build.r

In chenhaotian/Bayesian-Bricks: Bayesian Methods and Graphical Model Structures for Statistical Modeling

library(roxygen2)
library(devtools)
library(usethis)

VERSION <- "0.1.3.9000"
VERSION <- "0.1.4"
VERSION <- "0.1.5"

## remove previous build
system("rm -r man")
system("rm -r vignettes Meta doc")
system("rm NAMESPACE DESCRIPTION .Rbuildignore")

## create skeleton files
create_package("../bbricks",rstudio = FALSE)

## generate man/*.Rd files and NAMESPACE
devtools::document()

## add to .Rbuildignore to ignore non-package files
## "NEWS.md" is supported by CRAN, no need to exclude
usethis::use_build_ignore(c("^LICENSE\\.md$","^README\\.md$","^\\.travis\\.yml$","^build\\.r$","^\\.#build\\.r$","^README\\.raw\\.md$","^notes_pictures$","^cran-comments\\.md$","^index\\.html$","^CRAN-RELEASE$","^.*~$","^.*#$","^inst/WORDLIST$"),escape = FALSE)
## usethis::use_build_ignore(c("README.md",".travis.yml","build.r",".#build.r","README.raw.md","cran-comments.md"))

## Edit DESCRIPTIONN
## Version Reference:
##    http://r-pkgs.had.co.nz/release.html
##    Version format:  major.minor.patch.dev
## add to Collate: when there's new files added
Description <- paste0("Type: Package
Package: bbricks
Title: Bayesian Methods and Graphical Model Structures for Statistical Modeling
Version: ",VERSION,"
Authors@R: 
    person(given = \"Haotian\",
           family = \"Chen\",
           role = c(\"aut\", \"cre\"),
           email = \"chenhaotian.jtt@gmail.com\",
           comment = structure(\"0000-0001-9751-2093\", .Names = \"ORCID\"))
Description: A set of frequently used Bayesian parametric and nonparametric model structures, as well as a set of tools for common analytical tasks. Structures include linear Gaussian systems, Gaussian and Normal-Inverse-Wishart conjugate structure, Gaussian and Normal-Inverse-Gamma conjugate structure, Categorical and Dirichlet conjugate structure, Dirichlet Process on positive integers, Dirichlet Process in general, Hierarchical Dirichlet Process ... Tasks include updating posteriors, sampling from posteriors, calculating marginal likelihood, calculating posterior predictive densities, sampling from posterior predictive distributions, calculating \"Maximum A Posteriori\" (MAP) estimates ... See <https://chenhaotian.github.io/Bayesian-Bricks/> to get started.
License: What license it uses
URL: https://github.com/chenhaotian/Bayesian-Bricks
BugReports: https://github.com/chenhaotian/Bayesian-Bricks/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: ",packageVersion("roxygen2"),"
Collate: 
    'Bayesian_Bricks.r'
    'Categorical_Inference.r'
    'Gaussian_Inference.r'
    'Dirichlet_Process.r'
    'MCMC.r'
    'Gamma_Inference.r'
    'bbricks-package.R'
    'testData.r'
")
write(Description,file = "DESCRIPTION")



## Add license, run this will update the corresponding line in DESCRIPTION automatically
use_mit_license(name="Haotian Chen")

## Config travis CI
travis <- "language: r
r:
  - oldrel
  - release
  - devel
r_packages:
  - stats
"
write(travis,file = ".travis.yml")


## add vignette
## reference: https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-RSP_vignettes.html
use_vignette("bbricks-getting-started")

readme <- readLines("README.raw.md")
pics <- gsub("\\).*$","",gsub("^.*\\(","",grep("\\./notes_pictures/",readme,value = TRUE)))
if(length(pics)>0){
    if(length(dir("vignettes/notes_pictures/"))==0)
        system("mkdir vignettes/notes_pictures")
    system(paste("cp",paste(pics,collapse = " "),"vignettes/notes_pictures/"))
}
picsNotInline <- grep("^\\!.*\\./notes_pictures/.*\\)$",readme)
readme[picsNotInline] <- paste0(readme[picsNotInline],"{width=100%}")

