debug/build.R

In Sun-lab/SMASH: Subclone Multiplicity Allocation and Somatic Heterogeneity

# Steps to create/check/install package from directory

rm(list = ls())
git_dir = sprintf("%s/../..",getwd()); git_dir
pack = "SMASH"
pack_dir = file.path(git_dir,pack)
if( !file.exists(pack_dir) ) q("no")

chk_pack = tryCatch(find.package(pack),
	error = function(ee){NULL}); chk_pack
if( !is.null(chk_pack) ){
	remove.packages(pack)
	q("no")
}

req_packs = c("usethis","rmarkdown",
	"Rcpp","RcppArmadillo","devtools")
for(tmp_pack in req_packs){
	# tmp_pack = req_packs[8]; tmp_pack
	
	chk_pack2 = tryCatch(find.package(tmp_pack),
		error = function(ee){NULL})
	chk_pack2

	if( !is.null(chk_pack2) ){
		suppressPackageStartupMessages(library(tmp_pack,
			character.only = TRUE))
		next
	}
	
	if( tmp_pack == "Rtools" ){
		
		source(file.path(pack_dir,"R/inst_Rtools.R"))
		cat("Rtools is installed!\n")
		
	} else {
		bb = tryCatch(install.packages(tmp_pack),
			error = function(ee){NA})
		if( !is.null(bb) && is.na(bb) ) 
			stop(sprintf("Error with %s",tmp_pack))
		
	}
	
}

Sys.setenv('_R_CHECK_SYSTEM_CLOCK_' = 0)

compileAttributes(pkgdir = pack_dir)
document(pkg = pack_dir)
use_gpl3_license()
check_pandoc = pandoc_available(); check_pandoc
vign_dir = file.path(pack_dir,"vignettes")
chk_vign = length(list.files(vign_dir,pattern = "Rmd")) > 0
override_vign = !FALSE
make_vign = check_pandoc && chk_vign && override_vign; make_vign

# Check: takes some time
perf_chk = TRUE
if( perf_chk ){
	chk = tryCatch(check(pkg = pack_dir,
		manual = TRUE,cran = TRUE,
		error_on = "note",
		vignettes = make_vign),
		error = function(ee){NULL},
		warning = function(ww){NULL})
} else {
	chk = TRUE
}
chk

# Install
if( !is.null(chk) ){
	chk = tryCatch(install(pack_dir,
		build_vignettes = make_vign,
		upgrade = FALSE),
		error = function(ee){NULL},
		warning = function(ww){NULL})
}

# Build
if( !is.null(chk) ){
	desk_dir = sprintf("%s/../",git_dir)
	devtools::build(pkg = pack_dir,path = desk_dir)
}


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