rename default branch to main and update actions 2

pcastellanoescuder · Dec 7, 2023 · 303e4ae · 303e4ae
1 parent e9d0753
commit 303e4ae
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Showing 10 changed files with 68 additions and 107 deletions.
diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,49 @@
+
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+
diff --git a/.github/workflows/R-CMD-check.yml b/.github/workflows/R-CMD-check.yml
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@ inst/doc
 Dockerfile
 pkgdown/
 docs/
+.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: POMA
 Title: Tools for Omics Data Analysis   
-Version: 1.8.50
+Version: 1.8.51
 Authors@R: 
     c(person(given = "Pol",
              family = "Castellano-Escuder",

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# POMA 1.8.50
+# POMA 1.8.51
 
 * New POMA theme and colorblind-friendly palette
 * Available sample normalization (sum and quantile)
@@ -12,7 +12,6 @@
 * Other new functions: `PomaLM`, `PomaLMM`
 * Post-hoc pairwise comparisons in `PomaUnivariate`
 * Update tests and vignettes
-* Rename default GitHub branch from `master` to `main`
 
 # POMA 1.7.19
 

diff --git a/R/PomaUnivariate.R b/R/PomaUnivariate.R
@@ -137,7 +137,7 @@ PomaUnivariate <- function(data,
       # Post-hoc tests
       if (run_post_hoc) {
         post_hoc_tests <- list()
-        for (i in 1:nrow(SummarizedExperiment::assay(data))) {
+        for (i in seq_len(nrow(SummarizedExperiment::assay(data)))) {
           post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], 
                                                broom::tidy(TukeyHSD(aov(to_univariate[,i] ~ group_factor)))[,c(2, 7)])
         }
@@ -160,7 +160,7 @@ PomaUnivariate <- function(data,
       covariates_feat <- as.data.frame(cbind(to_univariate, covariates))
 
       result_cov <- vector(mode = "list", length = ncol(to_univariate))
-      for(i in 1:ncol(to_univariate)) {
+      for(i in seq_len(ncol(to_univariate))) {
         result_cov[[i]] <- broom::tidy(anova(aov(as.formula(paste(colnames(covariates_feat)[i], "~", model_names)),
                                                  data = covariates_feat))) %>% 
           dplyr::filter(term != "Residuals") %>% 
@@ -182,7 +182,7 @@ PomaUnivariate <- function(data,
       # Post-hoc tests
       if (run_post_hoc) {
         post_hoc_tests <- list()
-        for (i in 1:nrow(SummarizedExperiment::assay(data))) {
+        for (i in seq_len(nrow(SummarizedExperiment::assay(data)))) {
           post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], 
                                                as.data.frame(TukeyHSD(
                                                  aov(as.formula(paste(colnames(covariates_feat)[1], "~", model_names)),
@@ -238,7 +238,7 @@ PomaUnivariate <- function(data,
     # Post-hoc tests
     if (run_post_hoc) {
       post_hoc_tests <- list()
-      for (i in 1:nrow(SummarizedExperiment::assay(data))) {
+      for (i in seq_len(nrow(SummarizedExperiment::assay(data)))) {
         post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i],
                                              FSA::dunnTest(to_univariate[,i] ~ group_factor,
                                                            data = as.data.frame(to_univariate))$res

diff --git a/R/helpers.R b/R/helpers.R
@@ -1,8 +1,7 @@
 
 help_extract <- function(fun, 
-                         section = "Description",
-                         ...) {
-  x <- capture.output(tools:::Rd2txt(utils:::.getHelpFile(help(fun, ...)), options = list(sectionIndent = 0)))
+                         section = "Description") {
+  x <- capture.output(tools::Rd2txt(utils:::.getHelpFile(help(fun, ...)), options = list(sectionIndent = 0)))
   B <- grep("^_", x)
   x <- gsub("_\b", "", x, fixed = TRUE)
   X <- rep(FALSE, length(x))
@@ -21,17 +20,15 @@ help_extract <- function(fun,
   return(out)
 }
 
