cannot create GRanges object anymore
0
Entering edit mode
zhezhen • 0
@zhezhen-21686
Last seen 6 days 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
GenomicR GenomicRanges • 42 views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

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