Entering edit mode
zhezhen
•
0
@zhezhen-21686
Last seen 4.8 years ago
I am using R/3.6.1 and GenomicRanges/1.38.0 and for some reason, I am not able to create a GRanges object anymore starting last Monday. I have tried removing the package and reinstall but it still shows the same error.
x1 <- "chr2:56-125"
as(x1, "GRanges")
GRanges object with 1 range and 0 metadata columns:
Error in getListElement(x, i, ...) : IRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
gr0 <- GRanges(Rle(c("chr2", "chr2", "chr1", "chr3"), c(1, 3, 2, 4)), IRanges(1:10, width=10:1))
gr0
GRanges object with 10 ranges and 0 metadata columns:
Error in getListElement(x, i, ...) : IRanges objects don't support [[, as.list(), lapply(), or unlist() at the moment
sessionInfo( )
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPpeakAnno_3.20.0 VennDiagram_1.6.20 futile.logger_1.4.3 Biostrings_2.54.0
[5] XVector_0.26.0 nucleR_2.18.4 rtracklayer_1.46.0 GenomicRanges_1.38.0
[9] GenomeInfoDb_1.22.0 IRanges_2.20.0 S4Vectors_0.24.4 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] colorspace_1.4-1 seqinr_4.2-4 hwriter_1.3.2
[4] ellipsis_0.3.0 htmlTable_1.13.2 base64enc_0.1-3
[7] rstudioapi_0.10 bit64_0.9-7 AnnotationDbi_1.48.0
[10] splines_3.6.1 geneplotter_1.64.0 knitr_1.26
[13] ade4_1.7-13 Formula_1.2-3 Rsamtools_2.2.1
[16] annotate_1.64.0 cluster_2.1.0 GO.db_3.10.0
[19] dbplyr_1.4.2 graph_1.64.0 BiocManager_1.30.9
[22] compiler_3.6.1 httr_1.4.1 backports_1.1.5
[25] assertthat_0.2.1 Matrix_1.2-17 lazyeval_0.2.2
[28] limma_3.42.0 formatR_1.7 acepack_1.4.1
[31] htmltools_0.4.0 prettyunits_1.0.2 tools_3.6.1
[34] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.2
[37] dplyr_1.0.2 rappdirs_0.3.1 ShortRead_1.44.3
[40] Rcpp_1.0.3 Biobase_2.46.0 vctrs_0.3.2
[43] multtest_2.42.0 xfun_0.11 stringr_1.4.0
[46] lifecycle_0.2.0 ensembldb_2.10.2 XML_3.98-1.20
[49] idr_1.2 zlibbioc_1.32.0 MASS_7.3-51.4
[52] scales_1.1.1 BSgenome_1.54.0 ProtGenerics_1.18.0
[55] hms_0.5.2 SummarizedExperiment_1.16.0 RBGL_1.62.1
[58] AnnotationFilter_1.10.0 lambda.r_1.2.4 RColorBrewer_1.1-2
[61] curl_4.2 memoise_1.1.0 gridExtra_2.3
[64] ggplot2_3.3.2 biomaRt_2.42.0 rpart_4.1-15
[67] latticeExtra_0.6-28 stringi_1.4.3 RSQLite_2.1.2
[70] genefilter_1.68.0 checkmate_1.9.4 GenomicFeatures_1.38.1
[73] BiocParallel_1.20.0 rlang_0.4.7 pkgconfig_2.0.3
[76] matrixStats_0.55.0 bitops_1.0-6 lattice_0.20-38
[79] purrr_0.3.3 GenomicAlignments_1.22.1 htmlwidgets_1.5.1
[82] bit_1.1-14 tidyselect_1.1.0 magrittr_1.5
[85] DESeq2_1.26.0 R6_2.4.1 generics_0.0.2
[88] Hmisc_4.3-0 DelayedArray_0.12.3 DBI_1.0.0
[91] pillar_1.4.6 foreign_0.8-71 survival_2.44-1.1
[94] RCurl_1.95-4.12 nnet_7.3-12 tibble_3.0.3
[97] crayon_1.3.4 futile.options_1.0.1 BiocFileCache_1.10.2
[100] progress_1.2.2 locfit_1.5-9.1 data.table_1.12.6
[103] blob_1.2.0 digest_0.6.22 xtable_1.8-4
[106] regioneR_1.18.1 openssl_1.4.1 munsell_0.5.0
[109] askpass_1.1
