Hello,
Whenever I try to use getSeq from the BSGenome package to fetch a sequence i get this error:
getSeq(BSgenome.Hsapiens.UCSC.hg19,"chr7")
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains NAs or out-of-bounds indices
sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)
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] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.38.0 Biostrings_2.38.1 XVector_0.10.0
[5] biomaRt_2.26.0 rtracklayer_1.30.1 GenomicRanges_1.22.1 GenomeInfoDb_1.6.1
[9] IRanges_2.4.2 S4Vectors_0.8.3 BiocGenerics_0.16.1 reshape2_1.4.1
[13] ggplot2_1.0.1 shiny_0.12.2 BiocInstaller_1.20.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.2 futile.logger_1.4.1 plyr_1.8.3 futile.options_1.0.0 bitops_1.0-6 tools_3.2.2
[7] zlibbioc_1.16.0 digest_0.6.8 RSQLite_1.0.0 gtable_0.1.2 DBI_0.3.1 proto_0.3-10
[13] stringr_1.0.0 grid_3.2.2 Biobase_2.30.0 R6_2.1.1 AnnotationDbi_1.32.0 XML_3.98-1.3
[19] BiocParallel_1.4.0 lambda.r_1.1.7 magrittr_1.5 GenomicAlignments_1.6.1 scales_0.3.0 Rsamtools_1.22.0
[25] htmltools_0.2.6 MASS_7.3-45 SummarizedExperiment_1.0.1 mime_0.4 xtable_1.8-0 colorspace_1.2-6
[31] httpuv_1.3.3 stringi_1.0-1 RCurl_1.95-4.7 munsell_0.4.2
Actually, this happens also to other use cases of
getSeq
(the code below is taken fromGenomicFeatures
extractTranscriptSeqs
help page):Eventually this is caused by some updated package. I remember I did a package update today, but I can't remember which packages got updated (IRanges?).
Did you also update your packages recently?
cheers, jo
My session info: