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

[Vincent Carey]

Please provide sessionInfo()

The class is defined in AnnotationHub in devel.  Perhaps it is not suitably
exported.

On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:

> 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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