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Fix non cran2 (#4)
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alternative to:
#3

test those two together:
- insightsengineering/r.pkg.template#255
- #4

This would require additional inputs: `lookup-refs` action parameter. I
think that this is ok since we have to have an information where to find
non-cran dependencies. The Remotes field (if provided) will be used
instead of this.
See:
insightsengineering/teal.goshawk@main...refs/heads/fix_non_cran2
as an example

Tests:
-
https://github.com/insightsengineering/teal.goshawk/actions/workflows/scheduled.yaml?query=branch%3Afix_non_cran2
-
https://github.com/insightsengineering/teal.osprey/actions/workflows/scheduled.yaml?query=branch%3Afix_non_cran2

---------

Signed-off-by: Pawel Rucki <[email protected]>
Co-authored-by: Marcin <[email protected]>
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@pawelru @m7pr
pawelru and m7pr authored Oct 2, 2024
1 parent dd285cd commit c368cd4
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Showing 2 changed files with 113 additions and 76 deletions.
5 changes: 1 addition & 4 deletions action.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,10 +45,7 @@ runs:
export $(tr '\n' ' ' < /tmp/dotenv.env)
}
fi
echo ".libPaths(\" \", include.site = FALSE)" > .Rprofile
export R_LIBS_SITE=" "
export R_LIBS_USER=" "
time Rscript ${GITHUB_ACTION_PATH}/script.R '${{ inputs.repository-path }}' '${{ inputs.number-of-workers }}' '${{ inputs.timeout }}'
Rscript ${GITHUB_ACTION_PATH}/script.R '${{ inputs.repository-path }}' '${{ inputs.number-of-workers }}' '${{ inputs.timeout }}'
shell: bash
env:
GITHUB_PAT: "${{ inputs.github-token }}"
Expand Down
184 changes: 112 additions & 72 deletions script.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,54 @@ if_error <- function(x, y = NULL) {
`%||%` <- function(x, y) {
if (!length(x) || is.null(x)) y else x
}
check_if_pkg_available <- function(pkg, ver = NULL) {
length(
available.packages(
filters = list(
add = TRUE,
function(db) {
if (is.null(ver)) {
db[db[, "Package"] == pkg, ]
} else {
db[db[, "Package"] == pkg & db[, "Version"] == ver, ]
}
}
)
)
) > 0
}
add_to_minicran <- function(x, minicran_path) {
temp_dir <- tempfile()
on.exit(unlink(temp_dir))
dir.create(temp_dir)
# for GH packages we have `pkg_1.2.3.9000_hash.tar.gz` so we need to remove the hash and keep only `pkg_1.2.3.9000.tar.gz`

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file=/github/workspace/script.R,line=33,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 124 characters.
new_file_name <- gsub("(.*?_.*)_.*?(\\..*)", "\\1\\2", basename(x))
file.copy(x, file.path(temp_dir, new_file_name))
miniCRAN::addLocalPackage(gsub("_.*", "", basename(new_file_name)), temp_dir, minicran_path)
invisible(NULL)
}
add_cache_to_minicran <- function(pkg, version, minicran_path) {
i_cache <- pkgcache::pkg_cache_find(package = pkg, version = version, platform = "source")
if (nrow(i_cache) == 0) return(invisible(NULL))
cli::cli_inform(sprintf("Adding %s to miniCRAN...", pkg))
add_to_minicran(i_cache$fullpath[1], minicran_path)
invisible(NULL)
}
install_and_add_to_minicran <- function(ref, minicran_path) {
cli::cli_inform(sprintf("Installing and adding %s to miniCRAN...", ref))
x <- pak::pkg_install(ref, ask = FALSE)
for (i in seq_len(nrow(x))) {
i_package <- x$package[i]
i_version <- x$version[i]
if (check_if_pkg_available(i_package, i_version)) next
add_cache_to_minicran(i_package, i_version, minicran_path)
}
invisible(NULL)
}
is_installed_from_gh <- function(package_name) {
d <- packageDescription(package_name)
(!is.null(d$GithubSHA1)) || identical(d$RemoteType, "github")
}

args <- commandArgs(trailingOnly = TRUE)
setwd(normalizePath(file.path(args[1])))
Expand All @@ -18,9 +66,18 @@ timeout <- as.integer(args[3])

# Install required packages
catnl("Installing required packages...")
install.packages(c(
"pak"
))
if (!requireNamespace("pak", quietly = TRUE)) {
install.packages("pak", quiet = TRUE)
}
if (!requireNamespace("pkgcache", quietly = TRUE)) {
install.packages("pkgcache", quiet = TRUE)
}
options(
repos = c(
PPM = pkgcache::repo_resolve("PPM@latest"),
getOption("repos")
)
)
pak::pkg_install(c(
"cli",
"miniCRAN",
Expand Down Expand Up @@ -61,24 +118,11 @@ cli::cli_bullets(refs)
cli::cli_h1("Initiate pre-requisites")
cli::cli_progress_bar()

## install pkg
# cache pkg and its dependencies
cli::cli_progress_step("Installing the package...")
pkg_name <- read.dcf("DESCRIPTION")[1, "Package"][[1]]
crancache::install_packages(pkg_name, quiet = TRUE)

## revdepcheck
cli::cli_progress_step("Initiating `revdepcheck`...")
revdepcheck::revdep_reset()
unlink("./revdep/", recursive = TRUE)
revdepcheck:::db_disconnect(".")
usethis::use_revdep()
revdepcheck:::db_setup(".")

