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Fixes: deprecated wrap arg, and passing lib_paths to tools::pkgVignettes #160

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Fixes: deprecated wrap arg, and passing lib_paths to tools::pkgVignettes #160

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4cc42e6
Stop using deprecated `wrap` parameter.
vogr Jun 10, 2021
87edf16
Correctly pass lib_paths from gen_from_package/trace_from_source all the
vogr Aug 12, 2021
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18 changes: 10 additions & 8 deletions R/extract-package-code.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,9 @@
#' @export
#'
# TODO: support commentDontrun, commentDonttest
extract_package_code <- function(pkg, pkg_dir=find.package(pkg),
extract_package_code <- function(pkg,
lib_paths=NULL,
pkg_dir=find.package(pkg),
types=c("examples", "tests", "vignettes", "all"),
output_dir=tempfile(pattern="genthat-extract_package"),
filter=NULL) {
Expand Down Expand Up @@ -32,7 +34,7 @@ extract_package_code <- function(pkg, pkg_dir=find.package(pkg),
output <- file.path(output_dir, type)
stopifnot(dir.exists(output) || dir.create(output, recursive=TRUE))

files <- fun(pkg, pkg_dir, output_dir=output)
files <- fun(pkg, pkg_dir, output_dir=output, lib_paths=lib_paths)

if (!is.null(filter)) {
files <- files[grepl(filter, tools::file_path_sans_ext(files))]
Expand All @@ -44,7 +46,7 @@ extract_package_code <- function(pkg, pkg_dir=find.package(pkg),
}

#' @importFrom tools Rd_db Rd2ex
extract_package_examples <- function(pkg, pkg_dir, output_dir) {
extract_package_examples <- function(pkg, pkg_dir, output_dir, lib_paths=NULL) {
db <- tryCatch({
tools::Rd_db(basename(pkg_dir), lib.loc=dirname(pkg_dir))
}, error=function(e) {
Expand Down Expand Up @@ -82,7 +84,7 @@ extract_package_examples <- function(pkg, pkg_dir, output_dir) {
na.omit(examples)
}

extract_package_tests <- function(pkg, pkg_dir, output_dir) {
extract_package_tests <- function(pkg, pkg_dir, output_dir, lib_paths=NULL) {
test_dir <- file.path(pkg_dir, "tests")

if (!dir.exists(test_dir)) {
Expand All @@ -100,8 +102,8 @@ extract_package_tests <- function(pkg, pkg_dir, output_dir) {
}

#' @importFrom tools pkgVignettes checkVignettes
extract_package_vignettes <- function(pkg, pkg_dir, output_dir) {
vinfo <- tools::pkgVignettes(pkg, source=T)
extract_package_vignettes <- function(pkg, pkg_dir, output_dir, lib_paths=NULL) {
vinfo <- tools::pkgVignettes(pkg, source=T, lib.loc=lib_paths)
if (length(vinfo$docs) == 0) {
return(character())
}
Expand All @@ -111,11 +113,11 @@ extract_package_vignettes <- function(pkg, pkg_dir, output_dir) {
# sources in the R code. It might actually run the vignettes as well.
# That is a pity, but there is no way to tell it not to (the tangle is
# needed to it extracts the R code)
tools::checkVignettes(pkg, pkg_dir, tangle=TRUE, weave=FALSE, workdir="src")
tools::checkVignettes(pkg, pkg_dir, tangle=TRUE, weave=FALSE, workdir="src", lib.loc=lib_paths)
}

# check if there are some sources
vinfo <- tools::pkgVignettes(pkg, source=T)
vinfo <- tools::pkgVignettes(pkg, source=T, lib.loc=lib_paths)
files <- as.character(unlist(vinfo$sources))
if (length(files) == 0) {
return(character())
Expand Down
4 changes: 3 additions & 1 deletion R/genthat.R
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Original file line number Diff line number Diff line change
Expand Up @@ -45,6 +45,7 @@ gen_from_package <- function(pkgs_to_trace, pkgs_to_run=pkgs_to_trace,
filter=NULL,
prune_tests=FALSE,
quiet=TRUE,
lib_paths=NULL,
...) {

if (prune_tests) {
Expand All @@ -70,7 +71,7 @@ gen_from_package <- function(pkgs_to_trace, pkgs_to_run=pkgs_to_trace,
}

working_dir <- tempfile(pattern="genthat-gen_from_package")
files <- lapply(pkgs_to_run, extract_package_code, types=types, output_dir=working_dir, filter=filter)
files <- lapply(pkgs_to_run, extract_package_code, lib_paths=lib_paths, types=types, output_dir=working_dir, filter=filter)
files <- unlist(files)

if (length(files) == 0) {
Expand All @@ -82,6 +83,7 @@ gen_from_package <- function(pkgs_to_trace, pkgs_to_run=pkgs_to_trace,
files_to_run=files,
action=action,
quiet=quiet,
lib_paths=lib_paths,
...
)

Expand Down
2 changes: 1 addition & 1 deletion R/run-generated-tests.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ test_generated_file <- function(test) {
testthat::test_env()
}

testthat::test_file(test, reporter="stop", wrap=FALSE, env=env)
testthat::test_file(test, reporter="stop", env=env)
}

#' @export
Expand Down