Off topic:Usecase_AnnotationHub_GRanges.Rmd, genes = qhs[[1]] can't download UCSC 'refGene'. - Window 7, R 3.2.1, RStudio 0.99.484
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J.C. SUN • 0
@jc-sun
Last seen 3.0 years ago
Korea, Republic Of

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

annotationhub bioconductor for genomic data science • 799 views
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