cannot use de.method="wilcox" and plotMarkerHeatmap function.

[AmmyDK]

> library(SingleR)
pred.grun <- SingleR(test=sceG, ref=sceM, labels=sceM$label, de.method="wilcox")
table(pred.grun$labels)
Error in (function (x, groups, block = NULL, block.weight.policy = c("variable", :
unused arguments (compute.delta.detected = FALSE, compute.delta.mean = FALSE, compute.cohens.d = FALSE)

also if I run
> plotMarkerHeatmap(pred.grun, sceG, "beta")
Error in scrapper::scoreMarkers(test, predictions, num.threads = num.threads, :
unused arguments (compute.cohens.d = (order.by.effect == "cohens.d"), compute.delta.mean = (order.by.effect == "delta.mean"), compute.delta.detected = (order.by.effect == "delta.detected"))

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 9.2 (Plow)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.21.so; LAPACK version 3.9.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Stockholm
tzcode source: system (glibc)

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] SingleR_2.8.0 scater_1.34.0
[3] ggplot2_3.5.1 scuttle_1.16.0
[5] scRNAseq_2.20.0 SingleCellExperiment_1.28.1
[7] SummarizedExperiment_1.36.0 Biobase_2.66.0
[9] GenomicRanges_1.58.0 GenomeInfoDb_1.42.1
[11] IRanges_2.40.1 S4Vectors_0.44.0
[13] BiocGenerics_0.52.0 MatrixGenerics_1.18.0
[15] matrixStats_1.4.1

I tried 2.9.4 version as well, but I cannot apply de.method, same issue raised up as above. Please help, many thanks.

[LTLA]

I don't think you're using 2.8.0, the compute.* arguments were only added in 2.9+.

If you're going to use packages from the development stream like 2.9.4, make sure all other BioC packages are also from the devel stream. In this case, I would guess that you're mixing 2.9.4 with the release scrapper that lacks the compute.* arguments.