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.geistlin...@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.geistlin...@bio.ifi.lmu.de > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
