Here you go ... > sessionInfo() R Under development (unstable) (2015-03-09 r67969) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie)
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationHub_1.99.72 BiocInstaller_1.17.5 loaded via a namespace (and not attached): [1] Rcpp_0.11.5 IRanges_2.1.43 [3] digest_0.6.8 bitops_1.0-6 [5] mime_0.2 GenomeInfoDb_1.3.13 [7] R6_2.0.1 xtable_1.7-4 [9] DBI_0.3.1 stats4_3.2.0 [11] RSQLite_1.0.0 httr_0.6.1 [13] S4Vectors_0.5.22 RJSONIO_1.3-0 [15] stringr_0.6.2 Biobase_2.27.2 [17] RCurl_1.95-4.5 shiny_0.11.1 [19] httpuv_1.3.2 parallel_3.2.0 [21] BiocGenerics_0.13.6 AnnotationDbi_1.29.17 [23] htmltools_0.2.6 interactiveDisplayBase_1.5.1 > 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 >> âRNA-Sequencing and clinical data for 7706 tumor samples from The >> Cancer Genome Atlasâ of class ExpressionSet; reason: >> âExpressionSetResourceâ 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 >> > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
