[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
Hi,
As I pulled down the devel_core image (running boot2docker under OS X
Yosemite)
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
C...
# $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706
tum...
# $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"]]
or
> 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,
Ludwig
--
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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