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@nikhilashokjoshi-19417
Last seen 4.3 years 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
