From 559fd8974baa3142b20f080a40e0f383b25e4ec6 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 May 2026 19:12:00 +0200 Subject: [PATCH 1/9] Remove anndataR arg from readSpatialData --- vignettes/SpatialData.plot.Rmd | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd index 099e080..9eab0d0 100644 --- a/vignettes/SpatialData.plot.Rmd +++ b/vignettes/SpatialData.plot.Rmd @@ -50,7 +50,7 @@ are represented as `r BiocStyle::Biocpkg("SingleCellExperiment")` as tables. ```{r read-blobs} x <- file.path("extdata", "blobs.zarr") x <- system.file(x, package="SpatialData") -(x <- readSpatialData(x, anndataR=TRUE)) +(x <- readSpatialData(x)) ``` # Visualization @@ -169,7 +169,7 @@ Such labels could be morphological regions annotated by pathologists. ```{r merfish-read} dir.create(td <- tempfile()) pa <- get_demo_SDdata("merfish") -(x <- readSpatialData(pa, anndataR=TRUE)) +(x <- readSpatialData(pa)) ``` There are only `r length(SpatialData::shape(x, "cells"))` cells, but @@ -210,7 +210,7 @@ Mouse intestine, 1GB; 4 image resolutions and 3 shapes at 2, 8, and 16 $\mu$m. ```{r visiumhd-read, eval=FALSE} dir.create(td <- tempfile()) pa <- MouseIntestineVisHD(target=td) -(x <- readSpatialData(pa, images=4, shapes=3, anndataR=TRUE)) +(x <- readSpatialData(pa, images=4, shapes=3)) ``` ```{r visiumhd-plot, eval=FALSE} @@ -229,7 +229,7 @@ dir.create(td <- tempfile()) pa <- SpatialData.data:::.unzip_spd_demo( zipname="mibitof.zip", dest=td, source="biocOSN") -(x <- readSpatialData(pa, anndataR=TRUE)) +(x <- readSpatialData(pa)) ``` ```{r mibitof-plot, fig.width=10, fig.height=3} @@ -249,7 +249,7 @@ dir.create(td <- tempfile()) pa <- SpatialData.data:::.unzip_spd_demo( zipname="mcmicro_io.zip", dest=td, source="biocOSN") -(x <- readSpatialData(pa, anndataR=FALSE)) +(x <- readSpatialData(pa)) ``` Getting channel names for the image: @@ -278,7 +278,7 @@ dir.create(td <- tempfile()) pa <- SpatialData.data:::.unzip_spd_demo( zipname="steinbock_io.zip", dest=td, source="biocOSN") -x <- readSpatialData(pa, anndataR=TRUE) +x <- readSpatialData(pa) ``` ### channels From fc3190445d87916d8af5f157bf1250c86f6a0c3f Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 May 2026 21:01:54 +0200 Subject: [PATCH 2/9] Fix name matching multiple arguments --- vignettes/SpatialData.plot.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/SpatialData.plot.Rmd b/vignettes/SpatialData.plot.Rmd index 9eab0d0..60ae178 100644 --- a/vignettes/SpatialData.plot.Rmd +++ b/vignettes/SpatialData.plot.Rmd @@ -185,7 +185,7 @@ q <- p[sample(n, 1e3)] plotSpatialData() + plotImage(x, c="white") + new_scale_color() + - plotPoint(x, i="1k", c="cell_type", s=0.2) + + plotPoint(x, i="1k", c="cell_type", size=0.2) + new_scale_color() + plotShape(x, i="anatomical") + scale_color_manual(values=hcl.colors(6, "Spectral")) From b316a273b11e456fb1bfb7a5092cd92112f80a9e Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 May 2026 21:25:57 +0200 Subject: [PATCH 3/9] Fix missing import in tests --- tests/testthat/test-plotShape.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-plotShape.R b/tests/testthat/test-plotShape.R index 350159a..d392227 100644 --- a/tests/testthat/test-plotShape.R +++ b/tests/testthat/test-plotShape.R @@ -16,7 +16,7 @@ test_that("plotShape(),circles", { df <- st_coordinates(st_as_sf(data(y))) geom <- layer_data(q, 1)$geometry expect_s3_class(geom, "sfc_POLYGON") - geom <- st_centroid(geom) + geom <- sf::st_centroid(geom) fd <- st_coordinates(geom) expect_equivalent(as.matrix(df), as.matrix(fd)) # size From 02336452eeb0e6c40af7aebb260f0f10568d7d75 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 May 2026 21:27:37 +0200 Subject: [PATCH 4/9] Test standard workflow --- .github/workflows/R-CMD-check.yaml | 49 +++++ .github/workflows/check-bioc.yml | 340 ----------------------------- 2 files changed, 49 insertions(+), 340 deletions(-) create mode 100644 .github/workflows/R-CMD-check.yaml delete mode 100644 .github/workflows/check-bioc.yml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..b770f6f --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,49 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + pull_request: + +name: R-CMD-check.yaml + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v6 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml deleted file mode 100644 index 91cae76..0000000 --- a/.github/workflows/check-bioc.yml +++ /dev/null @@ -1,340 +0,0 @@ -## Read more about GitHub actions the features of this GitHub Actions workflow -## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action -## -## For more details, check the biocthis developer notes vignette at -## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html -## -## You can add this workflow to other packages using: -## > biocthis::use_bioc_github_action() -## -## Using