [`checkmate::AssertCollection`]. #' @param info (`string`)\cr extra information to be included in the -#' message for the testthat reporter, see [testthat::expect_that()]. +#' message for the `testthat` reporter, see [testthat::expect_that()]. #' @param label (`string`)\cr name of the checked object to print in #' messages. Defaults to the heuristic implemented in [checkmate::vname()]. #' diff --git a/R/checkmate.R b/R/checkmate.R index 979363c5..717025d5 100644 --- a/R/checkmate.R +++ b/R/checkmate.R @@ -120,11 +120,11 @@ assert_summary_funs <- function(x, null.ok = FALSE) { # nolint # assert_adtte_vars ---- -#' Check for ADTTE Variables +#' Check for `ADTTE` Variables #' #' @description `r lifecycle::badge("experimental")` #' -#' Check whether `x` is a list of ADTTE variables. +#' Check whether `x` is a list of `ADTTE` variables. #' #' @inheritParams assertion_arguments #' @seealso [`assertions`] for more details. diff --git a/R/km.R b/R/km.R index 40baf460..963b503f 100644 --- a/R/km.R +++ b/R/km.R @@ -1,9 +1,9 @@ -#' Teal Module for Kaplan-Meier Plot +#' Teal Module for `Kaplan-Meier` Plot #' #' @description `r lifecycle::badge("experimental")` #' -#' This teal module produces a grid style Kaplan-Meier plot for data with -#' ADaM structure. +#' This teal module produces a grid style `Kaplan-Meier` plot for data with +#' `ADaM` structure. #' #' @inheritParams module_arguments #' diff --git a/README.md b/README.md index 9767350e..800c9660 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/teal.modules.hermes/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/insightsengineering/teal.modules.hermes/_xml_coverage_reports/data/main/coverage.xml) ![GitHub forks](https://img.shields.io/github/forks/insightsengineering/teal.modules.hermes?style=social) -![GitHub Repo stars](https://img.shields.io/github/stars/insightsengineering/teal.modules.hermes?style=social) +![GitHub repo stars](https://img.shields.io/github/stars/insightsengineering/teal.modules.hermes?style=social) ![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/teal.modules.hermes) ![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/teal.modules.hermes) @@ -24,21 +24,21 @@ ### What is `teal`? `teal` is a shiny-based interactive exploration framework for analyzing clinical trials data. `teal` currently provides a dynamic filtering facility and diverse data viewers. `teal` shiny applications are built using standard [shiny modules](https://shiny.rstudio.com/articles/modules.html). -See [github](https://insightsengineering.github.io/teal) for more details. +See [`teal` page](https://insightsengineering.github.io/teal) for more details. ### What is `hermes`? `hermes` facilitates preprocessing, analyzing, and reporting of RNA-seq data. -The core functionality is built on the BioConductor ecosystem, especially the `SummarizedExperiment` class from which the `HermesData` class inherits. +The core functionality is built on the `BioConductor` ecosystem, especially the `SummarizedExperiment` class from which the `HermesData` class inherits. See the [vignette](https://insightsengineering.github.io/hermes/articles/hermes.html) for more details. ### So what is then `teal.modules.hermes`? -`teal.modules.hermes` provides `teal` modules (which can be used as part of any `teal` app), for interactive RNA-seq data analysis using `hermes`. Again it is heavily built on the BioConductor classes, in particular `MultiAssayExperiment` (MAE) which is expected to contain the `HermesData` experiments. +`teal.modules.hermes` provides `teal` modules (which can be used as part of any `teal` app), for interactive RNA-seq data analysis using `hermes`. Again it is heavily built on the `BioConductor` classes, in particular `MultiAssayExperiment` (MAE) which is expected to contain the `HermesData` experiments. ## Installation -For releases from August 2022 it is recommended that you [create and use a Github PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following: +For releases from August 2022 it is recommended that you [create and use a GitHub PAT](https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and-data-secure/creating-a-personal-access-token) to install the latest version of this package. Once you have the PAT, run the following: ```r Sys.setenv(GITHUB_PAT = "your_access_token_here") diff --git a/inst/WORDLIST b/inst/WORDLIST index 22fd530d..8d0da384 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,22 +1,13 @@ -ADTTE -ADaM -BioConductor Bové Forkers -Github -hoc Hoffmann -Kaplan Lyndsee Midori RNAseq -Repo Sabanés UI funder -github hermes pre reactives repo -testthat diff --git a/man/adtteSpecInput.Rd b/man/adtteSpecInput.Rd index 6161cd47..a1639a30 100644 --- a/man/adtteSpecInput.Rd +++ b/man/adtteSpecInput.