I am failing to load ENCODE RNAseq expression data with after downloading via AnnotationHub.
library(AnnotationHub) ah = AnnotationHub() dm <- query(ah, c("EncodeDCC", "Homo sapiens")) dm["AH1376"]
AnnotationHub with 1 record
# snapshotDate(): 2016-11-15
# names(): AH1376
# $dataprovider: EncodeDCC
# $species: Homo sapiens
# $rdataclass: GRanges
# $title: wgEncodeCshlLongRnaSeqHelas3CellPapGeneGencV7
# $description:
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: BED
# $sourceurl: http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeCshlLongRnaSeq/wgEncodeCshlLo...
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: c("011WC,012WC", "HeLa-S3", "wgEncodeCshlLongRnaSeq", "RnaSeq", "ENCODE Mar 2012 Freeze",
# "2011-07-13", "2012-04-13", "wgEncodeEH000173", "GSM765402", "Gingeras", "CSHL",
# "LID16633,LID16634", "iIDR", "cell", "9b6a25c6c8e577edf94e8a28f41f0f3a", "wgEncode", "2x76D",
# "longPolyA", "Illumina_GA2x", "2e+06", "Nist14", "4583", "gtf", "GeneGencV7")
# retrieve record with 'object[["AH1376"]]'
out <- dm[["AH1376"]]
require(“GenomicRanges”)
downloading from ‘https://annotationhub.bioconductor.org/fetch/1376’
retrieving 1 resource
|======================================================================================================| 100%
Error: failed to load resource
name: AH1376
title: wgEncodeCshlLongRnaSeqHelas3CellPapGeneGencV7
reason: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘1376’ has magic number 'chr16'
Use of save versions prior to 2 is deprecated
sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicRanges_1.26.1 GenomeInfoDb_1.10.1 IRanges_2.8.1 S4Vectors_0.12.0 AnnotationHub_2.6.1
[6] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.7 digest_0.6.10 mime_0.5
[4] R6_2.2.0 xtable_1.8-2 DBI_0.5-1
[7] RSQLite_1.0.0 BiocInstaller_1.24.0 httr_1.2.1
[10] zlibbioc_1.20.0 XVector_0.14.0 curl_2.2
[13] Biobase_2.34.0 shiny_0.14.2 httpuv_1.3.3
[16] AnnotationDbi_1.36.0 htmltools_0.3.5 interactiveDisplayBase_1.12.0
Is there a known problem here or have I missed something essential? Thanks in advance for any help you can offer!
Thanks for posting this bug. We are looking into it.
Valerie