Question: ChIPQC error: NCList object is too deep
0
gravatar for nikhil.ashok.joshi
4 months ago by
nikhil.ashok.joshi0 wrote:

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 • 114 views
ADD COMMENTlink modified 3 months ago by Thomas Carroll400 • written 4 months ago by nikhil.ashok.joshi0
Answer: ChIPQC error: NCList object is too deep
0
gravatar for Thomas Carroll
3 months ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:

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

ADD COMMENTlink written 3 months ago by Thomas Carroll400
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 298 users visited in the last hour