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Fix scheduled #59

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merged 6 commits into from
Oct 14, 2024
Merged

Fix scheduled #59

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8b10f38
update
pawelru Oct 9, 2024
97fd048
vbump testthat; add utils prefix to avoid R CMD NOTE
pawelru Oct 9, 2024
427d5d6
Apply suggestions from code review
pawelru Oct 10, 2024
95b92a8
use released pkgcache; add rmarkdown to vignettebuilder
pawelru Oct 11, 2024
fc3de91
use MultiAssayExperiment instead of SummarizedExperiment
pawelru Oct 14, 2024
d53d77c
rewrite test
pawelru Oct 14, 2024
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1 change: 1 addition & 0 deletions .Rbuildignore
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Expand Up @@ -21,3 +21,4 @@ images
^.revdeprefs\.yaml$
^revdep$
^\.covrignore$
^inst/training_202307$
17 changes: 9 additions & 8 deletions .github/workflows/scheduled.yaml
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Expand Up @@ -48,14 +48,15 @@ jobs:
uses: insightsengineering/r.pkg.template/.github/workflows/branch-cleanup.yaml@main
secrets:
REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
revdepcheck:
if: >
github.event_name == 'schedule' || (
github.event_name == 'workflow_dispatch' &&
inputs.chosen-workflow == 'revdepcheck'
)
name: revdepcheck ↩️
uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main
# disable until the first release
# revdepcheck:
# if: >
# github.event_name == 'schedule' || (
# github.event_name == 'workflow_dispatch' &&
# inputs.chosen-workflow == 'revdepcheck'
# )
# name: revdepcheck ↩️
# uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main
rhub:
if: >
github.event_name == 'schedule' || (
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11 changes: 5 additions & 6 deletions DESCRIPTION
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Expand Up @@ -17,9 +17,9 @@ Depends:
Imports:
cli (>= 3.6.0),
desc (>= 1.2),
gh,
gh (>= 1.1.0),
jsonlite,
pkgcache (>= 2.2.2.9000),
pkgcache (>= 2.2.3),
pkgdepends (>= 0.5.0),
rcmdcheck,
remotes (>= 2.2.0),
Expand All @@ -31,9 +31,7 @@ Suggests:
knitr (>= 1.42),
pingr,
rmarkdown (>= 2.23),
testthat (>= 3.0.4)
Remotes:
r-lib/pkgcache
testthat (>= 3.1.9)
Config/Needs/verdepcheck:
r-lib/cli,
r-lib/desc,
Expand All @@ -48,7 +46,8 @@ Config/Needs/verdepcheck:
r-lib/pingr,
r-lib/testthat
VignetteBuilder:
knitr
knitr,
rmarkdown
Encoding: UTF-8
Language: en-US
LazyData: true
Expand Down
8 changes: 4 additions & 4 deletions R/get_ref.R
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Expand Up @@ -527,7 +527,7 @@ get_release_date.remote_ref <- function(remote_ref) {
#' verdepcheck:::get_release_data("MultiAssayExperiment")
get_release_data <- function(package) {
cran_archive <- pkgcache::cran_archive_list(packages = package)[, c("package", "version", "mtime")]
cran_current <- head(
cran_current <- utils::head(
pkgcache::meta_cache_list(packages = package)[, c("type", "package", "version", "published")],
1
)
Expand Down Expand Up @@ -613,11 +613,11 @@ get_avail_date.remote_ref_cran <- function(remote_ref, start = get_release_date(
ppm_url <- get_ppm_snapshot_by_date(date)
date <- `if`(
grepl("/latest$", ppm_url),
tail(pkgcache::ppm_snapshots(), 1)$date,
utils::tail(pkgcache::ppm_snapshots(), 1)$date,
unname(as.Date(sub(".*/", "", ppm_url)))
)
if (remote_ref$atleast != "") {
data <- available.packages(
data <- utils::available.packages(
repos = ppm_url,
filters = list(
function(db) {
Expand All @@ -638,7 +638,7 @@ get_avail_date.remote_ref_cran <- function(remote_ref, start = get_release_date(
)
)
} else {
data <- available.packages(
data <- utils::available.packages(
repos = ppm_url,
filters = list(function(db) db[db[, "Package"] == remote_ref$package, ])
)
Expand Down
6 changes: 3 additions & 3 deletions R/utils.R
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Expand Up @@ -33,11 +33,11 @@ get_ppm_snapshot_by_date <- function(date = NA) {
if (is.na(date)) {
return(pkgcache::repo_resolve("PPM@latest"))
}
if (date >= tail(pkgcache::ppm_snapshots(), 1)$date) {
if (date >= utils::tail(pkgcache::ppm_snapshots(), 1)$date) {
return(pkgcache::repo_resolve("PPM@latest"))
}
if (date <= head(pkgcache::ppm_snapshots(), 1)$date) {
return(pkgcache::repo_resolve(sprintf("PPM@%s", head(pkgcache::ppm_snapshots(), 1)$date)))
if (date <= utils::head(pkgcache::ppm_snapshots(), 1)$date) {
return(pkgcache::repo_resolve(sprintf("PPM@%s", utils::head(pkgcache::ppm_snapshots(), 1)$date)))
}
tryCatch(
pkgcache::repo_resolve(sprintf("PPM@%s", as.character(as.Date(date) + 1))),
Expand Down
2 changes: 1 addition & 1 deletion tests/testthat/helper.R
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Expand Up @@ -69,7 +69,7 @@ test_proposal_common <- function(x,
# CRAN
if (is.null(pkg_gh_str) && is.null(pkg_ver_target)) {
pkg_ver_target <- package_version(
available.packages(
utils::available.packages(
repos = pkgcache::default_cran_mirror(),
filters = list(
add = TRUE, function(x) x[x[, "Package"] == pkg_name, ]
Expand Down
38 changes: 28 additions & 10 deletions tests/testthat/test-deps_installation_proposal.R
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Expand Up @@ -288,20 +288,26 @@ test_that("new_min_cohort_deps_installation_proposal correctly handles Bioc pack
skip_if_offline()
skip_if_empty_gh_token()

