cannot create GRanges object anymore
Entering edit mode
zhezhen • 0
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))
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

[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
Entering edit mode
Last seen 2 days ago
United States

There is no support offered for non-release versions. Please upgrade to R-4.0.3 and the current release version of Bioconductor.

Login before adding your answer.

Similar Posts
Loading Similar Posts
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.3