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/adtteSpec.R \name{adtteSpecInput} \alias{adtteSpecInput} -\title{Module Input for ADTTE Specification} +\title{Module Input for \code{ADTTE} Specification} \usage{ adtteSpecInput(inputId, label_paramcd = "Select Endpoint") } @@ -18,7 +18,7 @@ The UI part. \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -This defines the input for the ADTTE specification. +This defines the input for the \code{ADTTE} specification. } \seealso{ \code{\link[=adtteSpecServer]{adtteSpecServer()}} for the module server and a complete example. diff --git a/man/adtteSpecServer.Rd b/man/adtteSpecServer.Rd index a06ef287..6e9d1221 100644 --- a/man/adtteSpecServer.Rd +++ b/man/adtteSpecServer.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/adtteSpec.R \name{adtteSpecServer} \alias{adtteSpecServer} -\title{Module Server for ADTTE Specification} +\title{Module Server for \code{ADTTE} Specification} \usage{ adtteSpecServer( id, @@ -28,10 +28,10 @@ functions, holding all the data sets provided in the app initialization.} name of the MAE data used in the teal module.} \item{adtte_name}{(\code{string})\cr -name of the ADTTE dataset.} +name of the \code{ADTTE} dataset.} \item{adtte_vars}{(named \code{list} of \code{string})\cr -names of the variables to use in the ADTTE dataset. It should comprise elements: +names of the variables to use in the \code{ADTTE} dataset. It should comprise elements: \itemize{ \item \code{aval}: the numeric time-to-event variable. \item \code{avalu}: the variable holding the unit of \code{aval}. @@ -57,7 +57,7 @@ into.} \value{ List with the following elements: \itemize{ -\item \code{binned_adtte_subset}: reactive containing the joined ADTTE and gene data. +\item \code{binned_adtte_subset}: reactive containing the joined \code{ADTTE} and gene data. \item \code{gene_col}: reactive containing the string with the column name of the original numeric gene variable. \item \code{gene_factor}: string with the variable name for the binned gene data. @@ -67,8 +67,8 @@ numeric gene variable. \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -This defines the server part for the ADTTE specification. The resulting data -set \code{binned_adtte_subset} contains the subset of ADTTE selected by the time-to-event +This defines the server part for the \code{ADTTE} specification. The resulting data +set \code{binned_adtte_subset} contains the subset of \code{ADTTE} selected by the time-to-event endpoint, joined together with the gene information extracted from specified assay and experiment, as numeric and factor columns. The factor column is created by binning the numeric column according to the quantile cutoffs specified in \code{probs}. diff --git a/man/assert_adtte_vars.Rd b/man/assert_adtte_vars.Rd index 3c9004ca..bdd4f61f 100644 --- a/man/assert_adtte_vars.Rd +++ b/man/assert_adtte_vars.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/checkmate.R \name{assert_adtte_vars} \alias{assert_adtte_vars} -\title{Check for ADTTE Variables} +\title{Check for \code{ADTTE} Variables} \usage{ assert_adtte_vars(x) } @@ -12,7 +12,7 @@ assert_adtte_vars(x) \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -Check whether \code{x} is a list of ADTTE variables. +Check whether \code{x} is a list of \code{ADTTE} variables. } \examples{ assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u")) diff --git a/man/assertion_arguments.Rd b/man/assertion_arguments.Rd index a498b36d..536ce555 100644 --- a/man/assertion_arguments.Rd +++ b/man/assertion_arguments.Rd @@ -15,7 +15,7 @@ assertions; defaults to the heuristic implemented in \code{\link[checkmate:vname assertion messages, see \code{\link[checkmate:AssertCollection]{checkmate::AssertCollection}}.