rworkflows 1.0.2

neurogenomics · Nov 16, 2023 · eea1f6b · eea1f6b
1 parent b4e0170
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -10,6 +10,8 @@ rworkflows-merged
 ^reports
 ^inst/hex$
 ^hex$
+.*\.pdf$
+^CITATION$
 
 .*\.Rproj$
 ^\.Rproj\.user$

diff --git a/.Rhistory b/.Rhistory
@@ -1,9 +1,3 @@
-library(rworkflows)
-use_vignette_docker(force_new = T)
-use_vignette_docker("neurogenomics",force_new = T)
-library(rworkflows)
-use_vignette_docker("neurogenomics",force_new = T)
-library(rworkflows)
 use_vignette_docker("neurogenomics",force_new = T)
 cont
 library(rworkflows)
@@ -510,3 +504,9 @@ library(rworkflows)
 devtools::build_manual()
 devtools::build_manual(path = 'inst')
 ## Bug fixes
+testthat::test_check()
+testthat::test_check("rworkflows")
+?rstatix::anova_test
+?rstatix::Anova()
+?)
+?rstatix::cor_pmat
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: rworkflows
 Type: Package
 Title: Test, Document, Containerise, and Deploy R Packages
-Version: 1.0.1
+Version: 1.0.2
 Authors@R:
     c(person(given = "Brian",
            family = "Schilder",
@@ -59,7 +59,8 @@ Suggests:
     BiocPkgTools,
     biocViews,
     reticulate,
-    rvest
+    rvest,
+    tinytex
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

diff --git a/NAMESPACE b/NAMESPACE
@@ -6,6 +6,10 @@ export(construct_authors)
 export(construct_conda_yml)
 export(construct_cont)
 export(construct_runners)
+export(dependencies_latex)
+export(dependencies_linux)
+export(dependencies_macos)
+export(dependencies_windows)
 export(dt_to_desc)
 export(fill_description)
 export(get_description)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,26 @@
+# rworkflows 1.0.2
+
+## New features
+
+* *action.yml* 
+  - Condense steps
+  - Use new `rworkflows` funcs to specific system and latex deps
+* *Dockerfile*
+  - Use new `rworkflows` funcs to specific system and latex deps
+* New functions:
+  - `dependencies_linux`
+  - `dependencies_macos`
+  - `dependencies_windows`
+  - `dependencies_latex`
+* README: update and condense.
+
+## Bug fixes
+
+* Get rid of CRAN NOTE by reducing package size:
+  - Remove unused *inst* files.
+  - Change vignettes to use `rmarkdown::render` instead of `BiocStyle::html_document`.
+  - Add to *.Rbuildignore*: .`*\.pdf$`, `^CITATION$`
+
 # rworkflows 1.0.1
 
 ## New features
@@ -9,7 +32,7 @@
 - *action.yml* 
   - `repository: ${{ github.repository }}` --> `repository: ${{ env.packageName }}`
   - Add `env: GITHUB_TOKEN: ${{ inputs.GITHUB_TOKEN }}` to any checking steps 
-  (allows piggyback to download data from Relesases) 
+  (allows piggyback to download data from Releases) 
 
