Warning message: In size + sum(size_args, na.rm = FALSE) : NAs produced by integer overflow

[Sirin24]

I faced the following warning messages with ProjectData() step . I would appreciate it if you can help

filtered_obj_sketched <- FindNeighbors(filtered_obj_sketched, dims = 1:30, reduction = "pca")
filtered_obj_sketched <- FindClusters(filtered_obj_sketched, resolution = 2, cluster.name = "unintegrated_clusters_2")
filtered_obj_sketched <- FindClusters(filtered_obj_sketched, resolution = 1, cluster.name = "unintegrated_clusters_1")
filtered_obj_sketched <- FindClusters(filtered_obj_sketched, resolution = 0.5, cluster.name = "unintegrated_clusters_0.5")
filtered_obj_sketched <- RunUMAP(filtered_obj_sketched, dims = 1:30, reduction = "pca", reduction.name = "umap.unintegrated")

filtered_obj_sketched <- FindNeighbors(filtered_obj_sketched, reduction = "integrated.harmony", dims = 1:30)
filtered_obj_sketched <- FindClusters(filtered_obj_sketched, resolution = 2, cluster.name = "harmony_clusters_2")
filtered_obj_sketched <- FindClusters(filtered_obj_sketched, resolution = 1, cluster.name = "harmony_clusters_1")
filtered_obj_sketched <- FindClusters(filtered_obj_sketched, resolution = 0.5, cluster.name = "harmony_clusters_0.5")
filtered_obj_sketched <- RunUMAP(filtered_obj_sketched, reduction = "integrated.harmony", dims = 1:30, return.model = T, reduction.name = "umap.harmony")

filtered_obj_sketched  <- ProjectIntegration(object = filtered_obj_sketched,
                                             sketched.assay = "sketch",
                                             assay = "RNA",
                                             reduction = "pca")

> filtered_obj_sketched <- ProjectData(
+   object = filtered_obj_sketched,
+   assay = "RNA",
+   full.reduction = "pca.full",
+   sketched.assay = "sketch",
+   sketched.reduction = "pca",
+   umap.model = "umap.unintegrated",
+   dims = 1:30,
+   refdata = list(unintegrated_clusters_2_full = "unintegrated_clusters_2",
+                  unintegrated_clusters_1_full = "unintegrated_clusters_1",
+                  unintegrated_clusters_0.5_full = "unintegrated_clusters_0.5")
+ )
Finding sketch neighbors
Finding sketch weight matrix
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Transfering refdata from sketch
Warning messages:
1: In size + sum(size_args, na.rm = FALSE) :
  NAs produced by integer overflow
2: In TransferSketchLabels(object = object, sketched.assay = sketched.assay,  :
  umap.unintegrated does not have a stored umap model

filtered_obj_sketched  <- ProjectIntegration(object = filtered_obj_sketched,
                                           sketched.assay = "sketch",
                                           assay = "RNA",
                                           reduction = "integrated.harmony")

> filtered_obj_sketched <- ProjectData(
+   object = filtered_obj_sketched,
+   assay = "RNA",
+   full.reduction = "integrated.harmony.full",
+   sketched.assay = "sketch",
+   sketched.reduction = "integrated.harmony.full",
+   dims = 1:30,
+   refdata = list(harmony_clusters_2_full = "harmony_clusters_2",
+                  harmony_clusters_1_full = "harmony_clusters_1",
+                  harmony_clusters_0.5_full = "harmony_clusters_0.5"),
+   verbose = TRUE
+ )
Finding sketch neighbors
Transfering refdata from sketch
Warning message:
In size + sum(size_args, na.rm = FALSE) : NAs produced by integer overflow

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 9.3 (Blue Onyx)

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 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 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: UTC
tzcode source: system (glibc)