d_std_path <- local_description(list(SummarizedExperiment = "Import"))
d_std_path <- local_description(
list(MultiAssayExperiment = "Import"),
need_verdepcheck = c("bioc::MultiAssayExperiment")
)

x <- new_min_cohort_deps_installation_proposal(d_std_path)

withr::defer(unlink(x$get_config()$library))

test_proposal_common_bioc(x, "SummarizedExperiment")
test_proposal_common_bioc(x, "MultiAssayExperiment")
})

test_that("new_min_isolated_deps_installation_proposal correctly handles Bioc package", {
skip_if_offline()
skip_if_empty_gh_token()

d_std_path <- local_description(list(SummarizedExperiment = "Import"))
d_std_path <- local_description(
list(MultiAssayExperiment = "Import"),
need_verdepcheck = c("bioc::MultiAssayExperiment")
)

x <- new_min_isolated_deps_installation_proposal(d_std_path)

Expand All @@ -310,42 +316,51 @@ test_that("new_min_isolated_deps_installation_proposal correctly handles Bioc pa
# https://github.com/r-lib/pkgdepends/issues/365
withr::with_options(
opts_partial_match_old,
test_proposal_common_bioc(x, "SummarizedExperiment")
test_proposal_common_bioc(x, "MultiAssayExperiment")
)
})

test_that("new_release_deps_installation_proposal correctly handles Bioc package", {
skip_if_offline()
skip_if_empty_gh_token()

d_std_path <- local_description(list(SummarizedExperiment = "Import"))
d_std_path <- local_description(
list(MultiAssayExperiment = "Import"),
need_verdepcheck = c("bioc::MultiAssayExperiment")
)

x <- new_release_deps_installation_proposal(d_std_path)

withr::defer(unlink(x$get_config()$library))

test_proposal_common_bioc(x, "SummarizedExperiment")
test_proposal_common_bioc(x, "MultiAssayExperiment")
})

test_that("new_max_deps_installation_proposal correctly handles Bioc package", {
skip_if_offline()
skip_if_empty_gh_token()

d_std_path <- local_description(list(SummarizedExperiment = "Import"))
d_std_path <- local_description(
list(MultiAssayExperiment = "Import"),
need_verdepcheck = c("bioc::MultiAssayExperiment")
)

x <- new_max_deps_installation_proposal(d_std_path)

withr::defer(unlink(x$get_config()$library))

test_proposal_common_bioc(x, "SummarizedExperiment")
test_proposal_common_bioc(x, "MultiAssayExperiment")
})

# ################################################################

test_that("indirect dependencies in the config field - ignore on default", {
skip_if_offline()

d_std_path <- local_description(list(dplyr = "Import"), need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang"))
d_std_path <- local_description(
list(dplyr = "Import"),
need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang")
)

x <- new_max_deps_installation_proposal(d_std_path)

Expand All @@ -358,7 +373,10 @@ test_that("indirect dependencies in the config field - ignore on default", {
test_that("indirect dependencies in the config field - include on match with `extra_deps`", {
skip_if_offline()

d_std_path <- local_description(list(dplyr = "Import"), need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang"))
d_std_path <- local_description(
list(dplyr = "Import"),
need_verdepcheck = c("tidyverse/dplyr", "r-lib/rlang")
)

x <- new_max_deps_installation_proposal(d_std_path, extra_deps = "rlang")

Expand Down
4 changes: 3 additions & 1 deletion tests/testthat/test-get_ref.R
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Expand Up @@ -68,7 +68,9 @@ test_that("get_release_date with any class other than remote_ref.{github,cran,st
test_that("get_release_data returns date for Bioconductor", {
skip_if_offline()

expect_false(any(is.na(get_release_data("SummarizedExperiment")$mtime)))
result <- get_release_data("MultiAssayExperiment")$mtime
expect_length(result, 1)
expect_s3_class(result, "POSIXct")
})

test_that("get_ref_release returns a CRAN remote_reference if package exists", {
Expand Down
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