} \item{info}{(\code{string})\cr extra information to be included in the -message for the testthat reporter, see \code{\link[testthat:expect_that]{testthat::expect_that()}}.} +message for the \code{testthat} reporter, see \code{\link[testthat:expect_that]{testthat::expect_that()}}.} \item{label}{(\code{string})\cr name of the checked object to print in messages. Defaults to the heuristic implemented in \code{\link[checkmate:vname]{checkmate::vname()}}.} diff --git a/man/check_tag.Rd b/man/check_tag.Rd index 5803414e..fd408af8 100644 --- a/man/check_tag.Rd +++ b/man/check_tag.Rd @@ -27,7 +27,7 @@ assertions; defaults to the heuristic implemented in \code{\link[checkmate:vname assertion messages, see \code{\link[checkmate:AssertCollection]{checkmate::AssertCollection}}.} \item{info}{(\code{string})\cr extra information to be included in the -message for the testthat reporter, see \code{\link[testthat:expect_that]{testthat::expect_that()}}.} +message for the \code{testthat} reporter, see \code{\link[testthat:expect_that]{testthat::expect_that()}}.} \item{label}{(\code{string})\cr name of the checked object to print in messages. Defaults to the heuristic implemented in \code{\link[checkmate:vname]{checkmate::vname()}}.} diff --git a/man/h_km_mae_to_adtte.Rd b/man/h_km_mae_to_adtte.Rd index 4a3d7609..2544e53f 100644 --- a/man/h_km_mae_to_adtte.Rd +++ b/man/h_km_mae_to_adtte.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/adtteSpec.R \name{h_km_mae_to_adtte} \alias{h_km_mae_to_adtte} -\title{Data Preprocessing for ADTTE Module} +\title{Data Preprocessing for \code{ADTTE} Module} \usage{ h_km_mae_to_adtte( adtte, diff --git a/man/module_arguments.Rd b/man/module_arguments.Rd index 8b912f0c..b0c34675 100644 --- a/man/module_arguments.Rd +++ b/man/module_arguments.Rd @@ -15,10 +15,10 @@ menu item label of the module in the teal app.} the ID used to call the module input.} \item{adtte_name}{(\code{string})\cr -name of the ADTTE dataset.} +name of the \code{ADTTE} dataset.} \item{adtte_vars}{(named \code{list} of \code{string})\cr -names of the variables to use in the ADTTE dataset. It should comprise elements: +names of the variables to use in the \code{ADTTE} dataset. It should comprise elements: \itemize{ \item \code{aval}: the numeric time-to-event variable. \item \code{avalu}: the variable holding the unit of \code{aval}. diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd index 685a71fa..50d06fec 100644 --- a/man/tm_g_forest_tte.Rd +++ b/man/tm_g_forest_tte.Rd @@ -53,13 +53,13 @@ sample_tm_g_forest_tte() menu item label of the module in the teal app.} \item{adtte_name}{(\code{string})\cr -name of the ADTTE dataset.} +name of the \code{ADTTE} dataset.} \item{mae_name}{(\code{string})\cr name of the MAE data used in the teal module.} \item{adtte_vars}{(named \code{list} of \code{string})\cr -names of the variables to use in the ADTTE dataset. It should comprise elements: +names of the variables to use in the \code{ADTTE} dataset. It should comprise elements: \itemize{ \item \code{aval}: the numeric time-to-event variable. \item \code{avalu}: the variable holding the unit of \code{aval}. diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd index 924b69f4..c56a28ba 100644 --- a/man/tm_g_km.Rd +++ b/man/tm_g_km.Rd @@ -5,7 +5,7 @@ \alias{ui_g_km} \alias{srv_g_km} \alias{sample_tm_g_km} -\title{Teal Module for Kaplan-Meier Plot} +\title{Teal Module for \code{Kaplan-Meier} Plot} \usage{ tm_g_km( label, @@ -41,13 +41,13 @@ sample_tm_g_km() menu item label of the module in the teal app.} \item{adtte_name}{(\code{string})\cr -name of the ADTTE dataset.} +name of the \code{ADTTE} dataset.} \item{mae_name}{(\code{string})\cr name of the MAE data used in the teal module.