Skip to content

Add missing Suggests referenced in tests to DESCRIPTION #1531

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
EmilHvitfeldt merged 10 commits into from
Mar 31, 2026
Merged

Add missing Suggests referenced in tests to DESCRIPTION #1531

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
7ef1579
Cite mixOmics in DESCRIPTION
MichaelChirico Dec 6, 2025
3d52f71
Add fastICA, remove mixOmics
MichaelChirico Dec 6, 2025
34a1374
dimRed
MichaelChirico Dec 6, 2025
e58d1eb
Merged origin/main into MichaelChirico-patch-2
EmilHvitfeldt Dec 9, 2025
a7b77d7
Merged origin/main into MichaelChirico-patch-2
EmilHvitfeldt Mar 30, 2026
8dbcc7f
add mixOmics to description
EmilHvitfeldt Mar 31, 2026
33434fb
usethis::use_tidy_description()
EmilHvitfeldt Mar 31, 2026
d6fc322
skip install igraph on old GHA
EmilHvitfeldt Mar 31, 2026
e127ce4
new way of handling old version of igraph on GHA
EmilHvitfeldt Mar 31, 2026
5ef987b
add igraph ignore-before-r back in
EmilHvitfeldt Mar 31, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion .github/workflows/R-CMD-check.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ jobs:

- uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
extra-packages: any::rcmdcheck, igraph=?ignore-before-r=4.2.0
needs: check

- uses: r-lib/actions/check-r-package@v2
Expand Down
5 changes: 4 additions & 1 deletion DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,10 @@ Suggests:
covr,
ddalpha,
dials (>= 1.2.0),
dimRed,
fastICA,
ggplot2,
igraph,
igraph (>= 2.1.1),
kernlab,
knitr,
methods,
Expand All @@ -69,6 +71,7 @@ VignetteBuilder:
knitr
RdMacros:
lifecycle
biocViews: mixOmics
Config/Needs/website: tidyverse/tidytemplate, rmarkdown
Config/testthat/edition: 3
Config/usethis/last-upkeep: 2025-04-23
Expand Down
24 changes: 12 additions & 12 deletions tests/testthat/test-isomap.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ scrub_timestamp <- function(x) {
test_that("correct Isomap values", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand All @@ -74,7 +74,7 @@ test_that("correct Isomap values", {
test_that("No ISOmap", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand All @@ -97,7 +97,7 @@ test_that("No ISOmap", {
test_that("ISOmap fails gracefully", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand All @@ -115,7 +115,7 @@ test_that("ISOmap fails gracefully", {

test_that("ISOmap suppresses only messages, not errors", {
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand Down Expand Up @@ -157,7 +157,7 @@ test_that("ISOmap suppresses only messages, not errors", {
test_that("check_name() is used", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")
dat <- dplyr::as_tibble(dat1)
Expand Down Expand Up @@ -191,7 +191,7 @@ test_that("tunable", {
test_that("check_options() is used", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand All @@ -208,7 +208,7 @@ test_that("check_options() is used", {
test_that("bake method errors when needed non-standard role columns are missing", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand Down Expand Up @@ -262,7 +262,7 @@ test_that("empty selection tidy method works", {
test_that("keep_original_cols works", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand Down Expand Up @@ -308,7 +308,7 @@ test_that("keep_original_cols works", {
test_that("keep_original_cols - can prep recipes with it missing", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand All @@ -330,7 +330,7 @@ test_that("keep_original_cols - can prep recipes with it missing", {
test_that("printing", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand Down Expand Up @@ -359,7 +359,7 @@ test_that("tunable is setup to work with extract_parameter_set_dials", {
test_that("bad args", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand All @@ -380,7 +380,7 @@ test_that("bad args", {
test_that("0 and 1 rows data work in bake method", {
skip_on_cran()
skip_if_not_installed("RSpectra")
skip_if_not_installed("igraph")
skip_if_not_installed("igraph", minimum_version = "2.1.1")
skip_if_not_installed("RANN")
skip_if_not_installed("dimRed")

Expand Down
Loading