diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml index c02f032f..156df073 100644 --- a/.github/workflows/deploy.yaml +++ b/.github/workflows/deploy.yaml @@ -34,8 +34,12 @@ jobs: strategy: fail-fast: false matrix: - directory: ["basic-teal"] - repository: ["https://insightsengineering.r-universe.dev"] + directory: ["basic-teal", "RNA-seq"] + repository: + [ + "https://insightsengineering.r-universe.dev", + "https://pharmaverse.r-universe.dev", + ] steps: - name: Set CHANNEL run: | diff --git a/RNA-seq/renv.lock b/RNA-seq/renv.lock index c0743bf3..0fbe397e 100644 --- a/RNA-seq/renv.lock +++ b/RNA-seq/renv.lock @@ -1388,20 +1388,6 @@ ], "Hash": "63cb26d12517c7863f5abb006c5e0f25" }, - "formatters": { - "Package": "formatters", - "Version": "0.5.1", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "checkmate", - "grid", - "htmltools", - "methods" - ], - "Hash": "a68b4771f14ae9e662fc22f96ced77d3" - }, "fs": { "Package": "fs", "Version": "1.6.3", @@ -1973,19 +1959,6 @@ ], "Hash": "ef6270cb713747aa8211620d6a47188d" }, - "nestcolor": { - "Package": "nestcolor", - "Version": "0.1.2", - "Source": "Bioconductor", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "checkmate", - "ggplot2", - "lifecycle" - ], - "Hash": "1b54abe1a145b4df499a273baaea4475" - }, "nlme": { "Package": "nlme", "Version": "3.1-162", @@ -2384,22 +2357,6 @@ ], "Hash": "1de7ab598047a87bba48434ba35d497d" }, - "rtables": { - "Package": "rtables", - "Version": "0.6.2", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "formatters", - "grid", - "htmltools", - "magrittr", - "methods", - "stats" - ], - "Hash": "85fe6fcebbfb3dc8cbce39b49b2b7634" - }, "sass": { "Package": "sass", "Version": "0.4.7", @@ -2432,27 +2389,6 @@ ], "Hash": "906cb23d2f1c5680b8ce439b44c6fa63" }, - "scda": { - "Package": "scda", - "Version": "0.1.6", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "utils" - ], - "Hash": "bf70e1415684b9ec33d661672a111657" - }, - "scda.2022": { - "Package": "scda.2022", - "Version": "0.1.5", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R" - ], - "Hash": "425e70a2ce4a6ec7c5ec3a774190ccc2" - }, "shape": { "Package": "shape", "Version": "1.4.6", @@ -2678,290 +2614,6 @@ "Repository": "CRAN", "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" }, - "teal": { - "Package": "teal", - "Version": "0.14.0", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "checkmate", - "lifecycle", - "logger", - "magrittr", - "rlang", - "shiny", - "shinyjs", - "stats", - "teal.data", - "teal.logger", - "teal.reporter", - "teal.slice", - "teal.transform", - "teal.widgets", - "utils" - ], - "Hash": "404f9b53d5212ae28e4911d62d3a09d8" - }, - "teal.code": { - "Package": "teal.code", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "checkmate", - "grDevices", - "lifecycle", - "methods", - "rlang", - "shiny", - "styler" - ], - "Hash": "05bbdc13cf5440c53e94bf0f70b41c6b" - }, - "teal.data": { - "Package": "teal.data", - "Version": "0.3.0", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "R6", - "checkmate", - "digest", - "lifecycle", - "logger", - "methods", - "rlang", - "shiny", - "shinyjs", - "stats", - "teal.logger", - "utils", - "yaml" - ], - "Hash": "2f1e3270eb58d01f53b52b0f56625a25" - }, - "teal.logger": { - "Package": "teal.logger", - "Version": "0.1.1", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "glue", - "lifecycle", - "logger", - "shiny", - "withr" - ], - "Hash": "82bdd798040e2a3731d0f4f23ef6ad53" - }, - "teal.modules.general": { - "Package