Error reading bam files with getCounts after updating R
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tsourkas • 0
@ca6ba0a4
Last seen 2 days ago
United States

I recently updated R and am now getting an error when trying to read in bam files with getCounts. Prior to updating there were no issues with reading bam files. My code is as follows:

getCounts(bamFile, masterPeak, paired = TRUE, by_rg = FALSE, format = "bam")

The error message is:
Error in unlist_as_integer(x@subscript) : object 'fancy_mseq' not found

The traceback is:
23: unlist_as_integer(x@subscript)
22: .local(x, ...)
21: as.integer(i)
20: as.integer(i)
19: normalizeSingleBracketSubscript(i, x, allow.NAs = TRUE, allow.append = TRUE)
18: extractROWS(x@unlistData, idx_on_unlisted_x)
17: extractROWS(x@unlistData, idx_on_unlisted_x)
16: extractROWS(x, i)
15: extractROWS(x, i)
14: subset_along_ROWS(x, i, drop = drop)
13: .extract_groups_from_GenomicRanges(query)[q_group_idx]
12: .extract_groups_from_GenomicRanges(query)[q_group_idx]
11: findOverlaps_GNCList(query, subject, maxgap = maxgap, minoverlap = minoverlap, 
        type = type, select = select, ignore.strand = ignore.strand)
10: .local(query, subject, maxgap, minoverlap, type, select, ...)
9: findOverlaps(query, unlisted_subject, maxgap = maxgap, type = type, 
       select = "all", ignore.strand = ignore.strand)
8: findOverlaps(query, unlisted_subject, maxgap = maxgap, type = type, 
       select = "all", ignore.strand = ignore.strand)
7: .local(query, subject, maxgap, minoverlap, type, select, ...)
6: findOverlaps(query, subject, maxgap = maxgap, minoverlap = minoverlap, 
       type = type, ...)
5: findOverlaps(query, subject, maxgap = maxgap, minoverlap = minoverlap, 
       type = type, ...)
4: countOverlaps(peaks, fragments, type = "any", ignore.strand = TRUE)
3: countOverlaps(peaks, fragments, type = "any", ignore.strand = TRUE)
2: get_counts_from_bams(alignment_files, peaks, paired, by_rg, colData)
1: getCounts(bamFile, masterPeak, paired = TRUE, by_rg = FALSE, 
       format = "bam")

and the session info is:
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

time zone: America/Chicago
tzcode source: internal

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

other attached packages:
 [1] dplyr_1.1.3                             TxDb.Drerio.UCSC.danRer11.refGene_3.4.6
 [3] GenomicFeatures_1.54.2                  AnnotationDbi_1.64.1                   
 [5] ChIPseeker_1.26.2                       clusterProfiler_4.10.0                 
 [7] readr_2.1.5                             readxl_1.4.3                           
 [9] FusionExpressionPlot_0.1.2.9000         NMF_0.30.1                             
[11] cluster_2.1.6                           rngtools_1.5.2                         
[13] pkgmaker_0.32.10                        registry_0.5-1                         
[15] vioplot_0.4.0                           zoo_1.8-12                             
[17] sm_2.2-5.7.1                            corrplot_0.92                          
[19] ggpubr_0.6.0                            DESeq2_1.42.0                          
[21] SummarizedExperiment_1.32.0             Biobase_2.50.0                         
[23] MatrixGenerics_1.14.0                   matrixStats_1.2.0                      
[25] chromVAR_1.24.0                         GenomicRanges_1.42.0                   
[27] GenomeInfoDb_1.38.5                     IRanges_2.24.1                         
[29] S4Vectors_0.40.2                        BiocGenerics_0.48.1                    
[31] viridis_0.6.5                           viridisLite_0.4.2                      
[33] ggplot2_3.4.4                           stringr_1.5.1                          

