IntegrateData error

[MJoseMo]

Hi,

I'm trying to integrate 17 Seurat objects on RStudio. After a couple hours, I encountered this error.

split_spatial <- lapply(split_spatial, SCTransform, assay = "Spatial", vst.flavor = "v2", conserve.memory = TRUE)

spatial_features <- SelectIntegrationFeatures(split_spatial, verbose = FALSE)

split_spatial <- lapply(split_spatial, function(obj) {
    obj[["RNA"]] <- obj[["Spatial"]]
    return(obj)
})

library(future)
plan(sequential)
options(future.stdout = NA)
options(future.globals.maxSize = +Inf)
options(future.fork.enable = FALSE)
options(future.rng.onMisuse="ignore")
options(Seurat.future = FALSE)
options(Seurat.parallel = FALSE)


split_spatial <- PrepSCTIntegration(object.list = split_spatial, anchor.features = spatial_features,
                              verbose = FALSE)

spatial_anchors <- FindIntegrationAnchors(object.list = split_spatial, normalization.method = "SCT",
                                      verbose = FALSE, anchor.features = spatial_features)

spatial_integrated <- IntegrateData(anchorset = spatial_anchors, normalization.method = "SCT",
                                  verbose = FALSE)

Error en .M2C(newTMat(i = c(ij1[, 1], ij2[, 1]), j = c(ij1[, 2], ij2[, : 
  'R_Calloc' could not allocate memory (22989229 of 4 bytes)

[anashen]

Hi @MJoseMo, can you provide more details about your object & session? If your dataset is large, I would recommend trying a sketch-based analysis workflow.

This could also be helpful: https://stackoverflow.com/questions/1395229/increasing-or-decreasing-the-memory-available-to-r-processes

[MJoseMo]

Hi @anashen, is this pipeline adequated for spatial transcriptomics?

[MJoseMo]

Hi, my dataset contains 17 samples for two different treatment.

R version 4.5.2 (2025-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26200)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Spanish_Spain.utf8  LC_CTYPE=Spanish_Spain.utf8    LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C                   LC_TIME=Spanish_Spain.utf8    

time zone: Europe/Madrid
tzcode source: internal

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

other attached packages:
[1] sessioninfo_1.2.3

loaded via a namespace (and not attached):
 [1] compiler_4.5.2    fastmap_1.2.0     cli_3.6.5         htmltools_0.5.9   tools_4.5.2       otel_0.2.0        rstudioapi_0.18.0 yaml_2.3.12       rmarkdown_2.30    knitr_1.51        xfun_0.56         digest_0.6.39    
[13] rlang_1.1.7       evaluate_1.0.5