ChIPQC error: NCList object is too deep
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Entering edit mode
@nikhilashokjoshi-19417
Last seen 18 months ago

I am getting this error after calling "ChIPQCsample" on one of my samples. It works for most of them, but for 4 of the samples it produces this error. I found this post with the same problem, but it doesn't look like a solution was found (or if it was, it wasn't implemented). Any help would be appreciated.

  • Nik.
Error in .Call2("new_NCListAsINTSXP_from_NCList", nclist_xp, PACKAGE = "IRanges") : 
  compute_NCListAsINTSXP_length: NCList object is too deep (has more than
  100000 levels of nested ranges)
Calls: ChIPQCsample ... lapply -> lapply -> lapply -> FUN -> .nclist -> .Call2
Execution halted

SESSIONINFO:
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so

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

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

other attached packages:
 [1] ChIPQC_1.18.0               DiffBind_2.10.0            
 [3] SummarizedExperiment_1.10.1 DelayedArray_0.6.5         
 [5] BiocParallel_1.14.2         matrixStats_0.54.0         
 [7] Biobase_2.40.0              GenomicRanges_1.32.6       
 [9] GenomeInfoDb_1.16.0         IRanges_2.14.10            
[11] S4Vectors_0.18.3            BiocGenerics_0.26.0        
[13] ggplot2_3.0.0              

loaded via a namespace (and not attached):
  [1] amap_0.8-16                              
  [2] colorspace_1.3-2                         
  [3] rjson_0.2.20                             
  [4] hwriter_1.3.2                            
  [5] XVector_0.20.0                           
  [6] base64enc_0.1-3                          
  [7] ggrepel_0.8.0                            
  [8] bit64_0.9-7                              
  [9] AnnotationDbi_1.44.0                     
 [10] splines_3.5.0                            
 [11] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2  
 [12] Nozzle.R1_1.1-1                          
 [13] Rsamtools_1.34.0                         
 [14] annotate_1.58.0                          
 [15] GO.db_3.7.0                              
 [16] pheatmap_1.0.12                          
 [17] graph_1.60.0                             
 [18] TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2  
 [19] compiler_3.5.0                           
 [20] httr_1.3.1                               
 [21] GOstats_2.48.0                           
 [22] backports_1.1.2                          
 [23] assertthat_0.2.0                         
 [24] Matrix_1.2-14                            
 [25] lazyeval_0.2.1                           
 [26] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  
 [27] limma_3.36.2                             
 [28] prettyunits_1.0.2                        
 [29] tools_3.5.0                              
 [30] bindrcpp_0.2.2                           
 [31] gtable_0.2.0                             
 [32] glue_1.3.0                               
 [33] GenomeInfoDbData_1.1.0                   
 [34] Category_2.48.0                          
 [35] reshape2_1.4.3                           
 [36] systemPipeR_1.16.1                       
 [37] dplyr_0.7.6                              
 [38] ShortRead_1.40.0                         
 [39] Rcpp_0.12.18                             
 [40] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
 [41] TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2  
 [42] Biostrings_2.48.0                        
 [43] gdata_2.18.0                             
 [44] rtracklayer_1.40.4                       
 [45] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4 
 [46] stringr_1.3.1                            
 [47] gtools_3.8.1                             
 [48] XML_3.98-1.15                            
 [49] edgeR_3.22.3                             
 [50] zlibbioc_1.26.0                          
 [51] scales_1.0.0                             
 [52] hms_0.4.2                                
 [53] RBGL_1.58.1                              
 [54] RColorBrewer_1.1-2                       
 [55] BBmisc_1.11                              
 [56] memoise_1.1.0                            
 [57] biomaRt_2.36.1                           
 [58] latticeExtra_0.6-28                      
 [59] stringi_1.2.4                            
 [60] RSQLite_2.1.1                            
 [61] genefilter_1.62.0                        
 [62] checkmate_1.8.5                          
 [63] GenomicFeatures_1.34.1                   
 [64] caTools_1.17.1.1                         
 [65] chipseq_1.32.0                           
 [66] rlang_0.2.2                              
 [67] pkgconfig_2.0.2                          
 [68] BatchJobs_1.7                            
 [69] bitops_1.0-6                             
 [70] TxDb.Celegans.UCSC.ce6.ensGene_3.2.2     
 [71] lattice_0.20-35                          
 [72] purrr_0.2.5                              
 [73] bindr_0.1.1                              
 [74] GenomicAlignments_1.16.0                 
 [75] bit_1.1-14                               
 [76] tidyselect_0.2.4                         
 [77] GSEABase_1.44.0                          
 [78] AnnotationForge_1.24.0                   
 [79] plyr_1.8.4                               
 [80] magrittr_1.5                             
 [81] sendmailR_1.2-1                          
 [82] R6_2.2.2                                 
 [83] gplots_3.0.1                             
 [84] DBI_1.0.0                                
 [85] pillar_1.3.0                             
 [86] withr_2.1.2                              
 [87] survival_2.42-6                          
 [88] RCurl_1.95-4.11                          
 [89] tibble_1.4.2                             
 [90] crayon_1.3.4                             
 [91] KernSmooth_2.23-15                       
 [92] progress_1.2.0                           
 [93] locfit_1.5-9.1                           
 [94] grid_3.5.0                               
 [95] data.table_1.11.4                        
 [96] blob_1.1.1                               
 [97] Rgraphviz_2.26.0                         
 [98] digest_0.6.15                            
 [99] xtable_1.8-2                             
[100] brew_1.0-6                               
[101] munsell_0.5.0 
ChIPQC • 365 views
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Entering edit mode
@thomas-carroll-7019
Last seen 13 months ago
United States/New York/The Rockefeller …

hi Nik,

Sorry, this was fixed in release and not in development branch. I have fixed in release and development last night and it should be available in release version 1.18.1 now.

best,

tom

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