diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 891b236..a905549 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -28,12 +28,12 @@ jobs: cont: ghcr.io/bioconductor/bioconductor_docker:devel rspm: ~ - os: macOS-latest - bioc: release + bioc: devel r: auto cont: ~ rspm: ~ - os: windows-latest - bioc: release + bioc: devel r: auto cont: ~ rspm: ~ diff --git a/DESCRIPTION b/DESCRIPTION index 2a3ba1c..b1d801c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -24,6 +24,7 @@ biocViews: Depends: R (>= 4.3.0) Imports: + SummarizedExperiment, SpatialExperiment, tidySpatialExperiment, tidySummarizedExperiment, diff --git a/vignettes/Session_1_sequencing_assays.Rmd b/vignettes/Session_1_sequencing_assays.Rmd index 9fd02df..00025e5 100644 --- a/vignettes/Session_1_sequencing_assays.Rmd +++ b/vignettes/Session_1_sequencing_assays.Rmd @@ -195,9 +195,10 @@ Maynard and Torres et al., doi: [10.1038/s41593-020-00787-0](https://www.ncbi.nl library(spatialLIBD) library(ExperimentHub) -# To avoid error for SPE loading -# https://support.bioconductor.org/p/9161859/#9161863 -setClassUnion("ExpData", c("matrix", "SpatialExperiment")) +# # To avoid error for SPE loading +# # https://support.bioconductor.org/p/9161859/#9161863 +# library(methods) +# setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) spatial_data <- ExperimentHub::ExperimentHub() |> diff --git a/vignettes/Session_2_Tidy_spatial_analyses.Rmd b/vignettes/Session_2_Tidy_spatial_analyses.Rmd index 533120e..cba4229 100644 --- a/vignettes/Session_2_Tidy_spatial_analyses.Rmd +++ b/vignettes/Session_2_Tidy_spatial_analyses.Rmd @@ -57,25 +57,6 @@ style="width:100%; height:600px;" frameborder="0"> -### Installation - -let's make sure we get the latest packages available on github - -```{r, eval=FALSE} - -# In May 2025, the following packages should be installed from github repositories, to use the latest features. In case you have them pre installed, run the following command -BiocManager::install(c("lmweber/ggspavis", - "stemangiola/tidySummarizedExperiment", - "stemangiola/tidySingleCellExperiment", - "william-hutchison/tidySpatialExperiment", - "stemangiola/tidybulk", - "stemangiola/tidygate"), - update = FALSE) - -``` - -**Important:** Please restart your R session after installation to ensure the updated packages are loaded correctly. - Let's load the libraries needed for this session ```{r, message = FALSE} @@ -112,9 +93,10 @@ doi: [10.1038/s41593-020-00787-0](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8 library(spatialLIBD) library(ExperimentHub) -# To avoid error for SPE loading -# https://support.bioconductor.org/p/9161859/#9161863 -setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) +# # To avoid error for SPE loading +# # https://support.bioconductor.org/p/9161859/#9161863 +# library(methods) +# setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) spatial_data <- ExperimentHub::ExperimentHub() |> diff --git a/vignettes/Session_3_imaging_assays.Rmd b/vignettes/Session_3_imaging_assays.Rmd index f6c5819..33f6989 100644 --- a/vignettes/Session_3_imaging_assays.Rmd +++ b/vignettes/Session_3_imaging_assays.Rmd @@ -98,9 +98,10 @@ tx_small = tx[sample(seq_len(nrow(tx)), size = nrow(tx)/500),] ``` ```{r, echo=FALSE} -# To avoid error for SPE loading -# https://support.bioconductor.org/p/9161859/#9161863 -setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) +# # To avoid error for SPE loading +# # https://support.bioconductor.org/p/9161859/#9161863 +# library(methods) +# setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) options(timeout = max(300, getOption("timeout"))) tx_small_file = tempfile()