[Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Thu Apr 9 11:33:20 CEST 2015


As I pulled down the devel_core image (running boot2docker under OS X

docker run -ti bioconductor/release_core R

and then executed

> library(AnnotationHub)
> hub <- AnnotationHub()

and selected the recently integrated GSE62944 TCGA dataset (announced in
the latest BioC newsletter, April 2015)

> h <- hub[hub$rdataclass == "ExpressionSet"]
> h
AnnotationHub with 1 record
# snapshotDate(): 2015-03-26
# names(): AH28855
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: ExpressionSet
# $title: RNA-Sequencing and clinical data for 7706 tumor samples from The
# $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 #
$sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: TCGA, RNA-seq, Expression, Count
# retrieve record with 'object[["AH28855"]]'

and then tried to retrieve the record with either

> h[["AH28855"]]


> h[[1]]

I received the following error:

Error in value[[3L]](cond) :
  failed to create a 'AnnotationHubResource' instance for hub resource
    ‘RNA-Sequencing and clinical data for 7706 tumor samples from The
    Cancer Genome Atlas’ of class ExpressionSet; reason:
    “ExpressionSetResource” is not a defined class

Did I do something wrong?
Thank you for your help,

Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de

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