BUG: SCTransform invoked with do.call fails to finish #10153
Description
Issue Description
Even when the arguments and environment are exactly the same, SCTransform invoked in the form of do.call(SCTransform, list(object=so)) fails to finish, whereas when called directly i.e., SCTransform(object=so) it finishes with no problems.
Reproducing Code Example
# I can't replicate this with pbmc_small. I could only reproduce this with my own
# Seurat object, which has this form:
so
# An object of class Seurat
# 50871 features across 11568 samples within 2 assays
# Active assay: SCT (15385 features, 0 variable features)
# 3 layers present: counts, data, scale.data
# 1 other assay present: RNA
# Then, this works:
SCTransform(object=so, ncells=100)
# But not this:
do.call(SCTransform, list(object=so, ncells=100))Error Message
Additional Comments
The last message printed before the do.call hangs is:
Running SCTransform on assay: RNA
vst.flavor='v2' set. Using model with fixed slope and excluding poisson genes.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 15457 by 6450
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 100 cells
Found 212 outliers - those will be ignored in fitting/regularization step
Second step: Get residuals using fitted parameters for 15457 genes
Computing corrected count matrix for 15457 genes
Calculating gene attributes
Wall clock passed: Time difference of 13.61948 secs
Determine variable features
Session Info
> sessionInfo()
R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Red Hat Enterprise Linux 9.3 (Plow)
Matrix products: default
BLAS/LAPACK: /data/wanglf/home/e0175719/repos/batwing/.snakemake/conda/13ab51087dfaeaea761357a0ade3a749_/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
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: Asia/Singapore
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.4 forcats_1.0.1 stringr_1.5.2 dplyr_1.1.4
[5] purrr_1.1.0 readr_2.1.5 tidyr_1.3.1 tibble_3.3.0
[9] ggplot2_4.0.0 tidyverse_2.0.0 future_1.67.0 Seurat_5.3.0
[13] SeuratObject_5.2.0 sp_2.2-0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_2.0.0
[3] magrittr_2.0.4 spatstat.utils_3.2-0
[5] farver_2.1.2 zlibbioc_1.52.0
[7] vctrs_0.6.5 ROCR_1.0-11
[9] DelayedMatrixStats_1.28.0 spatstat.explore_3.5-3
[11] S4Arrays_1.6.0 htmltools_0.5.8.1
[13] SparseArray_1.6.0 sctransform_0.4.2
[15] parallelly_1.45.1 KernSmooth_2.23-26
[17] htmlwidgets_1.6.4 ica_1.0-3
[19] plyr_1.8.9 plotly_4.11.0
[21] zoo_1.8-14 igraph_2.1.4
[23] mime_0.13 lifecycle_1.0.4
[25] pkgconfig_2.0.3 Matrix_1.7-4
[27] R6_2.6.1 fastmap_1.2.0
[29] GenomeInfoDbData_1.2.13 MatrixGenerics_1.18.0
[31] fitdistrplus_1.2-4 shiny_1.11.1
[33] digest_0.6.37 patchwork_1.3.1
[35] S4Vectors_0.44.0 tensor_1.5.1
[37] RSpectra_0.16-2 irlba_2.3.5.1
[39] GenomicRanges_1.58.0 progressr_0.16.0
[41] spatstat.sparse_3.1-0 timechange_0.3.0
[43] httr_1.4.7 polyclip_1.10-7
[45] abind_1.4-8 compiler_4.4.3
[47] withr_3.0.2 S7_0.2.0
[49] fastDummies_1.7.5 MASS_7.3-65
[51] DelayedArray_0.32.0 tools_4.4.3
[53] lmtest_0.9-40 httpuv_1.6.16
[55] future.apply_1.20.0 goftest_1.2-3
[57] glmGamPoi_1.18.0 glue_1.8.0
[59] nlme_3.1-168 promises_1.3.3
[61] grid_4.4.3 Rtsne_0.17
[63] cluster_2.1.8.1 reshape2_1.4.4
[65] generics_0.1.4 gtable_0.3.6
[67] spatstat.data_3.1-8 tzdb_0.5.0
[69] data.table_1.17.8 hms_1.1.3
[71] XVector_0.46.0 BiocGenerics_0.52.0
[73] spatstat.geom_3.6-0 RcppAnnoy_0.0.22
[75] ggrepel_0.9.6 RANN_2.6.2
[77] pillar_1.11.1 spam_2.11-1
[79] RcppHNSW_0.6.0 later_1.4.4
[81] splines_4.4.3 lattice_0.22-7
[83] survival_3.8-3 deldir_2.0-4
[85] tidyselect_1.2.1 miniUI_0.1.2
[87] pbapply_1.7-4 gridExtra_2.3
[89] IRanges_2.40.0 SummarizedExperiment_1.36.0
[91] scattermore_1.2 stats4_4.4.3
[93] Biobase_2.66.0 matrixStats_1.5.0
[95] stringi_1.8.7 UCSC.utils_1.2.0
[97] lazyeval_0.2.2 codetools_0.2-20
[99] cli_3.6.5 uwot_0.2.3
[101] xtable_1.8-4 reticulate_1.43.0
[103] Rcpp_1.1.0 GenomeInfoDb_1.42.0
[105] globals_0.18.0 spatstat.random_3.4-2
[107] png_0.1-8 spatstat.univar_3.1-4
[109] parallel_4.4.3 dotCall64_1.2
[111] sparseMatrixStats_1.18.0 listenv_0.9.1
[113] viridisLite_0.4.2 scales_1.4.0
[115] ggridges_0.5.7 crayon_1.5.3
[117] rlang_1.1.6 cowplot_1.2.0