fix actions

pcastellanoescuder · Dec 14, 2023 · 4d86b64 · 4d86b64
1 parent f312208
commit 4d86b64
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Showing 7 changed files with 16 additions and 14 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: POMA
 Title: Tools for Omics Data Analysis   
-Version: 1.13.4
+Version: 1.13.5
 Authors@R: 
     c(person(given = "Pol",
              family = "Castellano-Escuder",
@@ -55,7 +55,7 @@ Imports:
     lme4,
     magrittr,
     MASS,
-    Matrix,
+    Matrix (<= 1.6.1),
     mixOmics,
     randomForest,
     RankProd (>= 3.14),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# POMA 1.13.4
+# POMA 1.13.5
 
 * New POMA theme and colorblind-friendly palette
 * Available sample normalization (sum and quantile)

diff --git a/R/PomaPLS.R b/R/PomaPLS.R
@@ -86,7 +86,7 @@ PomaPLS <- function(data,
 
   if (method == "pls") {
     dependent_variable <- SummarizedExperiment::colData(data) %>% 
-      as.data.frame() %>% 
+      dplyr::as_tibble() %>% 
       dplyr::select_if(is.numeric)
 
     if (ncol(dependent_variable) == 0) {
@@ -152,7 +152,7 @@ PomaPLS <- function(data,
 
   else if (method == "plsda") {
     dependent_variable <- SummarizedExperiment::colData(data) %>% 
-      as.data.frame() %>% 
+      dplyr::as_tibble() %>% 
       dplyr::select_if(is.factor)
 
     if (ncol(dependent_variable) == 0) {
@@ -263,7 +263,7 @@ PomaPLS <- function(data,
 
   else if (method == "splsda") {
     dependent_variable <- SummarizedExperiment::colData(data) %>% 
-      as.data.frame() %>% 
+      dplyr::as_tibble() %>% 
       dplyr::select_if(is.factor)
 
     if (ncol(dependent_variable) == 0) {

diff --git a/R/PomaUnivariate.R b/R/PomaUnivariate.R
@@ -122,8 +122,8 @@ PomaUnivariate <- function(data,
   }
 
   else if (method == "anova") {
-    covariates <- SummarizedExperiment::colData(data) %>%
-      as.data.frame() %>%
+    covariates <- SummarizedExperiment::colData(data) %>% 
+      dplyr::as_tibble() %>% 
       dplyr::select(-1)
 
     if (is.null(covs)) {

diff --git a/R/helpers.R b/R/helpers.R
@@ -1,7 +1,8 @@
 
 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(utils::help(fun, ...)), options = list(sectionIndent = 0)))
   B <- grep("^_", x)
   x <- gsub("_\b", "", x, fixed = TRUE)
   X <- rep(FALSE, length(x))
@@ -20,8 +21,9 @@ 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(utils::help(fun, ...)), options = list(sectionIndent = 0)))
   x <- gsub("_\b", "", x, fixed = TRUE)
   title <- x[1]
   return(title)

diff --git a/README.Rmd b/README.Rmd
@@ -16,7 +16,7 @@ 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-1.13.4-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) 	|
+| [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) 	|
 
   <!-- badges: end -->
 

diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ 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-1.13.4-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)   |
+| [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)   |
 
 <!-- badges: end -->