I'm getting an error when trying to load data from AnnotationHub. Here's an example of my code:
library(AnnotationHub)
ah <- AnnotationHub()
dat <- ah[["AH29067"]]
This gives:
Error: failed to load resource
name: AH29067
title: E017-DNase.hotspot.broad.bed.gz
reason: solving row 1: range cannot be determined from the supplied arguments (too many NAs)
This seems to happen for some but not all values of names in ah[["name"]]. My session info is:
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] rtracklayer_1.36.6 GenomicRanges_1.28.6 GenomeInfoDb_1.12.3
[4] IRanges_2.10.5 S4Vectors_0.14.7 AnnotationHub_2.8.3
[7] BiocGenerics_0.22.1 BiocInstaller_1.26.1
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 compiler_3.4.1
[3] XVector_0.16.0 bitops_1.0-6
[5] tools_3.4.1 zlibbioc_1.22.0
[7] digest_0.6.12 bit_1.1-12
[9] BSgenome_1.44.2 lattice_0.20-35
[11] RSQLite_2.0 memoise_1.1.0
[13] tibble_1.3.4 pkgconfig_2.0.1
[15] rlang_0.1.2 Matrix_1.2-10
[17] DelayedArray_0.2.7 shiny_1.0.5
[19] DBI_0.7 curl_3.0
[21] yaml_2.1.14 GenomeInfoDbData_0.99.0
[23] httr_1.3.1 knitr_1.17
[25] Biostrings_2.44.2 grid_3.4.1
[27] bit64_0.9-7 Biobase_2.36.2
[29] R6_2.2.2 AnnotationDbi_1.38.2
[31] BiocParallel_1.10.1 XML_3.98-1.9
[33] blob_1.1.0 matrixStats_0.52.2
[35] GenomicAlignments_1.12.2 Rsamtools_1.28.0
[37] htmltools_0.3.6 SummarizedExperiment_1.6.5
[39] mime_0.5 interactiveDisplayBase_1.14.0
[41] xtable_1.8-2 httpuv_1.3.5
[43] RCurl_1.95-4.8
Does anyone know how to resolve this error? Thanks!
Great, thanks! This does work in the meantime.