## miniCRAN
cli::cli_progress_step("Initiating `miniCRAN`...")
minicran_path <- tempfile()
dir.create(minicran_path)
on.exit(unlink(minicran_path, recursive = TRUE))
# added `rlang` as a dummy package as the `pkgs` arg cannot be empty
miniCRAN::makeRepo(pkgs = "rlang", path = minicran_path, type = c("source", .Platform$pkgType))
# add minicran repo path to repos so that revdepcheck can use it
Expand All @@ -88,61 +132,53 @@ options("repos" = c(
getOption("repos")
))

### install pkg - only if not available
pkg_name <- read.dcf("DESCRIPTION")[, "Package"]
if (isFALSE(check_if_pkg_available(pkg_name))) {
cli::cli_progress_step("Adding GH release to miniCRAN...")
# try to get the package reference from the DESCRIPTION file (URL field)
pkg_url <- gsub("\n|/$", "", strsplit(read.dcf("DESCRIPTION")[1, "URL"], ",")[[1]])
pkg_url_gh <- grep("github.com", pkg_url, value = TRUE)
pkg_ref_released <- paste0(gsub(".*github.com/", "", pkg_url_gh), "@*release")
if (length(pkg_ref_released) == 0) {
cli::cli_abort("Unable to automatically determine the package reference for GitHub release.")
return(NULL)
}
install_and_add_to_minicran(pkg_ref_released, minicran_path)
}

### add pkgs from GH to miniCRAN
cli::cli_progress_step("Adding packages from GH to miniCRAN...")
x <- pkgdepends::new_pkg_deps(".")
x$resolve()
pkgs_from_gh <- Filter(is_installed_from_gh, unique(x$get_resolution()$package))
for (pkg in pkgs_from_gh) {
add_cache_to_minicran(pkg, installed.packages()[pkg, "Version"], minicran_path)
}

## revdepcheck
cli::cli_progress_step("Initiating `revdepcheck`...")
revdepcheck::revdep_reset()
unlink("./revdep/", recursive = TRUE)
revdepcheck:::db_disconnect(".")
usethis::use_revdep()
revdepcheck:::db_setup(".")

cli::cli_progress_done()


cli::cli_h1("Add refs to revdepcheck")
# include refs in revdepcheck
## Add revdep to miniCRAN repo so that it can be found by the revdepcheck.
## miniCRAN accepts only prebuilt .tar.gz file and build requires all the dependencies pre-installed.
## This is why we need to install all the deps of revdep (incl. tested package).
## It's important to use `crancache` as much as possible to make use of caching.
## Algorithm:
## for ref in refs:
## - install dependencies using `crancache`
## - install pkg using `pak` - this also gives prebuilt .tar.gz file
## - move .tar.gz file to miniCRAN repo
## - add to revdep todo table
## Add refs revdepcheck and also to miniCRAN so that it can be found from there
cli::cli_progress_bar("Adding refs to revdepcheck", total = length(refs))
for (ref in refs) {
cli::cli_progress_message("Adding {ref}...")

ref_parsed <- pkgdepends::parse_pkg_ref(ref)
ref_pkg <- ref_parsed$package

if (!is(ref_parsed, "remote_ref_standard") && !is(ref_parsed, "remote_ref_cran")) {
cli::cli_progress_message("Installing dependencies of {ref}...")
ref_deps <- pkgdepends::new_pkg_deps(ref, config = list(dependencies = FALSE))
ref_deps$resolve()
ref_deps_df <- ref_deps$get_resolution()[1, "deps"][[1]]
ref_deps_hard <- ref_deps_df[
tolower(ref_deps_df$type) %in% tolower(pkgdepends::pkg_dep_types_hard()) & ref_deps_df$ref != "R",
"package"
]
crancache::install_packages(ref_deps_hard, quiet = TRUE)

cli::cli_progress_message("Installing {ref}...")
ref_install <- pak::pkg_install(ref)
ref_cache <- pkgcache::pkg_cache_find(package = ref_pkg)
ref_targz <- subset(
ref_cache,
(built == 1 | built == TRUE | built == "TRUE") & platform == "source" & version == ref_install$version[1],
fullpath
)[[1]]
# cache might have multiple files for a given package and version
# copy this file to the temp dir and add to miniCRAN from that dir
temp_dir <- tempfile()
dir.create(temp_dir)
file.copy(
ref_targz,
file.path(temp_dir, paste0(sub("(.*?_.*?)_.*", "\\1", basename(ref_targz)), ".tar.gz"))
)
miniCRAN::addLocalPackage(ref_pkg, temp_dir, minicran_path)

cli::cli_inform("Added {ref} to minicran!")
}
install_and_add_to_minicran(ref, minicran_path)

ref_pkg <- pkgdepends::parse_pkg_ref(ref)$package
revdepcheck::revdep_add(packages = ref_pkg)

cli::cli_inform("Added {ref} to revdep todo!")
cli::cli_progress_update()
}
Expand Down Expand Up @@ -182,17 +218,21 @@ catnl(readLines("revdep/cran.md", warn = FALSE))

cli::cli_h2("Check duration...")
# this does not include download and install times
print(
setNames(
do.call(
rbind.data.frame,
lapply(
revdepcheck::revdep_summary(),
function(i) c(i$package, if_error(i$old[[1]]$duration) %||% "?", if_error(i$new$duration) %||% "?")
)
),
c("package", "old", "new")
if (length(revdepcheck::revdep_summary())) {
print(
setNames(
do.call(
rbind.data.frame,
lapply(
revdepcheck::revdep_summary(),
function(i) c(i$package, if_error(i$old[[1]]$duration) %||% "?", if_error(i$new$duration) %||% "?")
)
),
c("package", "old", "new")
)
)
)
} else {
print("(empty)")
}

stopifnot(identical(readLines("revdep/problems.md", warn = FALSE), "*Wow, no problems at all. :)*"))

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