other/update_r_package.r

In darcyj/specificity: Calculate Environmental or Host Phylogenetic Specificity

#!/usr/bin/env Rscript


# to do before running this script:
# 1. increase version number in ../DESCRIPTION
# 2. describe changes in changelog.txt

# RUN FROM MAIN PACKAGE FOLDER, i.e. "specificity"
packwd <- getwd()
if(!file.exists("DESCRIPTION")){
	stop("Wrong directory!")
}

# add files to .Rbuildignore (files ignored during package building)
write("^specificity\\.Rproj$",     file=".Rbuildignore",append=FALSE)
write("^\\.Rproj\\.user$",         file=".Rbuildignore",append=TRUE)
write("^vignette$",                file=".Rbuildignore",append=TRUE)
write("^\\.travis.yml$",           file=".Rbuildignore",append=TRUE)
write("^other$",                   file=".Rbuildignore",append=TRUE)
write("specificity.pdf",           file=".Rbuildignore",append=TRUE)


library(devtools)
library(roxygen2)
library(Rcpp)
library(testthat)

usethis::use_package("ape")
usethis::use_package("parallel")
usethis::use_package("Rcpp")

if(packageVersion("Rcpp") < "1.0.0"){
  stop("Rcpp needs to be updated to 1.0.0 or above.")
}


# this looks for Rcpp::export in cpp files
Rcpp::compileAttributes("./")

document()

# ADD C++ namespace stuff to NAMESPACE file, because document() above OVERWRITES it:
# originally made via Rcpp::compileAttributes("./") above
lines2add <- readLines("other/additional_namespace/rcpp_namespace.txt")
write(lines2add, file="NAMESPACE", append=TRUE)

# add stuff to namespace that's not in BASE R but sure is in VANILLA R
# generated by (in shell):
#   cd ../
#   R CMD build specificity
#   R CMD check specificity_XYZ.tar.gz 
# look at specificity.Rcheck/00check.log
lines2add <- readLines("other/additional_namespace/vanillaR_namespace.txt")
write(lines2add, file="NAMESPACE", append=TRUE)



# install
install("../specificity")

# test
setwd("tests/")
### doing tests can take a minute! ###
capture.output(test_check("specificity"), file="../other/test_results.txt", split=TRUE)
setwd(packwd)

# document packageVersions used for this test and build:
pkgvers_fp <- "other/package_versions.txt"
write("Pagage versions used in this build and tests:", file=pkgvers_fp)
writepkgvers <- function(pkgname, fp=pkgvers_fp){
	write(paste0(pkgname, "=", packageVersion(pkgname)), file=fp, append=T)
}
writepkgvers("devtools")
writepkgvers("roxygen2")
writepkgvers("Rcpp")
writepkgvers("testthat")
writepkgvers("ape")
writepkgvers("parallel")
writepkgvers("fields")      # NOTE: only suggested now!
writepkgvers("specificity")

# make pdf manual
# texinfo required: sudo apt-get install texinfo
pack <- "specificity"
path <- find.package(pack)
system("rm specificity.pdf")
# commmand below requires: texlive-fonts-extra, texinfo (install both with apt)
system(paste(shQuote(file.path(R.home("bin"), "R")), "CMD", "Rd2pdf", shQuote(path)))