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cole-trapnell-lab / cicero

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Stuck on SimpleList error #12

Closed Austin-s-h closed 3 years ago

Austin-s-h commented 3 years ago

Hi! I think there was a major structural change to S4Vectors with R 4.0. I haven't encountered this error before. Could you help me track down what is going wrong? This was left running for 48 hours without any error or crash, but no progress as far as I can tell.

conns <- run_cicero(cicero_obj,
                           genomic_coords = genomic_lengths_hg38,
                           sample_num = 100)

Error in get(as.character(FUN), mode = "function", envir = envir) : object 'as.SimpleList' of mode 'function' was not found

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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       

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

other attached packages:
 [1] Rcpp_1.0.5                           ensembldb_2.14.0                    
 [3] AnnotationFilter_1.14.0              GenomicFeatures_1.42.1              
 [5] AnnotationDbi_1.52.0                 dplyr_1.0.2                         
 [7] AnnotationHub_2.20.2                 BiocFileCache_1.14.0                
 [9] dbplyr_2.0.0                         cicero_1.3.4.11                     
[11] Gviz_1.34.0                          monocle3_0.2.3.3                    
[13] SingleCellExperiment_1.10.1          SummarizedExperiment_1.20.0         
[15] MatrixGenerics_1.2.0                 matrixStats_0.57.0                  
[17] Biobase_2.50.0                       patchwork_1.1.0                     
[19] SeuratWrappers_0.3.0                 future_1.21.0                       
[21] stringr_1.4.0                        plotly_4.9.2.1                      
[23] ggplot2_3.3.2                        cowplot_1.1.0                       
[25] BSgenome.Ggallus.ENSEMBL.galGal6_0.1 BSgenome_1.58.0                     
[27] rtracklayer_1.50.0                   Biostrings_2.58.0                   
[29] XVector_0.30.0                       GenomicRanges_1.42.0                
[31] GenomeInfoDb_1.26.2                  IRanges_2.24.1                      
[33] S4Vectors_0.28.1                     BiocGenerics_0.36.0                 
[35] Signac_1.1.0                         Seurat_3.2.2                        

