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Merged
federicomarini merged 3 commits into from
May 16, 2026
Merged

Adapt to new roxygen2 and scrapper replacement for scuttle functions #3

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33a82af
Adapt to one-line requirement of roxygen2 8.0.0
csoneson May 15, 2026
6251425
Replace deprecated scuttle functions with scrapper equivalents
csoneson May 15, 2026
9c0e683
Update GHA
csoneson May 15, 2026
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2 changes: 2 additions & 0 deletions .Rbuildignore
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Expand Up @@ -5,3 +5,5 @@
^CODE_OF_CONDUCT\.md$
TODO.md$
^\.github$
^\.positai$
^\.claude$
6 changes: 3 additions & 3 deletions .github/workflows/R-CMD-check.yaml
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Expand Up @@ -52,9 +52,9 @@ jobs:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: 'devel', bioc: '3.21', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: 'devel', bioc: '3.21'}
- { os: windows-latest, r: 'devel', bioc: '3.21'}
- { os: ubuntu-latest, r: 'release', bioc: '3.24', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: 'release', bioc: '3.24'}
- { os: windows-latest, r: 'release', bioc: '3.24'}
## Check https://github.com/r-lib/actions/tree/master/examples
## for examples using the http-user-agent
env:
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -28,7 +28,8 @@ Suggests:
knitr,
rmarkdown,
BiocStyle,
testthat (>= 3.0.0)
testthat (>= 3.0.0),
scrapper
URL: https://github.com/iSEE/iSEEid
BugReports: https://github.com/iSEE/iSEEid/issues
VignetteBuilder: knitr
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15 changes: 3 additions & 12 deletions R/panel_SampleIdentificationCenter.R
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Expand Up @@ -23,17 +23,7 @@
#' @return A panel designed to work within the iSEE framework
#'
#' @aliases
#' SampleIdentificationCenter SampleIdentificationCenter-class
#' .createObservers,SampleIdentificationCenter-method
#' .defineDataInterface,SampleIdentificationCenter-method
#' .defineOutput,SampleIdentificationCenter-method
#' .definePanelTour,SampleIdentificationCenter-method
#' .fullName,SampleIdentificationCenter-method
#' .generateOutput,SampleIdentificationCenter-method
#' .multiSelectionResponsive,SampleIdentificationCenter-method
#' .panelColor,SampleIdentificationCenter-method
#' .renderOutput,SampleIdentificationCenter-method
#' initialize,SampleIdentificationCenter-method
#' SampleIdentificationCenter SampleIdentificationCenter-class .createObservers,SampleIdentificationCenter-method .defineDataInterface,SampleIdentificationCenter-method .defineOutput,SampleIdentificationCenter-method .definePanelTour,SampleIdentificationCenter-method .fullName,SampleIdentificationCenter-method .generateOutput,SampleIdentificationCenter-method .multiSelectionResponsive,SampleIdentificationCenter-method .panelColor,SampleIdentificationCenter-method .renderOutput,SampleIdentificationCenter-method initialize,SampleIdentificationCenter-method
#'
#' @examples
#' library(iSEE)
Expand All @@ -44,7 +34,8 @@
#' class(sce)
#'
#' library(scater)
#' sce <- logNormCounts(sce, exprs_values = "tophat_counts")
#' library(scrapper)
#' sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
#'
#' sce <- runPCA(sce, ncomponents=4)
#' sce <- runTSNE(sce)
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3 changes: 2 additions & 1 deletion README.Rmd
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Expand Up @@ -50,9 +50,10 @@ library("iSEEid")
library("iSEE")
library("scRNAseq")
library("scater")
library("scrapper")

sce <- ReprocessedAllenData(assays = "tophat_counts")
sce <- logNormCounts(sce, exprs_values = "tophat_counts")
sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
sce <- runPCA(sce, ncomponents = 4)
sce <- runTSNE(sce)

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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -44,9 +44,10 @@ library("iSEEid")
library("iSEE")
library("scRNAseq")
library("scater")
library("scrapper")

sce <- ReprocessedAllenData(assays = "tophat_counts")
sce <- logNormCounts(sce, exprs_values = "tophat_counts")
sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
sce <- runPCA(sce, ncomponents = 4)
sce <- runTSNE(sce)

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3 changes: 2 additions & 1 deletion man/SampleIdentificationCenter-class.Rd
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3 changes: 2 additions & 1 deletion vignettes/Introduction_to_iSEEid.Rmd
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Expand Up @@ -81,9 +81,10 @@ library("iSEE")
library("iSEEid")
library("scRNAseq")
library("scater")
library("scrapper")

sce <- ReprocessedAllenData(assays = "tophat_counts")
sce <- logNormCounts(sce, exprs_values = "tophat_counts")
sce <- normalizeRnaCounts.se(sce, assay.type = "tophat_counts", size.factors = NULL)
sce <- runPCA(sce, ncomponents = 4)
sce <- runTSNE(sce)

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