readme <- gsub("```R","```{r,eval=FALSE}",readme)

readme <- readme[-1]                    #remove the additional title

writeLines(c("---
title: \"bbricks-getting-started\"
output: rmarkdown::html_vignette
vignette: >
  %\\VignetteIndexEntry{bbricks: Getting Started}
  %\\VignetteEngine{knitr::rmarkdown}
  %\\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = \"#>\"
)
```
",readme),"vignettes/bbricks-getting-started.Rmd")

system("rm .#* *~")
build_vignettes()

## copy the vignette to github page:
system("cp doc/bbricks-getting-started.html index.html")
indexPage <- readLines("index.html")
headidx <- grep("^<head>",indexPage)+1L
## addd google search verify code to the html file
indexPage <- c(indexPage[1L:headidx],
               "<meta name=\"google-site-verification\" content=\"IemNx-2nFSn77OM1b1z4TL3ZqkPboC1yCsfHrCTJfRs\" />",
               indexPage[(headidx+1L):length(indexPage)])
writeLines(indexPage,"index.html")

## make sure github language detector won't detect html
writeLines("index.html linguist-generated
",".gitattributes")

## very important step, must make sure there's no  warnings and errors
## remove stupic emacs tmp file before check()
system("rm .#* *~")
devtools::check()

## somehow the S3 methods are not exported... export them mannually
## have to be after check(), otherwise it will be overwritten
namespace <- readLines("./NAMESPACE")
S3classes <- grep("^S3method\\(",namespace,value = TRUE)
S3classes <- unique(gsub(",.*$","",gsub("S3method\\(","",S3classes)))
funs <- gsub(".rd$","",dir("./man"),ignore.case = TRUE)
funs <- na.omit(sapply(funs,function(f){
    if(any(sapply(S3classes,function(s3){grepl(paste0("^",s3,"\\."),f)}))) f
    else as.character(NA)
},USE.NAMES = FALSE))
funs <- paste0("export(",funs,")")
namespace <- c(namespace,setdiff(funs,namespace)) #don't use union()
writeLines(namespace,"./NAMESPACE")

## spell check
## Remember to put the new ignore words to ./inst/WORDLIST
spell_check(use_wordlist = TRUE)        #ignore the words in file inst/WORDLIST

## check if all Rd files has \value
rdn <- dir("man",full.names = TRUE)
rdf <- sapply(rdn,function(f){
    paste(readLines(f),collapse = " ")
})
idx <- grep("\\value",rdf,invert = TRUE)
if(length(idx)>0) cat(paste(c("\\value tag do not exist in following functions:",rdn[idx]),collapse = "\n"),"\n")

## build the package
## remove stupid emacs tmp file before build()
system("find . -type f -name '*~' -delete")
system("find . -type f -name '*#' -delete")
system("find . -type f -name '#*' -delete")
system("find . -type f -name '.#*' -delete")
devtools::build()

## devtools::release()

install.packages(paste0("../bbricks_",VERSION,".tar.gz")) #different from install()
## install()                                        #different from install.packages()

library(bbricks)

## Very important step!!
system("cd .. && R CMD build bbricks")
system(paste0("R CMD check ../bbricks_",VERSION,".tar.gz"))


remove.packages("bbricks")
## uninstall()
## remove.packages("bbricks")


## check from rhub
check_rhub(interactive=FALSE)

## check from win builder
check_win_devel()

## If you are ready to sumit it to CRAN, run relsease, release will do following things:
## • Confirm that the package passes ‘R CMD check’ on relevant
##    platforms
## • Confirm that important files are up-to-date
## • Build the package
## • Submit the package to CRAN, using comments in
##    "cran-comments.md"
## release_questions <- function() {
##   c("Have you set the correct version number?",
##     "Have you removed the irrelevant code blocks?",
##     "Have you add {width=100%} to each inluded image?",
##     "Have you add all R files to DESCRIPTION?",
##     "Have you removed the unfinished lines from vignette?",
##     "Have you add all the references?",
##     "Have you built README.md from README.raw.md?")
## }
 
## check if any example changed the par setting
system("grep 'par(' ./man/*")

devtools::release()