": "teal.modules.general", - "Version": "0.2.16", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "DT", - "R", - "checkmate", - "dplyr", - "forcats", - "ggmosaic", - "ggplot2", - "grid", - "logger", - "magrittr", - "scales", - "shiny", - "shinyTree", - "shinyWidgets", - "shinyjs", - "shinyvalidate", - "stats", - "stringr", - "teal", - "teal.code", - "teal.logger", - "teal.reporter", - "teal.slice", - "teal.transform", - "teal.widgets", - "tern", - "tibble", - "tidyr", - "tidyselect", - "utils" - ], - "Hash": "70b3f00b57a2a2e6ad69bb32f4c5eaa2" - }, - "teal.modules.hermes": { - "Package": "teal.modules.hermes", - "Version": "0.1.5", - "Source": "Bioconductor", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "DT", - "MultiAssayExperiment", - "R", - "S4Vectors", - "SummarizedExperiment", - "checkmate", - "edgeR", - "forcats", - "ggplot2", - "hermes", - "lifecycle", - "logger", - "rtables", - "shiny", - "shinyRadioMatrix", - "shinyWidgets", - "stats", - "stringr", - "teal", - "teal.data", - "teal.logger", - "teal.reporter", - "teal.widgets", - "tern" - ], - "Hash": "fcad1a2ebebfd51ffaad9a259dddc516" - }, - "teal.reporter": { - "Package": "teal.reporter", - "Version": "0.2.0", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R6", - "bslib", - "checkmate", - "grid", - "htmltools", - "knitr", - "lifecycle", - "rmarkdown", - "shiny", - "shinyWidgets", - "yaml", - "zip" - ], - "Hash": "57479129ef12c4a3bcaa47cf97cbeef1" - }, - "teal.slice": { - "Package": "teal.slice", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "R6", - "bslib", - "checkmate", - "dplyr", - "grDevices", - "htmltools", - "jsonlite", - "lifecycle", - "logger", - "methods", - "plotly", - "shiny", - "shinyWidgets", - "shinycssloaders", - "shinyjs", - "teal.data", - "teal.logger", - "teal.widgets" - ], - "Hash": "31bf42079affad82082cf2bd92ed4da2" - }, - "teal.transform": { - "Package": "teal.transform", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "checkmate", - "dplyr", - "lifecycle", - "logger", - "magrittr", - "methods", - "rlang", - "shiny", - "shinyjs", - "shinyvalidate", - "stats", - "teal.data", - "teal.logger", - "teal.slice", - "teal.widgets", - "tidyr", - "tidyselect" - ], - "Hash": "c7887305e42dd13c94d2df2d14ea8ca6" - }, - "teal.widgets": { - "Package": "teal.widgets", - "Version": "0.4.0", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "bslib", - "checkmate", - "ggplot2", - "graphics", - "htmltools", - "lifecycle", - "methods", - "shiny", - "shinyWidgets", - "shinyjs", - "styler" - ], - "Hash": "00c70d4fe01ef4e2c4dac416021ca1fb" - }, - "tern": { - "Package": "tern", - "Version": "0.8.5", - "Source": "Repository", - "Repository": "https://insightsengineering.r-universe.dev", - "Requirements": [ - "R", - "Rdpack", - "broom", - "car", - "checkmate", - "cowplot", - "dplyr", - "emmeans", - "forcats", - "formatters", - "ggplot2", - "grid", - "gridExtra", - "gtable", - "labeling", - "lifecycle", - "magrittr", - "methods", - "rlang", - "rtables", - "scales", - "stats", - "survival", - "tibble", - "tidyr", - "utils" - ], - "Hash": "f386494470e7cdc4f8a817afcff342ff" - }, "testthat": { "Package": "testthat", "Version": "3.1.10", diff --git a/basic-teal/.Rprofile b/basic-teal/.Rprofile index b5022afe..81b960f5 100644 --- a/basic-teal/.Rprofile +++ b/basic-teal/.Rprofile @@ -1,7 +1 @@ source("renv/activate.R") - -for (package in renv::dependencies()$Package) { - if (!requireNamespace(package)) { - renv::install(package) - } -}