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

other attached packages:
[1] batchelor_1.20.0 SingleCellExperiment_1.26.0 SummarizedExperiment_1.34.0 Biobase_2.64.0
[5] GenomicRanges_1.56.0 GenomeInfoDb_1.40.1 IRanges_2.38.0 S4Vectors_0.42.0
[9] BiocGenerics_0.50.0 MatrixGenerics_1.16.0 matrixStats_1.3.0 SeuratWrappers_0.3.2
[13] patchwork_1.2.0 ggrepel_0.9.5 ggplot2_3.5.1 SeuratDisk_0.0.0.9021
[17] BPCells_0.2.0 data.table_1.16.0 SCopeLoomR_0.13.0 Seurat_5.1.0
[21] SeuratObject_5.0.2 sp_2.1-4 dplyr_1.1.4

loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.0 later_1.3.2 tibble_3.2.1
[5] R.oo_1.26.0 polyclip_1.10-7 fastDummies_1.7.4 lifecycle_1.0.4
[9] rprojroot_2.0.4 globals_0.16.3 lattice_0.22-6 hdf5r_1.3.11
[13] MASS_7.3-60.2 magrittr_2.0.3 plotly_4.10.4 rmarkdown_2.28
[17] yaml_2.3.10 remotes_2.5.0 httpuv_1.6.15 sctransform_0.4.1
[21] spam_2.10-0 spatstat.sparse_3.1-0 reticulate_1.37.0 cowplot_1.1.3
[25] pbapply_1.7-2 RColorBrewer_1.1-3 ResidualMatrix_1.14.1 abind_1.4-5
[29] zlibbioc_1.50.0 Rtsne_0.17 purrr_1.0.2 R.utils_2.12.3
[33] rappdirs_0.3.3 GenomeInfoDbData_1.2.12 irlba_2.3.5.1 listenv_0.9.1
[37] spatstat.utils_3.1-0 goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.3-1
[41] fitdistrplus_1.2-1 parallelly_1.38.0 DelayedMatrixStats_1.26.0 leiden_0.4.3.1
[45] codetools_0.2-20 DelayedArray_0.30.1 scuttle_1.14.0 DT_0.33
[49] tidyselect_1.2.1 farver_2.1.2 UCSC.utils_1.0.0 ScaledMatrix_1.12.0
[53] spatstat.explore_3.3-2 jsonlite_1.8.8 BiocNeighbors_1.22.0 progressr_0.14.0
[57] ggridges_0.5.6 survival_3.7-0 tools_4.4.0 ica_1.0-3
[61] Rcpp_1.0.13 glue_1.7.0 gridExtra_2.3 SparseArray_1.4.8
[65] xfun_0.47 here_1.0.1 withr_3.0.1 BiocManager_1.30.23
[69] fastmap_1.2.0 fansi_1.0.6 digest_0.6.37 rsvd_1.0.5
[73] R6_2.5.1 mime_0.12 colorspace_2.1-1 scattermore_1.2
[77] tensor_1.5 spatstat.data_3.1-2 R.methodsS3_1.8.2 RhpcBLASctl_0.23-42
[81] utf8_1.2.4 tidyr_1.3.1 generics_0.1.3 httr_1.4.7
[85] htmlwidgets_1.6.4 S4Arrays_1.4.1 uwot_0.2.2 pkgconfig_2.0.3
[89] gtable_0.3.5 lmtest_0.9-40 XVector_0.44.0 htmltools_0.5.8.1
[93] dotCall64_1.1-1 scales_1.3.0 png_0.1-8 harmony_1.2.1
[97] spatstat.univar_3.0-0 knitr_1.48 rstudioapi_0.16.0 reshape2_1.4.4
[101] nlme_3.1-165 zoo_1.8-12 stringr_1.5.1 KernSmooth_2.23-24
[105] parallel_4.4.0 miniUI_0.1.1.1 pillar_1.9.0 grid_4.4.0
[109] vctrs_0.6.5 RANN_2.6.2 promises_1.3.0 BiocSingular_1.20.0
[113] beachmat_2.20.0 xtable_1.8-4 cluster_2.1.6 evaluate_0.24.0
[117] cli_3.6.3 compiler_4.4.0 rlang_1.1.4 crayon_1.5.3
[121] future.apply_1.11.2 labeling_0.4.3 plyr_1.8.9 stringi_1.8.4
[125] viridisLite_0.4.2 deldir_2.0-4 BiocParallel_1.38.0 munsell_0.5.1
[129] lazyeval_0.2.2 spatstat.geom_3.3-2 Matrix_1.7-0 RcppHNSW_0.6.0
[133] sparseMatrixStats_1.16.0 bit64_4.0.5 future_1.34.0 shiny_1.9.1
[137] ROCR_1.0-11 igraph_2.0.3 bit_4.0.5