Hi,

I am following the tutorial as described at https://cole-trapnell-lab.github.io/monocle3/docs/clustering/

I performed function graph_test() to create gene IDs with which to find gene modules.

pr_graph_test_res <- graph_test(G3_mon, neighbor_graph="knn")
pr_deg_ids <- row.names(subset(pr_graph_test_res, morans_I > 0.01 & q_value < 0.05))

But find_gene_modules() executed like so:

gene_module_df <- find_gene_modules(G3_mon[pr_deg_ids,], resolution=1e-2) 

Is giving me the error message:

'variable_name' is not a global variable.
Error: methods::is(object = nn_control_default, class2 = "list") is not TRUE

Has anyone seen this error before or knows what it could mean?

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] magrittr_2.0.1              dplyr_1.0.7                 monocle3_1.2.2              SingleCellExperiment_1.14.1
 [5] SummarizedExperiment_1.22.0 GenomicRanges_1.44.0        GenomeInfoDb_1.28.1         IRanges_2.26.0             
 [9] S4Vectors_0.30.0            MatrixGenerics_1.4.3        matrixStats_0.60.1          Biobase_2.52.0             
[13] BiocGenerics_0.38.0         cli_3.1.0                  

loaded via a namespace (and not attached):
  [1] colorspace_2.0-2          grr_0.9.5                 deldir_0.2-10             ellipsis_0.3.2           
  [5] class_7.3-19              rprojroot_2.0.2           XVector_0.32.0            fs_1.5.0                 
  [9] rstudioapi_0.13           proxy_0.4-26              farver_2.1.0              remotes_2.4.1            
 [13] ggrepel_0.9.1             RSpectra_0.16-0           fansi_0.5.0               codetools_0.2-18         
 [17] splines_4.1.0             sparseMatrixStats_1.4.0   cachem_1.0.6              knitr_1.36               
 [21] pkgload_1.2.3             speedglm_0.3-3            RhpcBLASctl_0.21-247.1    pheatmap_1.0.12          
 [25] uwot_0.1.10               BiocManager_1.30.16       compiler_4.1.0            assertthat_0.2.1         
 [29] Matrix_1.3-3              fastmap_1.1.0             s2_1.0.7                  htmltools_0.5.2          
 [33] prettyunits_1.1.1         tools_4.1.0               igraph_1.2.6              coda_0.19-4              
 [37] gtable_0.3.0              glue_1.4.2                GenomeInfoDbData_1.2.6    reshape2_1.4.4           
 [41] wk_0.5.0                  gmodels_2.18.1            Rcpp_1.0.7                raster_3.5-2             
 [45] vctrs_0.3.8               spdep_1.1-11              gdata_2.18.0              nlme_3.1-152             
 [49] DelayedMatrixStats_1.14.3 lmtest_0.9-38             xfun_0.25                 stringr_1.4.0            
 [53] ps_1.6.0                  testthat_3.0.4            irlba_2.3.3               lifecycle_1.0.1          
 [57] gtools_3.9.2              devtools_2.4.2            terra_1.4-11              zoo_1.8-9                
 [61] LearnBayes_2.15.1         zlibbioc_1.38.0           MASS_7.3-54               scales_1.1.1             
 [65] expm_0.999-6              RColorBrewer_1.1-2        yaml_2.2.1                curl_4.3.2               
 [69] leidenbase_0.1.3          memoise_2.0.0             gridExtra_2.3             ggplot2_3.3.5            
 [73] Matrix.utils_0.9.8        stringi_1.7.4             desc_1.4.0                e1071_1.7-8              
 [77] boot_1.3-28               pkgbuild_1.2.0            spData_2.0.1              rlang_0.4.11             
 [81] pkgconfig_2.0.3           bitops_1.0-7              evaluate_0.14             lattice_0.20-44          
 [85] purrr_0.3.4               sf_1.0-3                  labeling_0.4.2            processx_3.5.2           
 [89] tidyselect_1.1.1          RcppAnnoy_0.0.19          plyr_1.8.6                R6_2.5.1                 
 [93] generics_0.1.1            DelayedArray_0.18.0       DBI_1.1.1                 pillar_1.6.4             
 [97] withr_2.4.2               units_0.7-2               RCurl_1.98-1.4            sp_1.4-5                 
[101] tibble_3.1.4              crayon_1.4.2              KernSmooth_2.23-20        utf8_1.2.2               
[105] rmarkdown_2.11            viridis_0.6.2             usethis_2.1.3             grid_4.1.0               
[109] callr_3.7.0               digest_0.6.27             classInt_0.4-3            pbmcapply_1.5.0          
[113] tidyr_1.1.3               openssl_1.4.5             munsell_0.5.0             viridisLite_0.4.0        
[117] askpass_1.1               sessioninfo_1.2.1