} \item{adtte_vars}{(named \code{list} of \code{string})\cr -names of the variables to use in the ADTTE dataset. It should comprise elements: +names of the variables to use in the \code{ADTTE} dataset. It should comprise elements: \itemize{ \item \code{aval}: the numeric time-to-event variable. \item \code{avalu}: the variable holding the unit of \code{aval}. @@ -89,8 +89,8 @@ Shiny module to be used in the teal app. \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -This teal module produces a grid style Kaplan-Meier plot for data with -ADaM structure. +This teal module produces a grid style \code{Kaplan-Meier} plot for data with +\code{ADaM} structure. } \section{Functions}{ \itemize{ diff --git a/tests/testthat/setup-skip_if_too_deep.R b/tests/testthat/setup-skip_if_too_deep.R index 89205740..6467ab93 100644 --- a/tests/testthat/setup-skip_if_too_deep.R +++ b/tests/testthat/setup-skip_if_too_deep.R @@ -22,7 +22,7 @@ testing_depth <- function() { # nolint # nousage testing_depth } -#' Skipping tests in the testthat pipeline under specific scope +#' Skipping tests in the `testthat` pipeline under specific scope #' @description This function should be used per each \code{testthat::test_that} call. #' Each of the call should specify an appropriate depth value. #' The depth value will set the appropriate scope so more/less time consuming tests could be recognized. From 1cf076454151fed605e3c70f4bd8f6aed2b88e45 Mon Sep 17 00:00:00 2001 From: m7pr Date: Fri, 30 Jun 2023 17:28:15 +0200 Subject: [PATCH 2/4] revert Kaplan-Meier --- NEWS.md | 2 +- R/km.R | 4 ++-- inst/WORDLIST | 1 + man/tm_g_km.Rd | 4 ++-- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/NEWS.md b/NEWS.md index 8e089934..4e7f9687 100644 --- a/NEWS.md +++ b/NEWS.md @@ -43,7 +43,7 @@ * `tm_g_barplot` is a barplot module for RNA-seq gene expression analysis. * `tm_g_boxplot` is a boxplot module for RNA-seq gene expression analysis. * `tm_g_forest_tte` is a survival forest plot module to analyze RNA-seq gene expression data together with survival data. -* `tm_g_km` is a `Kaplan-Meier` plot module to analyze RNA-seq gene expression data together with survival data. +* `tm_g_km` is a Kaplan-Meier plot module to analyze RNA-seq gene expression data together with survival data. * `tm_g_pca` is a principal components analysis plot module for RNA-seq gene expression analysis. * `tm_g_quality` is a quality control module for RNA-seq gene expression data. * `tm_g_scatterplot` is a scatterplot module for RNA-seq gene expression analysis. diff --git a/R/km.R b/R/km.R index 963b503f..2c34de8e 100644 --- a/R/km.R +++ b/R/km.R @@ -1,8 +1,8 @@ -#' Teal Module for `Kaplan-Meier` Plot +#' Teal Module for Kaplan-Meier Plot #' #' @description `r lifecycle::badge("experimental")` #' -#' This teal module produces a grid style `Kaplan-Meier` plot for data with +#' This teal module produces a grid style Kaplan-Meier plot for data with #' `ADaM` structure. #' #' @inheritParams module_arguments diff --git a/inst/WORDLIST b/inst/WORDLIST index 8d0da384..162d18ee 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,6 +1,7 @@ Bové Forkers Hoffmann +Kaplan Lyndsee Midori RNAseq diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd index c56a28ba..80cd2cc9 100644 --- a/man/tm_g_km.Rd +++ b/man/tm_g_km.Rd @@ -5,7 +5,7 @@ \alias{ui_g_km} \alias{srv_g_km} \alias{sample_tm_g_km} -\title{Teal Module for \code{Kaplan-Meier} Plot} +\title{Teal Module for Kaplan-Meier Plot} \usage{ tm_g_km( label, @@ -89,7 +89,7 @@ Shiny module to be used in the teal app. \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} -This teal module produces a grid style \code{Kaplan-Meier} plot for data with +This teal module produces a grid style Kaplan-Meier plot for data with \code{ADaM} structure. } \section{Functions}{ From bb749758fbe4003012a4584cb319dd8bd2ba339b Mon Sep 17 00:00:00 2001 From: m7pr Date: Fri, 30 Jun 2023 17:30:29 +0200 Subject: [PATCH 3/4] extend threshold for execution of examples --- .github/workflows/check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 8f18b5f2..8e2a70fc 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -27,6 +27,7 @@ jobs: with: additional-env-vars: | _R_CHECK_CRAN_INCOMING_REMOTE_=false + _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10 NOT_CRAN=true additional-r-cmd-check-params: --as-cran coverage: From ed9a20a50a47248fb0085c7df6a1f8090a9c30a0 Mon Sep 17 00:00:00 2001 From: m7pr Date: Fri, 30 Jun 2023 21:35:45 +0200 Subject: [PATCH 4/4] add BiocStyle to Suggests as it is used in vignette as BiocStyle::html_document --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index 9bae1ca3..17037f2c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -53,6 +53,7 @@ Imports: teal.widgets (>= 0.2.0), tern (>= 0.7.10) Suggests: + BiocStyle, covr, dplyr, globals,