Error in tcrossprod(x, y): requires numeric/complex matrix/vector arguments

[boluofen]

Hello Team,

When I run:Track_genes <- graph_test(cds,neighbor_graph="principal_graph", cores=6,verbose = T)

I encountered:
set_nn_control: call stack: graph_test() => set_nn_control()
nn_control:
method: annoy
metric: euclidean
n_trees: 50
search_k: 2500
cores: 1
grain_size: 1
retrieve the matrices for Moran's I test...
set_nn_control: call stack: graph_test() => tryCatch() => tryCatchList() => tryCatchOne() => doTryCatch() => calculateLW() => make_nn_index() => set_nn_control()
nn_control:
method: annoy
metric: euclidean
n_trees: 50
search_k: NA
cores: NA
grain_size: NA
make_nn_index:
nn_control:
method: annoy
metric: euclidean
n_trees: 50
search_k: NA
cores: NA
grain_size: NA
make_nn_index: build time 3.29 seconds.
Identify connecting principal point pairs ...
set_nn_control: call stack: graph_test() => tryCatch() => tryCatchList() => tryCatchOne() => doTryCatch() => calculateLW() => tryCatch() => tryCatchList() => tryCatchOne() => doTryCatch() => search_nn_index() => set_nn_control()
nn_control:
method: annoy
metric: euclidean
n_trees: NA
search_k: 2500
cores: 1
grain_size: 1
search_nn_index:
k: 26
nn_control:
method: annoy
metric: euclidean
n_trees: NA
search_k: 2500
cores: 1
grain_size: 1
search_nn_index: search time: 14.02 seconds.
count_nn_missing_self_index:
0 out of 23861 rows are missing the row index
'recall': 100%
Error in value[3L] :
Error in tcrossprod(x, y): requires numeric/complex matrix/vector arguments

• error in graph_test

My session Info:
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0

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

time zone: Asia/Shanghai
tzcode source: system (glibc)

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

other attached packages:
[1] Matrix_1.6-5 monocle3_1.4.26 ggsci_3.0.0
[4] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 GenomicRanges_1.54.1
[7] GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2
[10] MatrixGenerics_1.14.0 matrixStats_1.5.0 Biobase_2.62.0
[13] BiocGenerics_0.48.1

loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.3.1 later_1.4.4
[4] bitops_1.0-7 tibble_3.3.0 polyclip_1.10-7
[7] fastDummies_1.7.5 lifecycle_1.0.4 Rdpack_2.6.4
[10] globals_0.18.0 processx_3.8.6 lattice_0.22-7
[13] MASS_7.3-60 magrittr_2.0.4 plotly_4.11.0
[16] remotes_2.5.0 httpuv_1.6.16 Seurat_5.3.0
[19] sctransform_0.4.1 spam_2.11-1 sp_2.2-0
[22] sessioninfo_1.2.2 pkgbuild_1.4.2 spatstat.sparse_3.1-0
[25] reticulate_1.43.0 cowplot_1.1.1 pbapply_1.7-4
[28] minqa_1.2.8 RColorBrewer_1.1-3 abind_1.4-8
[31] pkgload_1.4.1 zlibbioc_1.48.2 Rtsne_0.17
[34] purrr_1.1.0 RCurl_1.98-1.17 GenomeInfoDbData_1.2.11
[37] ggrepel_0.9.6 irlba_2.3.5.1 listenv_0.9.0
[40] spatstat.utils_3.2-0 pheatmap_1.0.13 goftest_1.2-3
[43] RSpectra_0.16-2 spatstat.random_3.4-2 fitdistrplus_1.2-4
[46] parallelly_1.36.0 codetools_0.2-20 DelayedArray_0.28.0
[49] tidyselect_1.2.1 farver_2.1.2 lme4_1.1-37
[52] spatstat.explore_3.5-3 jsonlite_2.0.0 ellipsis_0.3.2
[55] progressr_0.17.0 ggridges_0.5.7 survival_3.8-3
[58] tools_4.3.1 ica_1.0-3 Rcpp_1.1.0
[61] glue_1.8.0 gridExtra_2.3 SparseArray_1.2.4
[64] usethis_3.2.1 dplyr_1.1.4 withr_3.0.2
[67] BiocManager_1.30.22 fastmap_1.2.0 boot_1.3-32
[70] callr_3.7.6 digest_0.6.37 R6_2.6.1
[73] mime_0.13 scattermore_1.2 tensor_1.5.1
[76] dichromat_2.0-0.1 spatstat.data_3.1-8 tidyr_1.3.1
[79] generics_0.1.4 data.table_1.17.8 prettyunits_1.2.0
[82] httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.2.1
[85] uwot_0.2.3 pkgconfig_2.0.3 gtable_0.3.6
[88] lmtest_0.9-40 XVector_0.42.0 htmltools_0.5.8.1
[91] profvis_0.4.0 dotCall64_1.2 SeuratObject_5.2.0
[94] scales_1.4.0 png_0.1-8 spatstat.univar_3.1-4
[97] reformulas_0.4.1 rstudioapi_0.17.1 reshape2_1.4.4
[100] nlme_3.1-168 nloptr_2.2.1 zoo_1.8-14
[103] cachem_1.1.0 stringr_1.5.2 KernSmooth_2.23-26
[106] parallel_4.3.1 miniUI_0.1.2 pillar_1.11.1
[109] grid_4.3.1 vctrs_0.6.5 RANN_2.6.2
[112] urlchecker_1.0.1 promises_1.3.3 xtable_1.8-4
[115] cluster_2.1.4 cli_3.6.1 compiler_4.3.1
[118] rlang_1.1.6 crayon_1.5.3 future.apply_1.11.0
[121] ps_1.9.1 plyr_1.8.9 fs_1.6.6
[124] stringi_1.8.7 viridisLite_0.4.2 deldir_2.0-4
[127] assertthat_0.2.1 lazyeval_0.2.2 devtools_2.4.5
[130] spatstat.geom_3.6-0 RcppHNSW_0.6.0 patchwork_1.3.2.9000
[133] future_1.33.0 ggplot2_3.5.2 shiny_1.11.1
[136] rbibutils_2.3 ROCR_1.0-11 igraph_1.5.1
[139] memoise_2.0.1

If you can help me with this bug I would be grateful

Regards