Update .github files (these files were already up to date), README, p…

…kgdown config, ran dev/04_update.R

DESCRIPTION

@@ -76,5 +76,5 @@ URL: https://github.com/leekgroup/recount
 BugReports: https://support.bioconductor.org/t/recount/
 biocViews: Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing,
     Software, DataImport, ImmunoOncology
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)

R/add_metadata.R

@@ -61,8 +61,9 @@
 #' ## Obtain all the recount_brain_v2 metadata if you want to
 #' ## explore the metadata manually
 #' recount_brain_v2 <- add_metadata(source = "recount_brain_v2")
-add_metadata <- function(rse, source = "recount_brain_v2", is_tcga = FALSE,
-    verbose = TRUE) {
+add_metadata <- function(
+        rse, source = "recount_brain_v2", is_tcga = FALSE,
+        verbose = TRUE) {
     stopifnot(length(source) == 1)
 
     ## For a NOTE in R CMD check

R/add_predictions.R

@@ -65,21 +65,22 @@
 #'
 #' ## Download all the latest predictions
 #' PredictedPhenotypes <- add_predictions()
-add_predictions <- function(rse, is_tcga = FALSE, version = "latest",
-    verbose = TRUE) {
-
+add_predictions <- function(
+        rse, is_tcga = FALSE, version = "latest",
+        verbose = TRUE) {
     ## For a NOTE in R CMD check
     PredictedPhenotypes <- NULL
     if (version == "latest") {
-        version <- tryCatch(suppressWarnings(readLines(
-            "https://raw.githubusercontent.com/leekgroup/recount-website/master/predictions/latestVersion.txt"
-        ))[1],
-        error = function(e) {
-            print(e)
-            v <- "0.0.05"
-            message(paste(Sys.time(), "Failed to check the latest version, using version", v))
-            return(v)
-        }
+        version <- tryCatch(
+            suppressWarnings(readLines(
+                "https://raw.githubusercontent.com/leekgroup/recount-website/master/predictions/latestVersion.txt"
+            ))[1],
+            error = function(e) {
+                print(e)
+                v <- "0.0.05"
+                message(paste(Sys.time(), "Failed to check the latest version, using version", v))
+                return(v)
+            }
         )
     }
 

R/coverage_matrix.R

@@ -68,9 +68,10 @@
 #'     ## One row per region
 #'     identical(length(regions), nrow(rse))
 #' }
-coverage_matrix <- function(project, chr, regions, chunksize = 1000,
-    bpparam = NULL, outdir = NULL, chrlen = NULL, verbose = TRUE,
-    verboseLoad = verbose, scale = TRUE, round = FALSE, ...) {
+coverage_matrix <- function(
+        project, chr, regions, chunksize = 1000,
+        bpparam = NULL, outdir = NULL, chrlen = NULL, verbose = TRUE,
+        verboseLoad = verbose, scale = TRUE, round = FALSE, ...) {
     ## Check inputs
     stopifnot(is.character(project) & length(project) == 1)
     stopifnot(is.character(chr) & length(chr) == 1)

R/download_retry.R

@@ -26,8 +26,9 @@
 #' download_retry(
 #'     recount_url$url[which(recount_url$file_name == "files_info.tsv")[1]]
 #' )
-download_retry <- function(url, destfile = basename(url), mode = "wb",
-    N.TRIES = 3L, ...) {
+download_retry <- function(
+        url, destfile = basename(url), mode = "wb",
+        N.TRIES = 3L, ...) {
     ## Based on http://bioconductor.org/developers/how-to/web-query/
     ## and downloader::download()
 

R/download_study.R

@@ -99,8 +99,9 @@
 #' expect_equivalent(rse_gene, rse_gene_SRP009615)
 #' }
 #'
-download_study <- function(project, type = "rse-gene", outdir = project,
-    download = TRUE, version = 2, ...) {
+download_study <- function(
+        project, type = "rse-gene", outdir = project,
+        download = TRUE, version = 2, ...) {
     ## Check inputs
     stopifnot(is.character(project) & length(project) == 1)
     stopifnot(version %in% c(1, 2))

R/expressed_regions.R

@@ -54,8 +54,9 @@
 #' single <- unlist(GRangesList(regs))
 #' }
 #'
-expressed_regions <- function(project, chr, cutoff, outdir = NULL,
-    maxClusterGap = 300L, chrlen = NULL, verbose = TRUE, ...) {
+expressed_regions <- function(
+        project, chr, cutoff, outdir = NULL,
+        maxClusterGap = 300L, chrlen = NULL, verbose = TRUE, ...) {
     ## Check inputs
     stopifnot(is.character(project) & length(project) == 1)
     stopifnot(is.character(chr) & length(chr) == 1)