-title_extract <- function(fun, 
-                          ...) {
-  x <- capture.output(tools:::Rd2txt(utils:::.getHelpFile(help(fun, ...)), options = list(sectionIndent = 0)))
+title_extract <- function(fun) {
+  x <- capture.output(tools::Rd2txt(utils:::.getHelpFile(help(fun, ...)), options = list(sectionIndent = 0)))
   x <- gsub("_\b", "", x, fixed = TRUE)
   title <- x[1]
   return(title)
 }
 
 make_legend <- function(fun, 
-                        html = FALSE, 
-                        ...) {
+                        html = FALSE) {
   description <- help_extract(fun, package = POMA, section = "Description")
   title <- title_extract(fun, package = POMA)
   if (html) {

diff --git a/README.Rmd b/README.Rmd
@@ -7,7 +7,8 @@ output: github_document
   <!-- badges: start -->
 
   [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
-  [![Actions Status](https://github.com/pcastellanoescuder/POMA/workflows/R-CMD-check/badge.svg)](https://github.com/pcastellanoescuder/POMA/actions) 
+  <!-- [![Actions Status](https://github.com/pcastellanoescuder/POMA/workflows/R-CMD-check/badge.svg)](https://github.com/pcastellanoescuder/POMA/actions)  -->
+  [![R-CMD-check](https://github.com/pcastellanoescuder/POMA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pcastellanoescuder/POMA/actions/workflows/R-CMD-check.yaml)
   [![Codecov test coverage](https://codecov.io/gh/pcastellanoescuder/POMA/branch/master/graph/badge.svg)](https://codecov.io/gh/pcastellanoescuder/POMA?branch=master)
   [![CodeFactor](https://www.codefactor.io/repository/github/pcastellanoescuder/POMA/badge)](https://www.codefactor.io/repository/github/pcastellanoescuder/POMA)
   [![Last Commit](https://img.shields.io/github/last-commit/pcastellanoescuder/POMA.svg)](https://github.com/pcastellanoescuder/POMA/commits/master)
@@ -16,7 +17,7 @@ output: github_document
 | _BioC_ branch 	| Status 	| Version 	| Dependencies 	| Rank 	|
 |-	|-	|-	|-	|-	|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) 	| [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) 	| [![BioC released version](https://img.shields.io/badge/release%20version-1.6.0-blue.svg)](https://www.bioconductor.org/packages/POMA) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.8.50-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) 	| [![BioC devel version](https://img.shields.io/badge/devel%20version-1.8.51-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) 	| [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) 	| [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) 	|
 
   <!-- badges: end -->
 

diff --git a/README.md b/README.md
@@ -5,8 +5,8 @@
 
 [![Lifecycle:
 stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
-[![Actions
-Status](https://github.com/pcastellanoescuder/POMA/workflows/R-CMD-check/badge.svg)](https://github.com/pcastellanoescuder/POMA/actions)
+<!-- [![Actions Status](https://github.com/pcastellanoescuder/POMA/workflows/R-CMD-check/badge.svg)](https://github.com/pcastellanoescuder/POMA/actions)  -->
+[![R-CMD-check](https://github.com/pcastellanoescuder/POMA/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pcastellanoescuder/POMA/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
 coverage](https://codecov.io/gh/pcastellanoescuder/POMA/branch/master/graph/badge.svg)](https://codecov.io/gh/pcastellanoescuder/POMA?branch=master)
 [![CodeFactor](https://www.codefactor.io/repository/github/pcastellanoescuder/POMA/badge)](https://www.codefactor.io/repository/github/pcastellanoescuder/POMA)
@@ -18,7 +18,7 @@ v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/li
 | *BioC* branch                                                           | Status                                                                                                                                                  | Version                                                                                                                                            | Dependencies                                                                                                                                         | Rank                                                                                                                         |
 |-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
 | [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [![Bioc release status](https://bioconductor.org/shields/build/release/bioc/POMA.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [![BioC released version](https://img.shields.io/badge/release%20version-1.6.0-blue.svg)](https://www.bioconductor.org/packages/POMA)              | [![Dependencies](http://bioconductor.org/shields/dependencies/release/POMA.svg)](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [![Rank](http://www.bioconductor.org/shields/downloads/release/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA) |
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.8.50-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since)     | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html)     | [![Bioc devel status](https://bioconductor.org/shields/build/devel/bioc/POMA.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/)       | [![BioC devel version](https://img.shields.io/badge/devel%20version-1.8.51-blue.svg)](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [![Dependencies](http://bioconductor.org/shields/dependencies/devel/POMA.svg)](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since)     | [![Rank](http://www.bioconductor.org/shields/downloads/devel/POMA.svg)](https://bioconductor.org/packages/stats/bioc/POMA)   |
 
 <!-- badges: end -->