Hi....
During my coursera course, Bioconductor for Genomic Data Science , I've found out the below issue which seems to be a bug.
I can't download UCSC 'refGene'.
1. Below is the error message.
> ah <- AnnotationHub()
> ah <- subset(ah, species == "Homo sapiens")
> qhs <- query(ah, "RefSeq")
> qhs
AnnotationHub with 8 records
# snapshotDate(): 2015-08-26
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description, tags, sourceurl,
# sourcetype
# retrieve records with, e.g., 'object[["AH5040"]]'
title
AH5040 | RefSeq Genes
AH5041 | Other RefSeq
AH5155 | RefSeq Genes
AH5156 | Other RefSeq
AH5306 | RefSeq Genes
AH5307 | Other RefSeq
AH5431 | RefSeq Genes
AH5432 | Other RefSeq
> genes <- qhs[qhs$genome == "hg19" & qhs$title == "RefSeq Genes"]
> genes
AnnotationHub with 1 record
# snapshotDate(): 2015-08-26
# names(): AH5040
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# $title: RefSeq Genes
# $description: GRanges object from UCSC track 'RefSeq Genes'
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: UCSC track
# $sourceurl: rtracklayer://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/re
# $sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: refGene, UCSC, track, Gene, Transcript, Annotation
# retrieve record with 'object[["AH5040"]]'
> genes <- qhs[[1]]
Error in value[[3L]](cond) :
failed to load hub resource ‘RefSeq Genes’ of class GRanges; reason: bad
restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘5040’ has magic number '<meta'
Use of save versions prior to 2 is deprecated
> genes = qhs[[2]]
retrieving 1 resources
|==========================================================================================| 100%
There were 50 or more warnings (use warnings() to see the first 50)
> genes
UCSC track 'xenoRefGene'
UCSCData object with 161800 ranges and 5 metadata columns:
2. Below is the sessionInfo() for reference.
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
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 methods base
other attached packages:
[1] BiocInstaller_1.18.4 AnnotationHub_2.0.3 rtracklayer_1.28.10 GenomicRanges_1.20.6
[5] GenomeInfoDb_1.4.2 IRanges_2.2.7 S4Vectors_0.6.5 BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.0 AnnotationDbi_1.30.1 XVector_0.8.0
[4] magrittr_1.5 zlibbioc_1.14.0 GenomicAlignments_1.4.1
[7] BiocParallel_1.2.21 xtable_1.7-4 R6_2.1.1
[10] stringr_1.0.0 httr_1.0.0 tools_3.2.1
[13] Biobase_2.28.0 DBI_0.3.1 lambda.r_1.1.7
[16] futile.logger_1.4.1 htmltools_0.2.6 digest_0.6.8
[19] interactiveDisplayBase_1.6.0 shiny_0.12.2 futile.options_1.0.0
[22] bitops_1.0-6 curl_0.9.3 RCurl_1.95-4.7
[25] mime_0.4 RSQLite_1.0.0 stringi_0.5-5
[28] Biostrings_2.36.4 Rsamtools_1.20.4 XML_3.98-1.3
[31] httpuv_1.3.3
Smiles