no slot of name "ptr" for this object of class "SpatRaster"

[Elena983]

Hi, I am reproducing the visium example

sfe <- McKellarMuscleData("full")

if (!file.exists("tissue_lowres_5a.jpeg")) {
download.file("https://raw.githubusercontent.com/pachterlab/voyager/main/vignettes/tissue_lowres_5a.jpeg",
destfile = "tissue_lowres_5a.jpeg")
}

sfe <- addImg(sfe,
imageSource = "/Users/elena/Desktop/spatial_course/geospatial/tissue_lowres_5a.jpeg",
sample_id = "Vis5A",
image_id = "lowres",
scale_fct = 1024/22208)

this got me the error

Error in methods::slot(value, what) :
no slot of name "ptr" for this object of class "SpatRaster"

Thanks

[lambdamoses]

What version of SpatialFeatureExperiment and Bioconductor are you using? It sounds like an error from an old version that has already been fixed. The code runs with the newest version on my computer without error.

[Elena983]

BiocManager::version()
[1] ‘3.20’

packageVersion("SpatialFeatureExperiment")
[1] ‘1.8.4’

it is not only on mine PC

[lambdamoses]

OK, I was running the devel version. Now Bioc 3.20 branch is frozen as release of 3.21 is coming soon. Can you try installing Bioc 3.21 and see if the error persists?

[Elena983]

Thanks for the prompt answers. I am on Mac, and the latest available is 4.4.3 for R, and Bioconductor needs 4.5 at least, so only 3.20 for now

[lambdamoses]

You can still install devel version of SFE from GitHub without R devel

[abaghian]

Unable to convert seurat v5 object to SFE and getting

Error in [[<-.data.frame(*tmp*, i, value = list()) :
replacement has 0 rows, data has 2859

Is this package compatible with Seurat V5?

Thanks

[lambdamoses]

What Bioconductor version are you using? I though I fixed this a long time ago.

[abaghian]

bioc v3.21
here's the code:

sfe_conv_vis <-toSpatialFeatureExperiment(x = cSCC_post_data,
image_scalefactors = "lowres",
unit = "micron",
BPPARAM = BPPARAM

thank you

[abaghian]

also tried coercing from spaceranger and go the same error..

dir <- "/Users/ab/Desktop/ST_project"
sample_ids <- c("sample")
samples <- file.path(dir, sample_ids)
sfe3 <- read10xVisiumSFE(samples, sample_id = sample_ids,

•                      type = "sparse", 
  

•                      data = "filtered", images = "hires")
  

10X Visium data will be loaded: outs

Error in methods::slot(value, what) :
no slot of name "ptr" for this object of class "SpatRaster"

traceback()
13: methods::slot(value, what)
12: asMethod(object, Class, value)
11: as<-(*tmp*, Classi, value = obj)
10: initialize(value, ...)
9: initialize(value, ...)
8: new("SpatRasterImage", img)
7: .get_imgData(img_fns[j], sample_id = sample_id, image_id = names(img_fns)[j],
extent = NULL, scale_fct = scale_imgs[[j]], flip = (flip ==
"image"))
6: FUN(X[[i]], ...)
5: lapply(seq_along(img_fns), function(j) {
.get_imgData(img_fns[j], sample_id = sample_id, image_id = names(img_fns)[j],
extent = NULL, scale_fct = scale_imgs[[j]], flip = (flip ==
"image"))
})
4: .read10xVisium(dirs[i], sample_id[i], type, data, images, row.names = row.names,
flip = flip, VisiumHD = FALSE, unit = unit, zero.policy = zero.policy,
style = style)
3: FUN(X[[i]], ...)
2: lapply(seq_along(samples), function(i) {
o <- .read10xVisium(dirs[i], sample_id[i], type, data, images,
row.names = row.names, flip = flip, VisiumHD = FALSE,
unit = unit, zero.policy = zero.policy, style = style)
fn <- file.path(dirs[i], "spatial", "spatial_enrichment.csv")
if (file.exists(fn)) {
enrichment <- read.csv(fn)
row_inds <- match(rownames(o), enrichment[[enrichment_feature]])
if (i == 1L) {
rowData(o) <- cbind(rowData(o), Feature.Type = enrichment[row_inds,
"Feature.Type"])
}
cols_use <- c("I", "P.value", "Adjusted.p.value", "Feature.Counts.in.Spots.Under.Tissue",
"Median.Normalized.Average.Counts", "Barcodes.Detected.per.Feature")
enrichment2 <- enrichment[row_inds, cols_use]
names(enrichment2) <- paste(names(enrichment2), sample_id[i],
sep = "_")
rowData(o) <- cbind(rowData(o), enrichment2)
}
fn2 <- file.path(dirs[i], "", "spatial", "barcode_fluorescence_intensity.csv")
...
1: read10xVisiumSFE(samples, sample_id = sample_ids, type = "sparse",
data = "filtered", images = "hires")
list.files(file.path(samples[1]))
[1] "analysis" "filtered_feature_bc_matrix.h5"
[3] "other" "outs"
[5] "raw_feature_bc_matrix.h5"
list.files(file.path(samples[1], "outs"))
[1] "filtered_feature_bc_matrix" "filtered_feature_bc_matrix.h5"
[3] "raw_feature_bc_matrix" "raw_feature_bc_matrix.h5"
[5] "spatial"
list.files(file.path(samples[1], "outs", "filtered_feature_bc_matrix"))
[1] "barcodes.tsv.gz" "features.tsv.gz" "matrix.mtx.gz"
list.files(file.path(samples[1], "outs", "spatial"))
[1] "aligned_fiducials.jpg" "detected_tissue_image.jpg" "scalefactors_json.json"
[4] "spatial_enrichment.csv" "tissue_hires_image.png" "tissue_lowres_image.png"
[7] "tissue_positions.csv"

sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
[1] devtools_2.4.5 usethis_3.2.1 patchwork_1.3.2
[4] pheatmap_1.0.13 scico_1.5.0 ragg_1.5.0
[7] scran_1.36.0 png_0.1-8 remotes_2.5.0
[10] SpatialExperiment_1.18.1 bluster_1.18.0 textshaping_1.0.3
[13] DropletUtils_1.28.1 spdep_1.4-1 spData_2.3.4
[16] dplyr_1.1.4 rhdf5_2.52.1 Seurat_5.3.0
[19] SeuratObject_5.2.0 sp_2.2-0 BiocManager_1.30.26
[22] terra_1.8-60 scater_1.35.0 ggplot2_3.5.2
[25] sf_1.0-21 scuttle_1.18.0 SingleCellExperiment_1.30.1
[28] SummarizedExperiment_1.38.1 Biobase_2.68.0 GenomicRanges_1.60.0
[31] GenomeInfoDb_1.44.2 IRanges_2.42.0 S4Vectors_0.46.0
[34] BiocGenerics_0.54.0 generics_0.1.4 MatrixGenerics_1.20.0
[37] matrixStats_1.5.0 stringr_1.5.1 Matrix_1.7-4
[40] rjson_0.2.23 Voyager_1.10.0 SpatialFeatureExperiment_1.9.7
[43] R.utils_2.13.0 R.oo_1.27.1 R.methodsS3_1.8.2
[46] RBioFormats_1.8.0 rJava_1.0-11