loaded via a namespace (and not attached):
  [1] reticulate_1.18               tidyselect_1.1.0             
  [3] RSQLite_2.2.1                 htmlwidgets_1.5.3            
  [5] BiocParallel_1.24.1           Rtsne_0.15                   
  [7] munsell_0.5.0                 codetools_0.2-16             
  [9] ica_1.0-2                     chron_2.3-56                 
 [11] miniUI_0.1.1.1                withr_2.3.0                  
 [13] colorspace_2.0-0              OrganismDbi_1.30.0           
 [15] knitr_1.30                    rstudioapi_0.13              
 [17] ROCR_1.0-11                   tensor_1.5                   
 [19] listenv_0.8.0                 GenomeInfoDbData_1.2.4       
 [21] polyclip_1.10-0               pheatmap_1.0.12              
 [23] bit64_4.0.5                   farver_2.0.3                 
 [25] parallelly_1.22.0             vctrs_0.3.5                  
 [27] generics_0.1.0                xfun_0.19                    
 [29] biovizBase_1.38.0             lsa_0.73.2                   
 [31] ggseqlogo_0.1                 R6_2.5.0                     
 [33] RcppEigen_0.3.3.7.0           rsvd_1.0.3                   
 [35] VGAM_1.1-4                    RcppArmadillo_0.10.1.2.0     
 [37] bitops_1.0-6                  spatstat.utils_1.17-0        
 [39] reshape_0.8.8                 DelayedArray_0.16.0          
 [41] assertthat_0.2.1              promises_1.1.1               
 [43] scales_1.1.1                  nnet_7.3-14                  
 [45] gtable_0.3.0                  globals_0.14.0               
 [47] goftest_1.2-2                 ggbio_1.36.0                 
 [49] rlang_0.4.9                   RcppRoll_0.3.0               
 [51] splines_4.0.2                 lazyeval_0.2.2               
 [53] dichromat_2.0-0               checkmate_2.0.0              
 [55] yaml_2.2.1                    BiocManager_1.30.10          
 [57] reshape2_1.4.4                abind_1.4-5                  
 [59] backports_1.2.1               httpuv_1.5.4                 
 [61] Hmisc_4.4-2                   RBGL_1.64.0                  
 [63] tools_4.0.2                   qdapTools_1.3.5              
 [65] ellipsis_0.3.1                RColorBrewer_1.1-2           
 [67] ggridges_0.5.2                plyr_1.8.6                   
 [69] base64enc_0.1-3               progress_1.2.2               
 [71] zlibbioc_1.36.0               purrr_0.3.4                  
 [73] RCurl_1.98-1.2                prettyunits_1.1.1            
 [75] rpart_4.1-15                  openssl_1.4.3                
 [77] deldir_0.2-3                  viridis_0.5.1                
 [79] pbapply_1.4-3                 zoo_1.8-8                    
 [81] ggrepel_0.8.2                 cluster_2.1.0                
 [83] tinytex_0.27                  magrittr_2.0.1               
 [85] data.table_1.13.4             lmtest_0.9-38                
 [87] RANN_2.6.1                    SnowballC_0.7.0              
 [89] ProtGenerics_1.22.0           fitdistrplus_1.1-3           
 [91] evaluate_0.14                 hms_0.5.3                    
 [93] mime_0.9                      xtable_1.8-4                 
 [95] XML_3.99-0.5                  jpeg_0.1-8.1                 
 [97] gridExtra_2.3                 compiler_4.0.2               
 [99] biomaRt_2.46.0                tibble_3.0.4                 
[101] KernSmooth_2.23-17            crayon_1.3.4                 
[103] htmltools_0.5.0               mgcv_1.8-31                  
[105] later_1.1.0.1                 Formula_1.2-4                
[107] tidyr_1.1.2                   DBI_1.1.0                    
[109] tweenr_1.0.1                  MASS_7.3-51.6                
[111] rappdirs_0.3.1                readr_1.4.0                  
[113] Matrix_1.2-18                 igraph_1.2.6                 
[115] pkgconfig_2.0.3               GenomicAlignments_1.26.0     
[117] foreign_0.8-80                xml2_1.3.2                   
[119] VariantAnnotation_1.36.0      digest_0.6.27                
[121] sctransform_0.3.1             RcppAnnoy_0.0.17             
[123] graph_1.66.0                  spatstat.data_1.5-2          
[125] rmarkdown_2.5                 leiden_0.3.6                 
[127] fastmatch_1.1-0               htmlTable_2.1.0              
[129] uwot_0.1.9                    curl_4.3                     
[131] shiny_1.5.0                   Rsamtools_2.6.0              
[133] glasso_1.11                   lifecycle_0.2.0              
[135] nlme_3.1-148                  jsonlite_1.7.2               
[137] viridisLite_0.3.0             askpass_1.1                  
[139] pillar_1.4.7                  lattice_0.20-41              
[141] GGally_2.0.0                  fastmap_1.0.1                
[143] httr_1.4.2                    survival_3.1-12              
[145] interactiveDisplayBase_1.26.3 remotes_2.2.0                
[147] glue_1.4.2                    FNN_1.1.3                    
[149] spatstat_1.64-1               png_0.1-7                    
[151] BiocVersion_3.11.1            bit_4.0.4                    
[153] ggforce_0.3.2                 stringi_1.5.3                
[155] blob_1.2.1                    latticeExtra_0.6-29          
[157] memoise_1.1.0                 irlba_2.3.3                  
[159] future.apply_1.6.0
hpliner commented 3 years ago

Hi Austin, The checks are currently running on R 4.0.2 with no problems. Can you try restarting your R session, loading only cicero and monocle3 and running again? You have a lot going on in your sessionInfo which makes it tough to narrow down the trouble. In addition, do you run into the same problem with the example dataset as described on the website? https://cole-trapnell-lab.github.io/cicero-release/docs_m3/#abstract

hpliner commented 3 years ago

I'm going to close, reopen if this remains an issue