1. POMA
  2. Commit 4d86b6409be5b78c621034e0c52769d8ce643ab4
Browse code

fix actions

pcastellanoescuder authored on 14/12/2023 19:52:19
Showing 7 changed files
DESCRIPTION
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@@ -1,6 +1,6 @@
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 Package: POMA
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 Title: Tools for Omics Data Analysis
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-Version: 1.13.4
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+Version: 1.13.5
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 Authors@R:
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     c(person(given = "Pol",
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              family = "Castellano-Escuder",
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@@ -55,7 +55,7 @@ Imports:
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     lme4,
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     magrittr,
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     MASS,
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-    Matrix,
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+    Matrix (<= 1.6.1),
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     mixOmics,
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     randomForest,
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     RankProd (>= 3.14),
NEWS.md
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@@ -1,4 +1,4 @@
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-# POMA 1.13.4
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+# POMA 1.13.5
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 * New POMA theme and colorblind-friendly palette
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 * Available sample normalization (sum and quantile)
R/PomaPLS.R
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@@ -86,7 +86,7 @@ PomaPLS <- function(data,
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   if (method == "pls") {
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     dependent_variable <- SummarizedExperiment::colData(data) %>%
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-      as.data.frame() %>%
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+      dplyr::as_tibble() %>%
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       dplyr::select_if(is.numeric)
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     if (ncol(dependent_variable) == 0) {
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@@ -152,7 +152,7 @@ PomaPLS <- function(data,
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   else if (method == "plsda") {
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     dependent_variable <- SummarizedExperiment::colData(data) %>%
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-      as.data.frame() %>%
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+      dplyr::as_tibble() %>%
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       dplyr::select_if(is.factor)
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     if (ncol(dependent_variable) == 0) {
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@@ -263,7 +263,7 @@ PomaPLS <- function(data,
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   else if (method == "splsda") {
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     dependent_variable <- SummarizedExperiment::colData(data) %>%
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-      as.data.frame() %>%
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+      dplyr::as_tibble() %>%
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       dplyr::select_if(is.factor)
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     if (ncol(dependent_variable) == 0) {
R/PomaUnivariate.R
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@@ -122,8 +122,8 @@ PomaUnivariate <- function(data,
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   }
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   else if (method == "anova") {
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-    covariates <- SummarizedExperiment::colData(data) %>%
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-      as.data.frame() %>%
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+    covariates <- SummarizedExperiment::colData(data) %>%
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+      dplyr::as_tibble() %>%
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       dplyr::select(-1)
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     if (is.null(covs)) {
R/helpers.R
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@@ -1,7 +1,8 @@
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 help_extract <- function(fun,
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-                         section = "Description") {
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-  x <- capture.output(tools::Rd2txt(utils:::.getHelpFile(help(fun, ...)), options = list(sectionIndent = 0)))
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+                         section = "Description",
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+                         ...) {
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+  x <- capture.output(tools::Rd2txt(utils:::.getHelpFile(utils::help(fun, ...)), options = list(sectionIndent = 0)))
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   B <- grep("^_", x)
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   x <- gsub("_\b", "", x, fixed = TRUE)
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   X <- rep(FALSE, length(x))
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@@ -20,8 +21,9 @@ help_extract <- function(fun,
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   return(out)
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 }
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-title_extract <- function(fun) {
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-  x <- capture.output(tools::Rd2txt(utils:::.getHelpFile(help(fun, ...)), options = list(sectionIndent = 0)))
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+title_extract <- function(fun,
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+                          ...) {
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+  x <- capture.output(tools::Rd2txt(utils:::.getHelpFile(utils::help(fun, ...)), options = list(sectionIndent = 0)))
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   x <- gsub("_\b", "", x, fixed = TRUE)
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   title <- x[1]
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   return(title)
README.Rmd
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@@ -16,7 +16,7 @@ output: github_document
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 | _BioC_ branch 	| Status 	| Version 	| Dependencies 	| Rank 	|
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 |-	|-	|-	|-	|-	|
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 | [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) 	|
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-| [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-1.13.4-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) 	|
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+| [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-1.13.5-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) 	|
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   <!-- badges: end -->
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README.md
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@@ -17,7 +17,7 @@ v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/li
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 | *BioC* branch                                                           | Status                                                                                                                                                  | Version                                                                                                                                            | Dependencies                                                                                                                                         | Rank                                                                                                                         |
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 |-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------|
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 | [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) |
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-| [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-1.13.4-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)   |
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+| [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-1.13.5-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)   |
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 <!-- badges: end -->
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