In brouwern/compbio4all: Datasets and helpful functions for learning bioinformatics and computational biology

knitr::opts_chunk$set(
  collapse = TRUE,
  eval  = F,
  comment = "#>"
)

Introduction

This code is used to build, re-build, and trouble shoot the building of the package, including

1. Building/compiling diffrent components
2. Building the pkgdown website

These are mostly commands that can be launched from within RStudio via the GUI, except pkgdown::build_site()

devtools functions

library(devtools)

Clean vignettes

"This uses a fairly rudimentary algorithm where any files in ‘inst/doc’ with a name that exists in ‘vignettes’ are removed."

devtools::clean_vignettes() 

Build vignettes

"Builds package vignettes using the same algorithm that R CMD build does"

devtools::build_vignettes()

Build documentation

document()

devtools::document(roclets=c('rd', 'collate', 'namespace'))

Load all

devtools::load_all(".")

Check

devtools::check()

check_failures

pckgdown functions

Build package down website

Single function to build whole site: "This will generate a docs/ directory. The home page will be generated from your package’s README.md, and a function reference will be generated from the documentation in the man/ directory."

pkgdown::build_site()

Build piece by piece

pkgdown::clean_site (pkg = ".")

-- Initializing site

pkgdown::init_site(pkg = ".")

Building home

pkgdown::build_home(pkg = ".")

Building function reference

pkgdown::build_reference(pkg = ".")

Build vignettes

pkgdown::build_articles(pkg = ".")

pkgdown::build_news()

Explore dependencies

report1 <- CreatePackageReport(pkg_name = "FACavian")

Build pdf manual

https://stackoverflow.com/questions/16986422/r-create-reference-manual-with-r-cmd-check R CMD Rd2pdf mypackage

https://stackoverflow.com/questions/30607496/making-an-r-package-pdf-manual-using-devtools

pack <- "FACavian"
path <- find.package(pack)
system(paste(shQuote(file.path(R.home("bin"), "R")),
    "CMD", "Rd2pdf", shQuote(path)))

remove manual

file.remove("FACavian.pdf")

check(cleanup = FALSE,manual = TRUE,path = getwd())

Keep logs files (?)

options(keep.source.pkgs = TRUE)
devtools::check()

Rcmd.exe

"Clean and rebuild" ==> Rcmd.exe INSTALL --preclean --no-multiarch --with-keep.source mammalsmilk

"Install restart" ==> Rcmd.exe INSTALL --no-multiarch --with-keep.source mammalsmilk

devtools::check(env_vars = )

devtools::check()

See 'C:/Users/lisanjie/Documents/1_R/git/git-aviary/FACavian.Rcheck/00install.out' for details. Information on the location(s) of code generating the 'Note's can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to 'yes'.

brouwern/compbio4all documentation built on Dec. 19, 2021, 11:47 a.m.