 # rworkflows 1.0.0
 

diff --git a/R/dependencies_latex.R b/R/dependencies_latex.R
@@ -0,0 +1,48 @@
+#' Latex dependencies
+#' 
+#' Install extra latex package dependencies.
+#' @param install Install the packages with \link[tinytex]{tlmgr_install}
+#'  (\code{TRUE}). Otherwise, return a character vector of the packages to
+#'  install.
+#' @inheritParams dependencies_linux
+#' @inheritDotParams tinytex::tlmgr_install
+#' @returns A character vector of extra latex packages.
+#' 
+#' @export
+#' @examples
+#' dependencies_latex(install=FALSE)
+dependencies_latex <- function(extra=c("bera",
+                                       "nowidow",
+                                       "parnotes",
+                                       "marginfix",
+                                       "etoolbox",
+                                       "titlesec",
+                                       "sectsty",
+                                       "framed",
+                                       "enumitem",
+                                       "parskip",
+                                       "soul",
+                                       "placeins",
+                                       "footmisc",
+                                       "changepage",
+                                       "xstring",
+                                       "caption",
+                                       "mathtools",
+                                       "fancyhdr",
+                                       "preprint",
+                                       "ragged2e",
+                                       "pdfcrop",
+                                       "titling",
+                                       "silence",
+                                       "everysel"),
+                               install=TRUE,
+                               ...){
+  requireNamespace("tinytex")
+
+  if(isTRUE(install)){
+    tinytex::tlmgr_install(pkgs = unique(extra),
+                           ...)
+  } else {
+    extra
+  }
+}
diff --git a/R/dependencies_linux.R b/R/dependencies_linux.R
@@ -0,0 +1,38 @@
+#' Linux dependencies
+#' 
+#' Construct a command to install system dependencies for the 
+#' Linux OS environment.
+#' Includes all dependencies listed by \link[remotes]{system_requirements}, 
+#' in addition to user-specified dependencies via \code{extra}.
+#' @param prefix Prefix to prepend to the command.
+#' @param extra Additional dependencies to install.
+#' @param verbose Print messages.
+#' @inheritParams remotes::system_requirements
+#' @inheritDotParams remotes::system_requirements
+#' @returns Command to install system dependencies.
+#' 
+#' @export
+#' @examples
+#' dependencies_linux(package="rworkflows")
+dependencies_linux <- function(os = "ubuntu", 
+                               os_release = "20.04",
+                               extra=c("qpdf",
+                                       "rsync"),
+                               prefix=paste("apt-get update -y",
+                                            "apt-get install -y",
+                                            sep=" && "),
+                               verbose = TRUE,
+                                ...
+                                ){ 
+  # devoptera::args2vars(linux_dependencies)
+
+  deps <- gsub("apt-get install -y ", "", 
+                    remotes::system_requirements(os = os,
+                                                 os_release = os_release,
+                                                 ...)
+               )
+  deps <- unique(c(deps,extra))
+  cmd <- paste(prefix,paste(deps,collapse = " "))
+  messager(cmd,v=verbose)
+  cat(cmd)
+}
diff --git a/R/dependencies_macos.R b/R/dependencies_macos.R
@@ -0,0 +1,53 @@
+#' MacOS dependencies
+#' 
+#' Construct a command to install system dependencies for the 
+#' Mac OS environment.
+#' 
+#'### --- Justifications for each package --- ####
+#'## libxml2 ###
+#' Enable installing XML from source if needed
+#'## imagemagick@6 ###
+#' Required to install magick as noted at
+#' https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
+#'## harfbuzz fribidi ###
+#' For textshaping, required by ragg, and required by pkgdown
+#'## libgit2 ###
+#' For installing usethis's dependency gert
+#'## xquartz --cask ###
+#' Required for tcltk
+#'## libxfont ###
+#' Required for some ggplot2 functions
+#'## texlive ###
+#' Required for rendering Sweave files (even with r-lib/actions/setup-tinytex)
+#' @param cask Additional dependencies to install via cask.
+#' @inheritParams dependencies_linux
+#' @returns Command to install system dependencies.
+#' 
+#' @export
+#' @examples
+#' dependencies_macos()
+dependencies_macos <- function(extra=c("libxml2",
+                                       "harfbuzz",
+                                       "fribidi",
+                                       "libgit2",
+                                       "texlive",
+                                       "imagemagick@6",
+                                       "rsync"),
+                               cask = c("xquartz"),
+                               prefix="brew install",
+                               verbose=TRUE){ 
+  # devoptera::args2vars(macos_dependencies)  
+
+  ### Install normally ###
+  cmd <- paste(prefix,paste(extra,collapse=" "))
+  ### Install via cask ###
+  if(length(cask) > 0){
+    cmd <- paste(
+      cmd,
+      paste(prefix,paste(cask,collapse=" "),"--cask"),
+      sep=" && "
+    ) 
+  } 
+  messager(cmd,v=verbose)
+  cat(cmd)
+}
diff --git a/R/dependencies_windows.R b/R/dependencies_windows.R
@@ -0,0 +1,19 @@
+#' Windows dependencies
+#' 
+#' Construct a command to install system dependencies for the 
+#' Windows environment. 
+#' @inheritParams dependencies_linux
+#' @returns Command to install system dependencies.
+#' 
+#' @export
+#' @examples
+#' dependencies_windows()
+dependencies_windows <- function(extra=c("curl"),
+                                 prefix="npm install",
+                                 verbose=TRUE){ 
+  # devoptera::args2vars(windows_dependencies)  
+
+  cmd <- paste(prefix,paste(extra,collapse=" ")) 
+  messager(cmd,v=verbose)
+  cat(cmd)
+}
diff --git a/R/use_vignette_docker.R b/R/use_vignette_docker.R
@@ -54,7 +54,7 @@ use_vignette_docker <- function(package = names(get_description()),
                                                "vignettes",
                                                "docker.Rmd"),
                                 output=list(
-                                  "BiocStyle::html_document"= list(
+                                  "rmarkdown::html_document"= list(
                                     "md_extensions"="-autolink_bare_uris"
                                     )
                                   ),

diff --git a/R/use_vignette_getstarted.R b/R/use_vignette_getstarted.R
@@ -19,7 +19,7 @@ use_vignette_getstarted <- function(package = names(get_description()),
                                     path=file.path(save_dir,
                                                    "vignettes",
                                                    paste0(package,".Rmd")),
-                                    output="BiocStyle::html_document",
+                                    output="rmarkdown::html_document",
                                     force_new=FALSE,
                                     show=FALSE,
                                     verbose=TRUE){