packager
is a set of functions I use to create and maintain most of my R
-packages
using a build process such as fakemake
or, GNU make.
It borrows heavily from packages devtools
, usethis
, rcmdcheck
, remotes
and lintr
.
withr
Due to the CRAN policy
of not writing "anywhere else on the
file system apart from the R session's temporary directory",
throughout this vignette I use R's temporary directory, often by using
path <- file.path(tempdir(), "my_path")
followed by
withr::with_dir(path, ...)
or the like.
I do this because this is a vignette and its codes are run on
CRAN.
In real life, we would skip the temporary directory stuff.
To create a new package I use:
path <- file.path(tempdir(), "myFirstPackage") packager::create(path, fakemake = "check")
The package is built, tested, checked and committed into git:
list.files(path, recursive = FALSE) r <- git2r::repository(path) summary(r) git2r::status(r)
We can look at some of the files
(the directory myFirstPackage.Rcheck
might be of interest):
cat(readLines(file.path(path, "log", "spell.Rout")), sep = "\n") tail(readLines(file.path(path, "log", "check.Rout")), sep = "\n")
And we see what`s left to do:
cat(readLines(file.path(path, "TODO.md")), sep = "\n")
We see that the package's DESCRIPTION is filled with default values.
cat(readLines(file.path(path, "DESCRIPTION")), sep = "\n")
We could set the package information on the existing package, but we rather create a new one now. So we get rid of our first package
unlink(path, recursive = TRUE) if ("myFirstPackage" %in% .packages()) detach("package:myFirstPackage", unload = TRUE)
and customize the package creation (but we skip the process of testing, building and checking for the sake of CPU time, we just build the docs):
package_title <- "veryImportantPackage" path <- file.path(tempdir(), package_title) a <- utils::person(given = "Your", family = "Name", email = "some@whe.re", role = c("aut", "cre")) packager::create(path, author_at_r = a, title = package_title, description = "This is very important.", details = "At least to me.", fakemake = "roxygen2")
cat(readLines(file.path(path, "DESCRIPTION")), sep = "\n")
The package's man page is set up accordingly:
pkgload::load_all(path) help(paste0(package_title, "-package"))
pkgload::load_all(path) # insert developement page help_file <- system.file("man", paste0(package_title, "-package.Rd"), package = devtools::as.package(path)$package) captured <- gsub('_\b', '', capture.output(tools:::Rd2txt(help_file) )) cat(captured, sep = "\n")
I use
adc <- utils::person(given = "Andreas Dominik", family = "Cullmann", email = "fvafrcu@mailbox.org", role = c("aut", "cre")) pop <- as.list(getOption("packager")) pop[["whoami"]] <- adc options(packager = pop)
in one of my startup files to set the author information globally.
fakemake
Our brand new package r devtools::as.package(path)[["package"]]
is checked into git already:
r <- git2r::repository(path) summary(r) git2r::status(r)
but we have so far only built the documentation from the roxygen
comments:
list.files(file.path(path, "log"))
So we get a makelist
and look at its targets and aliases:
ml <- packager::get_package_makelist(is_cran = TRUE) cbind(lapply(ml, function(x) x[["target"]]), lapply(ml, function(x) x[["alias"]]))
We choose to build the package:
suppressMessages(withr::with_dir(path, print(fakemake::make("build", ml, verbose = FALSE))))
We note the warning
cat(git2r::diff(r, as_char = TRUE, path = file.path(".Rbuildignore")))
and see that now there are untracked files in our package's log directory and that some files changed.
git2r::status(r) cat(diff(r, as_char = TRUE, path = ".Rbuildignore"))
After inspecting the change, we commit:
withr::with_dir(path, packager::git_add_commit(path = ".", untracked = TRUE, message = "make build")) git2r::status(r)
So now we want the check the package:
suppressMessages(withr::with_dir(path, print(fakemake::make("check", ml, verbose = FALSE))))
We again see new files and changes to old files.
git2r::status(r)
Note that the RUnit
test files are run while checking the tarball, hence we
see output from RUnit
in our log directory.
We assume that we passed the check:
cat(tail(readLines(file.path(path, "log", "check.Rout")), n = 7), sep = "\n") check_log <- file.path(path, "log", "check.Rout") status <- packager::get_check_status(check_log) RUnit::checkEqualsNumeric(status[["status"]][["errors"]], 0)
and commit again
withr::with_dir(path, packager::git_add_commit(path = ".", untracked = TRUE, message = "make check"))
If we choose to rerun the check without touching any files "down the make chain" (i.e. no files that any of our make targets depend on), we see there's nothing to be done:
system.time(withr::with_dir(path, print(fakemake::make("check", ml, verbose = FALSE))))
This is the big difference between running the check via fakemake
with a set of dependencies (set up with packager
) and
running the check (be it using R CMD check
or rcmdcheck::rcmdcheck
or its wrapper devtools::check
) unconditionally: the latter method rebuilds and checks the whole package every time. This is why I wrote packager
and fakemake
.
Now we would like to submit our package to CRAN (which we will not do here, but we want to!) We provide comments to CRAN:
withr::with_dir(path, print(fakemake::make("cran_comments", ml, verbose = FALSE))) cat(readLines(file.path(path, "cran-comments.md")), sep = "\n")
After editing the contents we feel ready to submit:
try(packager::submit(path))
Oops: we need to commit git first:
packager::git_add_commit(path = path, untracked = TRUE, message = "prepare for CRAN") git2r::status(r)
Now we try and fail again, because this vignette is built in batch mode and there's a security query which then fails:
try(packager::submit(path))
Should you run this code interactively, you will be prompted for the security query
(as you might be used from devtools::release()
).
Best you know how to write R extensions and
the CRAN policies.
Anyway, we might want to tag the current commit and commence developing our package:
packager::git_tag(path = path, message = "A Tag") packager::use_dev_version(path = path) desc::desc_get("Version", file = path) cat(readLines(file.path(path, "NEWS.md")), sep = "\n")
This is close to the workflow I have been using for most of my packages,
substituting fakemake
with GNU make whenever possible.
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