R/geo_info.R

@@ -25,8 +25,9 @@
 #'
 #' @examples
 #' geo_info("GSM836270")
-geo_info <- function(geoid, verbose = FALSE, sleep = 1 / 2, getGPL = FALSE,
-    destdir = tempdir(), ...) {
+geo_info <- function(
+        geoid, verbose = FALSE, sleep = 1 / 2, getGPL = FALSE,
+        destdir = tempdir(), ...) {
     if (is.na(geoid)) {
         return(NULL)
     }

R/scale_counts.R

@@ -67,9 +67,9 @@
 #' identical(rse_gene, rse_gene_SRP009615)
 #' }
 #'
-scale_counts <- function(rse, by = "auc", targetSize = 4e7, L = 100,
-    factor_only = FALSE, round = TRUE) {
-
+scale_counts <- function(
+        rse, by = "auc", targetSize = 4e7, L = 100,
+        factor_only = FALSE, round = TRUE) {
     ## Check inputs
     stopifnot(is(rse, "RangedSummarizedExperiment"))
     stopifnot(length(targetSize) == 1)

README.Rmd

@@ -16,17 +16,18 @@ knitr::opts_chunk$set(
 # recount <img src="man/figures/logo.png" align="right" width="400px" />
 
 <!-- badges: start -->
-[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/recount.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/recount)
 [![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/recount.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount)
-[![Codecov test coverage](https://codecov.io/gh/leekgroup/recount/branch/master/graph/badge.svg)](https://codecov.io/gh/leekgroup/recount?branch=master)
-[![R build status](https://github.com/leekgroup/recount/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/leekgroup/recount/actions)
-[![GitHub issues](https://img.shields.io/github/issues/leekgroup/recount)](https://github.com/leekgroup/recount/issues)
 [![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/recount.svg)](http://bioconductor.org/packages/stats/bioc/recount/)
 [![Bioc support](https://bioconductor.org/shields/posts/recount.svg)](https://support.bioconductor.org/tag/recount)
 [![Bioc history](https://bioconductor.org/shields/years-in-bioc/recount.svg)](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
 [![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/recount.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount/)
 [![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/recount.svg)](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
+[![Codecov test coverage](https://codecov.io/gh/leekgroup/recount/branch/devel/graph/badge.svg)](https://codecov.io/gh/leekgroup/recount?branch=devel)
+[![R build status](https://github.com/leekgroup/recount/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/leekgroup/recount/actions)
+[![GitHub issues](https://img.shields.io/github/issues/leekgroup/recount)](https://github.com/leekgroup/recount/issues)
+[![GitHub pulls](https://img.shields.io/github/issues-pr/leekgroup/recount)](https://github.com/leekgroup/recount/pulls)
 <!-- badges: end -->
 
 Explore and download data from the recount project available at the [recount2 website](https://jhubiostatistics.shinyapps.io/recount/). Using the `recount` package you can download _RangedSummarizedExperiment_ objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The _RangedSummarizedExperiment_ objects can be used by different packages for performing differential expression analysis. Using [derfinder](http://bioconductor.org/packages/derfinder) you can perform annotation-agnostic differential expression analyses with the data from the recount project. 

README.md

@@ -6,17 +6,11 @@
 <!-- badges: start -->
 
 [![Lifecycle:
-stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable)
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Bioc release
 status](http://www.bioconductor.org/shields/build/release/bioc/recount.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/recount)
 [![Bioc devel
 status](http://www.bioconductor.org/shields/build/devel/bioc/recount.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/recount)
-[![Codecov test
-coverage](https://codecov.io/gh/leekgroup/recount/branch/master/graph/badge.svg)](https://codecov.io/gh/leekgroup/recount?branch=master)
-[![R build
-status](https://github.com/leekgroup/recount/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/leekgroup/recount/actions)
-[![GitHub
-issues](https://img.shields.io/github/issues/leekgroup/recount)](https://github.com/leekgroup/recount/issues)
 [![Bioc downloads
 rank](https://bioconductor.org/shields/downloads/release/recount.svg)](http://bioconductor.org/packages/stats/bioc/recount/)
 [![Bioc
@@ -27,6 +21,14 @@ history](https://bioconductor.org/shields/years-in-bioc/recount.svg)](https://bi
 commit](https://bioconductor.org/shields/lastcommit/devel/bioc/recount.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/recount/)
 [![Bioc
 dependencies](https://bioconductor.org/shields/dependencies/release/recount.svg)](https://bioconductor.org/packages/release/bioc/html/recount.html#since)
+[![Codecov test
+coverage](https://codecov.io/gh/leekgroup/recount/branch/devel/graph/badge.svg)](https://codecov.io/gh/leekgroup/recount?branch=devel)
+[![R build
+status](https://github.com/leekgroup/recount/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/leekgroup/recount/actions)
+[![GitHub
+issues](https://img.shields.io/github/issues/leekgroup/recount)](https://github.com/leekgroup/recount/issues)
+[![GitHub
+pulls](https://img.shields.io/github/issues-pr/leekgroup/recount)](https://github.com/leekgroup/recount/pulls)
 <!-- badges: end -->
 