GitHub Actions exposes you to many details about how R packages are -## compiled and installed in several operating system.s -### If you need help, please follow the steps listed at -## https://github.com/r-lib/actions#where-to-find-help -## -## If you found an issue specific to biocthis's GHA workflow, please report it -## with the information that will make it easier for others to help you. -## Thank you! - -## Acronyms: -## * GHA: GitHub Action -## * OS: operating system - -on: - push: - pull_request: - -name: R-CMD-check-bioc - -## These environment variables control whether to run GHA code later on that is -## specific to testthat, covr, and pkgdown. -## -## If you need to clear the cache of packages, update the number inside -## cache-version as discussed at https://github.com/r-lib/actions/issues/86. -## Note that you can always run a GHA test without the cache by using the word -## "/nocache" in the commit message. -env: - has_testthat: 'true' - run_covr: 'false' - run_pkgdown: 'false' - has_RUnit: 'false' - cache-version: 'cache-v1' - run_docker: 'false' - -jobs: - build-check: - runs-on: ${{ matrix.config.os }} - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - container: ${{ matrix.config.cont }} - ## Environment variables unique to this job. - - strategy: - fail-fast: false - matrix: - config: - - { os: ubuntu-latest, r: '4.5', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } - - { os: ubuntu-latest, r: '4.6', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } - - { os: macOS-latest, r: 'devel', bioc: 'devel'} - - { os: windows-latest, r: 'devel', bioc: 'devel'} - ## Check https://github.com/r-lib/actions/tree/master/examples - ## for examples using the http-user-agent - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - NOT_CRAN: true - TZ: UTC - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - ## Set the R library to the directory matching the - ## R packages cache step further below when running on Docker (Linux). - - name: Set R Library home on Linux - if: runner.os == 'Linux' - run: | - mkdir /__w/_temp/Library - echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile - - ## Most of these steps are the same as the ones in - ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml - ## If they update their steps, we will also need to update ours. - - name: Checkout Repository - uses: actions/checkout@v3 - - ## R is already included in the Bioconductor docker images - - name: Setup R from r-lib - if: runner.os != 'Linux' - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} - - ## pandoc is already included in the Bioconductor docker images - - name: Setup pandoc from r-lib - if: runner.os != 'Linux' - uses: r-lib/actions/setup-pandoc@v2 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - shell: Rscript {0} - - - name: Restore R package cache - if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" - uses: actions/cache@v3 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5- - - - name: Cache R packages on Linux - if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " - uses: actions/cache@v3 - with: - path: /home/runner/work/_temp/Library - key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5- - - # - name: Install Linux system dependencies - # if: runner.os == 'Linux' - # run: | - # sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))') - # echo $sysreqs - # sudo -s eval "$sysreqs" - - - name: Install macOS system dependencies - if: matrix.config.os == 'macOS-latest' - run: | - ## Enable installing XML from source if needed - brew install libxml2 - echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV - - ## ## Required to install magick as noted at - ## ## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 - ## brew install imagemagick@6 - - ## For textshaping, required by ragg, and required by pkgdown - brew install harfbuzz fribidi - - ## For installing usethis's dependency gert - brew install libgit2 - - ## Required for tcltk - brew install xquartz --cask - - - name: Install Windows system dependencies - if: runner.os == 'Windows' - run: | - ## Edit below if you have any Windows system dependencies - shell: Rscript {0} - - - name: Install BiocManager - run: | - message(paste('****', Sys.time(), 'installing BiocManager ****')) - remotes::install_cran("BiocManager") - shell: Rscript {0} - - - name: Set BiocVersion - run: | - BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) - shell: Rscript {0} - - - name: Install dependencies pass 1 - run: | - ## Try installing the package dependencies in steps. First the local - ## dependencies, then any remaining dependencies to avoid the - ## issues described at - ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html - ## https://github.com/r-lib/remotes/issues/296 - ## Ideally, all dependencies should get