[Bioc-devel] AnnotationHub: ExpressionSetResource Error in Docker devel_core
Ludwig Geistlinger
Ludwig.Geistlinger at bio.ifi.lmu.de
Thu Apr 9 14:57:47 CEST 2015
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.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
>> 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.Geistlinger at bio.ifi.lmu.de
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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