loaded via a namespace (and not attached):
  [1] fs_1.6.3                                bitops_1.0-6                           
  [3] enrichplot_1.22.0                       DirichletMultinomial_1.44.0            
  [5] TFBSTools_1.40.0                        HDO.db_0.99.1                          
  [7] httr_1.4.7                              RColorBrewer_1.1-3                     
  [9] doParallel_1.0.17                       tools_4.3.2                            
 [11] backports_1.4.1                         utf8_1.2.3                             
 [13] R6_2.5.1                                DT_0.31                                
 [15] lazyeval_0.2.2                          withr_3.0.0                            
 [17] prettyunits_1.2.0                       gridExtra_2.3                          
 [19] cli_3.6.1                               scatterpie_0.2.1                       
 [21] Rsamtools_2.6.0                         yulab.utils_0.1.4                      
 [23] gson_0.1.0                              DOSE_3.28.2                            
 [25] R.utils_2.12.3                          parallelly_1.36.0                      
 [27] plotrix_3.8-4                           BSgenome_1.70.1                        
 [29] rstudioapi_0.15.0                       RSQLite_2.2.8                          
 [31] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 generics_0.1.3                         
 [33] gridGraphics_0.5-1                      RApiSerialize_0.1.2                    
 [35] BiocIO_1.12.0                           vroom_1.6.5                            
 [37] gtools_3.9.4                            car_3.1-2                              
 [39] dendextend_1.17.1                       GO.db_3.12.1                           
 [41] Matrix_1.6-1.1                          fansi_1.0.4                            
 [43] abind_1.4-5                             R.methodsS3_1.8.2                      
 [45] lifecycle_1.0.4                         yaml_2.3.7                             
 [47] snakecase_0.11.1                        carData_3.0-5                          
 [49] gplots_3.1.3                            BiocFileCache_2.10.1                   
 [51] qvalue_2.34.0                           SparseArray_1.2.3                      
 [53] grid_4.3.2                              blob_1.2.4                             
 [55] promises_1.2.1                          crayon_1.5.2                           
 [57] miniUI_0.1.1.1                          lattice_0.21-9                         
 [59] annotate_1.80.0                         KEGGREST_1.42.0                        
 [61] pillar_1.9.0                            knitr_1.45                             
 [63] fgsea_1.16.0                            boot_1.3-28.1                          
 [65] rjson_0.2.21                            codetools_0.2-19                       
 [67] fastmatch_1.1-4                         glue_1.6.2                             
 [69] ggfun_0.1.4                             data.table_1.14.8                      
 [71] vctrs_0.6.3                             png_0.1-8                              
 [73] treeio_1.26.0                           cellranger_1.1.0                       
 [75] gtable_0.3.4                            poweRlaw_0.80.0                        
 [77] assertthat_0.2.1                        cachem_1.0.6                           
 [79] xfun_0.41                               S4Arrays_1.2.0                         
 [81] mime_0.12                               tidygraph_1.2.1                        
 [83] pracma_2.4.4                            iterators_1.0.14                       
 [85] tinytex_0.49                            interactiveDisplayBase_1.40.0          
 [87] ellipsis_0.3.2                          nlme_3.1-164                           
 [89] ggtree_3.10.0                           bit64_4.0.5                            
 [91] progress_1.2.3                          filelock_1.0.3                         
 [93] KernSmooth_2.23-22                      colorspace_2.1-0                       
 [95] seqLogo_1.68.0                          DBI_1.2.1                              
 [97] tidyselect_1.2.0                        curl_5.0.2                             
 [99] bit_4.0.4                               compiler_4.3.2                         
[101] xml2_1.3.5                              DelayedArray_0.28.0                    
[103] plotly_4.10.4                           shadowtext_0.1.3                       
[105] stringfish_0.15.8                       rtracklayer_1.62.0                     
[107] scales_1.3.0                            caTools_1.18.2                         
[109] rappdirs_0.3.3                          digest_0.6.33                          
[111] XVector_0.30.0                          htmltools_0.5.7                        
[113] pkgconfig_2.0.3                         dbplyr_2.4.0                           
[115] fastmap_1.1.1                           rlang_1.1.1                            
[117] htmlwidgets_1.6.4                       shiny_1.8.0                            
[119] farver_2.1.1                            jsonlite_1.8.8                         
[121] BiocParallel_1.24.1                     GOSemSim_2.28.1                        
[123] R.oo_1.26.0                             RCurl_1.98-1.2                         
[125] magrittr_2.0.3                          GenomeInfoDbData_1.2.11                
[127] ggplotify_0.1.2                         patchwork_1.2.0                        
[129] munsell_0.5.0                           Rcpp_1.0.7                             
[131] ape_5.7-1                               stringi_1.7.12                         
[133] ggraph_2.0.5                            zlibbioc_1.36.0                        
[135] MASS_7.3-60                             AnnotationHub_3.10.0                   
[137] plyr_1.8.8                              DO.db_2.9                              
[139] parallel_4.3.2                          listenv_0.9.1                          
[141] ggrepel_0.9.3                           CNEr_1.38.0                            
[143] Biostrings_2.58.0                       graphlayouts_0.8.0                     
[145] splines_4.3.2                           hms_1.1.3                              
[147] locfit_1.5-9.8                          igraph_1.3.0                           
[149] ggsignif_0.6.4                          biomaRt_2.58.2                         
[151] reshape2_1.4.4                          TFMPvalue_0.0.9                        
[153] BiocVersion_3.18.1                      XML_3.99-0.8                           
[155] evaluate_0.23                           RcppParallel_5.1.7                     
[157] BiocManager_1.30.22                     tzdb_0.4.0                             
[159] foreach_1.5.2                           tweenr_1.0.2                           
[161] httpuv_1.6.14                           tidyr_1.3.1                            
[163] purrr_1.0.2                             polyclip_1.10-4                        
[165] qs_0.25.5                               future_1.33.1                          
[167] gridBase_0.4-7                          ggforce_0.3.3                          
[169] broom_1.0.5                             xtable_1.8-4                           
[171] restfulr_0.0.15                         tidytree_0.4.6                         
[173] rstatix_0.7.2                           later_1.3.2                            
[175] tibble_3.2.1                            aplot_0.2.2                            
[177] memoise_2.0.1                           GenomicAlignments_1.26.0               
[179] globals_0.16.2

Thank you.

chromVAR chrom • 78 views
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