installed in the first pass. - - ## For running the checks - message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) - install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) - - ## Pass #1 at installing dependencies - message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) - remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) - continue-on-error: true - shell: Rscript {0} - - - name: Install dependencies pass 2 - run: | - ## Pass #2 at installing dependencies - message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) - remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force = TRUE) - shell: Rscript {0} - - - name: Install BiocGenerics - if: env.has_RUnit == 'true' - run: | - ## Install BiocGenerics - BiocManager::install("BiocGenerics") - shell: Rscript {0} - - - name: Install covr - if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' - run: | - remotes::install_cran("covr") - shell: Rscript {0} - - - name: Install pkgdown - if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' - run: | - remotes::install_cran("pkgdown") - shell: Rscript {0} - - - name: Session info - run: | - options(width = 100) - pkgs <- installed.packages()[, "Package"] - sessioninfo::session_info(pkgs, include_base = TRUE) - shell: Rscript {0} - - - name: Run CMD check - env: - _R_CHECK_CRAN_INCOMING_: false - DISPLAY: 99.0 - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck( - args = c("--no-manual", "--no-vignettes", "--timings"), - build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), - error_on = "error", - check_dir = "check" - ) - shell: Rscript {0} - - ## Might need an to add this to the if: && runner.os == 'Linux' - - name: Reveal testthat details - if: env.has_testthat == 'true' - run: find . -name testthat.Rout -exec cat '{}' ';' - - - name: Run RUnit tests - if: env.has_RUnit == 'true' - run: | - BiocGenerics:::testPackage() - shell: Rscript {0} - - - name: Run BiocCheck - env: - DISPLAY: 99.0 - run: | - BiocCheck::BiocCheck( - dir('check', 'tar.gz$', full.names = TRUE), - `quit-with-status` = TRUE, - `no-check-R-ver` = TRUE, - `no-check-bioc-help` = TRUE, - `no-check-remotes` = TRUE - ) - shell: Rscript {0} - - - name: Test coverage - if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' - run: | - covr::codecov(coverage = covr::package_coverage(type = "all")) - shell: Rscript {0} - - - name: Install package - if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' - run: R CMD INSTALL . - - - name: Build pkgdown site - if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' - run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) - shell: Rscript {0} - ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) - ## at least one locally before this will work. This creates the gh-pages - ## branch (erasing anything you haven't version controlled!) and - ## makes the git history recognizable by pkgdown. - - - name: Install deploy dependencies - if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' - run: | - apt-get update && apt-get -y install rsync - - - name: Deploy pkgdown site to GitHub pages 🚀 - if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' - uses: JamesIves/github-pages-deploy-action@releases/v4 - with: - clean: false - branch: gh-pages - folder: docs - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@master - with: - name: ${{ runner.os }}-biocversion-devel-r-4.5-results - path: check - - - ## Code adapted from - ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92 - docker-build-and-push: - runs-on: ubuntu-latest - needs: build-check - steps: - - name: Checkout Repository - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" - uses: actions/checkout@v3 - - - name: Register repo name - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" - id: reg_repo_name - run: | - echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV - - - name: Set up QEMU - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" - uses: docker/setup-qemu-action@v2 - - - name: Set up Docker Buildx - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" - uses: docker/setup-buildx-action@v2 - - - name: Login to Docker Hub - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" - uses: docker/login-action@v2 - with: - username: ${{ secrets.DOCKERHUB_USERNAME }} - password: ${{ secrets.DOCKERHUB_TOKEN }} - ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub - ## account, not your actual dockerhub account password. You can get it - ## from https://hub.docker.com/settings/security. - ## Check https://github.com/docker/build-push-action/tree/v4.0.0 - ## for more details. - ## Alternatively, try checking - ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html. - - - name: Build and Push Docker - if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()" - uses: docker/build-push-action@v4 - with: - context: . - push: true - tags: > - ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, - ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel From edce02a4f70151559e2eefcaa165d41654ef2a22 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 May 2026 21:35:35 +0200 Subject: [PATCH 5/9] Restrict run on push to specific branches --- .github/workflows/R-CMD-check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index b770f6f..19919be 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -2,6 +2,7 @@ # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: + branches: [main, devel] pull_request: name: R-CMD-check.yaml From 0c4bae3a896852b478936539644bf5fa285bd911 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Mon, 4 May 2026 21:35:50 +0200 Subject: [PATCH 6/9] Remove run on oldrel --- .github/workflows/R-CMD-check.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 19919be..0182129 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -23,7 +23,6 @@ jobs: - {os: windows-latest, r: 'release'} - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - {os: ubuntu-latest, r: 'release'} - - {os: ubuntu-latest, r: 'oldrel-1'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} From 995e01ff7db905d823870916b59282a8d26b7564 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Tue, 5 May 2026 07:40:03 +0200 Subject: [PATCH 7/9] Remove anndataR arg from examples --- R/data.R | 2 +- R/plotFrame.R | 2 +- R/plotLabel.R | 2 +- man/blobs.Rd | 2 +- man/plotFrame.Rd | 2 +- man/plotLabel.Rd | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/data.R b/R/data.R index 2183eeb..9c6daa6 100644 --- a/R/data.R +++ b/R/data.R @@ -9,5 +9,5 @@ #' @examples #' x <- file.path("extdata", "blobs.zarr") #' x <- system.file(x, package="SpatialData") -#' (x <- readSpatialData(x, anndataR=FALSE)) +#' (x <- readSpatialData(x)) NULL \ No newline at end of file diff --git a/R/plotFrame.R b/R/plotFrame.R index 81fd8de..95df194 100644 --- a/R/plotFrame.R +++ b/R/plotFrame.R @@ -11,7 +11,7 @@ #' @examples #' x <- file.path("extdata", "blobs.zarr") #' x <- system.file(x, package="SpatialData") -#' x <- readSpatialData(x, anndataR=TRUE) +#' x <- readSpatialData(x) #' #' # shapes #' p <- plotSpatialData() diff --git a/R/plotLabel.R b/R/plotLabel.R index a3aedc7..4718a46 100644 --- a/R/plotLabel.R +++ b/R/plotLabel.R @@ -20,7 +20,7 @@ #' @examples #' x <- file.path("extdata", "blobs.zarr") #' x <- system.file(x, package="SpatialData") -#' x <- readSpatialData(x, anndataR=TRUE) +#' x <- readSpatialData(x) #' #' i <- "blobs_labels" #' p <- plotSpatialData() diff --git a/man/blobs.Rd b/man/blobs.Rd index 06f7664..1aad279 100644 --- a/man/blobs.Rd +++ b/man/blobs.Rd @@ -9,5 +9,5 @@ data were retrieved on Nov. 11th, 2024, from \href{https://github.com/scverse/sp \examples{ x <- file.path("extdata", "blobs.zarr") x <- system.file(x, package="SpatialData") -(x <- readSpatialData(x, anndataR=FALSE)) +(x <- readSpatialData(x)) } diff --git a/man/plotFrame.Rd b/man/plotFrame.Rd index 2be54e3..5d1835a 100644 --- a/man/plotFrame.Rd +++ b/man/plotFrame.Rd @@ -27,7 +27,7 @@ specifies which \code{assay} data to use (see \code{\link{valTable}}). \examples{ x <- file.path("extdata", "blobs.zarr") x <- system.file(x, package="SpatialData") -x <- readSpatialData(x, anndataR=TRUE) +x <- readSpatialData(x) # shapes p <- plotSpatialData() diff --git a/man/plotLabel.Rd b/man/plotLabel.Rd index 3ba6f09..02bc7cf 100644 --- a/man/plotLabel.Rd +++ b/man/plotLabel.Rd @@ -48,7 +48,7 @@ specifies which \code{assay} data to use (see \code{\link{valTable}}).} \examples{ x <- file.path("extdata", "blobs.zarr") x <- system.file(x, package="SpatialData") -x <- readSpatialData(x, anndataR=TRUE) +x <- readSpatialData(x) i <- "blobs_labels" p <- plotSpatialData() From bb984ef4c1d33194fb9a256954000e3f691d02de Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Tue, 5 May 2026 07:43:06 +0200 Subject: [PATCH 8/9] Prefix filter() call --- R/plotFrame.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/plotFrame.R b/R/plotFrame.R index 95df194..8bc4948 100644 --- a/R/plotFrame.R +++ b/R/plotFrame.R @@ -43,7 +43,7 @@ NULL if (is(y, "PointFrame")) { if (!is.null(key)) { fk <- feature_key(y) - y@data <- filter(data(y), .data[[fk]] %in% key) + y@data <- dplyr::filter(data(y), .data[[fk]] %in% key) } } if (is.finite(n)) { From 5a3babd7b85c32228cfb75aecd22fef6e05e5e13 Mon Sep 17 00:00:00 2001 From: Hugo Gruson Date: Tue, 5 May 2026 07:43:53 +0200 Subject: [PATCH 9/9] Error on R CMD check error only for now --- .github/workflows/R-CMD-check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0182129..13c2168 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -47,3 +47,4 @@ jobs: with: upload-snapshots: true build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' + error-on: '"error"'