 Explore and download data from the recount project available at the
@@ -69,7 +71,6 @@ Please run this yourself to check for any updates on how to cite
 
 ``` r
 print(citation("recount"), bibtex = TRUE)
-#> 
 #> To cite package 'recount' in publications use:
 #> 
 #>   Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD,
@@ -128,7 +129,7 @@ print(citation("recount"), bibtex = TRUE)
 #>   Jaffe AE, Langmead B, Leek JT (2023). _Explore and download data from
 #>   the recount project_. doi:10.18129/B9.bioc.recount
 #>   <https://doi.org/10.18129/B9.bioc.recount>,
-#>   https://github.com/leekgroup/recount - R package version 1.25.1,
+#>   https://github.com/leekgroup/recount - R package version 1.27.0,
 #>   <http://www.bioconductor.org/packages/recount>.
 #> 
 #> A BibTeX entry for LaTeX users is
@@ -138,7 +139,7 @@ print(citation("recount"), bibtex = TRUE)
 #>     author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek},
 #>     year = {2023},
 #>     url = {http://www.bioconductor.org/packages/recount},
-#>     note = {https://github.com/leekgroup/recount - R package version 1.25.1},
+#>     note = {https://github.com/leekgroup/recount - R package version 1.27.0},
 #>     doi = {10.18129/B9.bioc.recount},
 #>   }
 #> 
@@ -218,7 +219,7 @@ By contributing to this project, you agree to abide by its terms.
   *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized
   to use [Bioconductor’s docker
   containers](https://www.bioconductor.org/help/docker/) and
-  *[BiocCheck](https://bioconductor.org/packages/3.16/BiocCheck)*.
+  *[BiocCheck](https://bioconductor.org/packages/3.17/BiocCheck)*.
 - Code coverage assessment is possible thanks to
   [codecov](https://codecov.io/gh) and
   *[covr](https://CRAN.R-project.org/package=covr)*.
@@ -234,7 +235,7 @@ By contributing to this project, you agree to abide by its terms.
 For more details, check the `dev` directory.
 
 This package was developed using
-*[biocthis](https://bioconductor.org/packages/3.16/biocthis)*.
+*[biocthis](https://bioconductor.org/packages/3.17/biocthis)*.
 
 ## Teams involved
 

dev/02_git_github_setup.R

@@ -34,7 +34,7 @@ rstudioapi::restartSession()
 ## Now run use_github()
 usethis::use_github()
 ## Follow any prompts, such as running on the terminal:
-## git push --set-upstream origin master
+## git push --set-upstream origin devel
 
 
 ## Move to the next step: setting up your package core files

dev/03_core_files.R

@@ -9,7 +9,7 @@ rstudioapi::navigateToFile(usethis::proj_path("dev", "02_git_github_setup.R"))
 ## Check http://r-pkgs.had.co.nz/description.html for details
 ## as well as http://bioconductor.org/developers/package-guidelines/#description
 
-## Check https://github.com/lcolladotor/biocthis/blob/master/DESCRIPTION
+## Check https://github.com/lcolladotor/biocthis/blob/devel/DESCRIPTION
 ## for an example.
 
 ## You'll at least want to edit the version to 0.99.0 (or lower) since that's

tests/testthat/test-data.R

@@ -155,7 +155,6 @@ if (.Platform$OS.type != "windows") {
                 )
             )
         })
-
     }
 }
 
@@ -212,7 +211,6 @@ if (!is.null(snap)) {
         expect_equal(snap_gtex$type == "GTEx:I", TRUE)
         expect_equal(snap_tcga$type == "TCGA:I", TRUE)
     })
-
 } else {
     warning("Snaptron_query() is not working! See https://github.com/ChristopherWilks/snaptron/issues/17 for more details.")
 }