Add R package basics

Author: bschilder

.Rbuildignore

@@ -0,0 +1,17 @@
+.*\.Rproj$
+^\.Rproj\.user$
+^README.Rmd
+^\.github$
+^doc$
+^Meta$
+^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+Dockerfile
+^LICENSE
+^action.yml$
+
+node_modules$
+package-lock\.json$
+package\.json$

.Rhistory

@@ -3,3 +3,4 @@ biocthis::use_bioc_description()
 biocthis::use_bioc_description("test")
 biocthis::use_bioc_description("testytest")
 ?remotes::install_cran()
+devtools::build()

.gitignore

@@ -1,3 +1,15 @@
+# R project files
+*.Rproj
+.Rproj.user
+.Ruserdata 
+# History files
+.Rhistory
+.Rapp.history
+# Session Data files
+.RData
+# User-specific files
+.Ruserdata
+# .DS_Store
 # find . -name .DS_Store -print0 | xargs -0 git rm -f --ignore-unmatch
 .DS_Store
 ./.DS_Store
@@ -7,4 +19,25 @@
 ./**/**/**/**/.DS_Store
 ./**/**/**/**/**/.DS_Store
 ./**/**/**/**/**/**/.DS_Store
-.Rproj.user
+# Example code in package build process
+*-Ex.R
+# Output files from R CMD build
+/*.tar.gz
+# Output files from R CMD check
+/*.Rcheck/
+# RStudio files
+.Rproj.user/
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+vignettes/*.R
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+# R Environment Variables
+.Renviron 

DESCRIPTION

@@ -0,0 +1,32 @@
+Package: rworkflows
+Type: Package
+Title: packageTitle
+Version: 0.99.0
+Authors@R: c( 
+     person(given = "yourGivenName",
+           family = "yourFamilyName",
+           role = c("cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "yourOrcidId"))
+    )
+Description: packageDescription.
+URL: https://github.com/neurogenomics/r_workflows
+BugReports: https://github.com/neurogenomics/r_workflows/issues
+Encoding: UTF-8
+Depends: R (>= 4.2)
+biocViews:
+    Genetics, FunctionalGenomics, SystemsBiology
+Suggests:
+    markdown,
+    rmarkdown,
+    magick,
+    remotes,
+    knitr,
+    BiocStyle,
+    covr,
+    testthat (>= 3.0.0),
+    badger
+RoxygenNote: 7.2.1.9000
+VignetteBuilder: knitr
+License: GPL-3
+Config/testthat/edition: 3

NAMESPACE

@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+

R/message_parallel.R

@@ -0,0 +1,8 @@
+#' Message parallel
+#' 
+#' Send messages to console even from within parallel processes
+#' @return Null
+#' @keywords internal
+message_parallel <- function(...) {
+    system(sprintf('echo "%s"', paste0(..., collapse = "")))
+}

R/messager.R

@@ -0,0 +1,21 @@
+#' Print messages 
+#' 
+#' Conditionally print messages.
+#'  Allows developers to easily control verbosity of functions, 
+#'  and meet Bioconductor requirements that dictate the message 
+#'  must first be stored to a variable before passing to \link[base]{message}. 
+#' 
+#' @param v Whether to print messages or not.
+#' @param parallel Whether to enable message print when wrapped 
+#' in parallelised functions.
+#' 
+#' @return Null 
+#' @keywords internal 
+messager <- function(..., v = TRUE, parallel = FALSE) {
+    if(parallel){
+        if(v) try({message_parallel(...)})
+    } else {
+        msg <- paste(...)
+        if (v) try({message(msg)})
+    }
+}

man/message_parallel.Rd

@@ -11,3 +11,7 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source