Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting a method for function '[<-': default method not implemented for type 'S4'

[chaiepi]

Describe the bug
Running the example in monocle3, and cluster_cells() function reports an error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting a method for function '[<-': default method not implemented for type 'S4'

To Reproduce
The code that produced the bug:
cell_metadata <- readRDS(system.file('extdata',
'worm_embryo/worm_embryo_coldata.rds',
package='monocle3'))
gene_metadata <- readRDS(system.file('extdata',
'worm_embryo/worm_embryo_rowdata.rds',
package='monocle3'))
expression_matrix <- readRDS(system.file('extdata',
'worm_embryo/worm_embryo_expression_matrix.rds',
package='monocle3'))

cds <- new_cell_data_set(expression_data=expression_matrix,
cell_metadata=cell_metadata,
gene_metadata=gene_metadata)

cds <- preprocess_cds(cds)
cds <- reduce_dimension(cds)
cds <- cluster_cells(cds)

traceback()
traceback()
5: h(simpleError(msg, call))
4: .handleSimpleError(function (cond)
.Internal(C_tryCatchHelper(addr, 1L, cond)), "default method not implemented for type 'S4'",
base::quote(is.nan(num_links)))
3: [<-(*tmp*, is.nan(num_links), value = 0)
2: compute_partitions(cluster_result$g, cluster_result$optim_res,
partition_qval, verbose)
1: cluster_cells(cds)

sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.12.so

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

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

other attached packages:
[1] tidyr_1.2.1 dplyr_1.0.10 patchwork_1.1.2 SeuratWrappers_0.3.0
[5] sp_1.5-0 SeuratObject_4.1.1 Seurat_4.1.1 monocle3_1.3.7
[9] SingleCellExperiment_1.18.1 SummarizedExperiment_1.26.1 GenomicRanges_1.48.0 GenomeInfoDb_1.32.4
[13] IRanges_2.30.1 S4Vectors_0.34.0 MatrixGenerics_1.8.1 matrixStats_0.62.0
[17] Biobase_2.56.0 BiocGenerics_0.42.0

loaded via a namespace (and not attached):
[1] plyr_1.8.7 igraph_2.0.3 lazyeval_0.2.2 splines_4.2.1
[5] listenv_0.8.0 scattermore_0.8 usethis_2.1.6 ggplot2_3.3.6
[9] digest_0.6.29 htmltools_0.5.3 fansi_1.0.3 memoise_2.0.1
[13] magrittr_2.0.3 tensor_1.5 cluster_2.1.4 ROCR_1.0-11
[17] remotes_2.4.2 globals_0.16.1 R.utils_2.12.0 spatstat.sparse_2.1-1
[21] prettyunits_1.1.1 colorspace_2.0-3 ggrepel_0.9.1 xfun_0.33
[25] crayon_1.5.1 callr_3.7.2 RCurl_1.98-1.8 jsonlite_1.8.0
[29] lme4_1.1-35.3 progressr_0.11.0 spatstat.data_2.2-0 survival_3.4-0
[33] zoo_1.8-11 glue_1.6.2 polyclip_1.10-0 gtable_0.3.1
[37] zlibbioc_1.42.0 XVector_0.36.0 leiden_0.4.3 DelayedArray_0.22.0
[41] pkgbuild_1.3.1 future.apply_1.9.1 abind_1.4-5 scales_1.2.1
[45] DBI_1.1.3 spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.12
[49] viridisLite_0.4.1 xtable_1.8-4 reticulate_1.26 spatstat.core_2.4-4
[53] rsvd_1.0.5 profvis_0.3.7 htmlwidgets_1.5.4 httr_1.4.4
[57] RColorBrewer_1.1-3 ellipsis_0.3.2 ica_1.0-3 urlchecker_1.0.1
[61] pkgconfig_2.0.3 R.methodsS3_1.8.2 uwot_0.1.14 deldir_1.0-6
[65] utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.5 reshape2_1.4.4
[69] later_1.3.0 cachem_1.0.6 munsell_0.5.0 tools_4.2.1
[73] cli_3.4.0 generics_0.1.3 devtools_2.4.4 ggridges_0.5.3
[77] evaluate_0.16 stringr_1.4.1 fastmap_1.1.0 goftest_1.2-3
[81] processx_3.7.0 fs_1.5.2 knitr_1.40 fitdistrplus_1.1-8
[85] purrr_0.3.4 RANN_2.6.1 sparseMatrixStats_1.8.0 pbapply_1.5-0
[89] future_1.28.0 nlme_3.1-159 mime_0.12 R.oo_1.25.0
[93] compiler_4.2.1 rstudioapi_0.14 plotly_4.10.0 png_0.1-7
[97] spatstat.utils_2.3-1 tibble_3.1.8 stringi_1.7.8 ps_1.7.1
[101] highr_0.9 rgeos_0.5-9 lattice_0.20-45 Matrix_1.5-1
[105] nloptr_2.0.3 vctrs_0.4.1 pillar_1.8.1 lifecycle_1.0.2
[109] BiocManager_1.30.18 spatstat.geom_2.4-0 lmtest_0.9-40 RcppAnnoy_0.0.19
[113] data.table_1.14.2 cowplot_1.1.1 bitops_1.0-7 irlba_2.3.5
[117] httpuv_1.6.6 R6_2.5.1 promises_1.2.0.1 KernSmooth_2.23-20
[121] gridExtra_2.3 parallelly_1.32.1 sessioninfo_1.2.2 codetools_0.2-18
[125] pkgload_1.3.0 boot_1.3-28 MASS_7.3-58.1 assertthat_0.2.1
[129] leidenbase_0.1.25 sctransform_0.3.5 GenomeInfoDbData_1.2.8 mgcv_1.8-40
[133] parallel_4.2.1 grid_4.2.1 rpart_4.1.16 minqa_1.2.4
[137] DelayedMatrixStats_1.18.2 Rtsne_0.16 shiny_1.7.2

[pavsol]

Having the same issue

[FuduanPeng]

anyone solved this problem?

[Allanware]

Having the same issue

[sqh614]

Having the same issue

[Biometeor]

The occurrence of this issue is attributed to a submission with the commit (1336cc9). It is regrettable that the developers have not yet addressed this problem. As an immediate workaround, I have temporarily forked the 'moncle3' repository and commented out the problematic sections of the code. For others who urgently require a quick solution, they can utilize the alternative installation method :

devtools::install_github('Biometeor/monocle3', ref="master").

This is a provisional measure, and I earnestly hope that the developers will take notice of this issue and resolve it. Once the issue is resolved, I will remove this forked repository."