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

[Martin Morgan]

On 04/09/2015 05:57 AM, Ludwig Geistlinger wrote:
> 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

Yes, this should be AnnotationHub 1.99.81. Should be installed with

   BiocInstaller::biocLite("AnnotationHub")

You can check that status of your Bioconductor installation with

   BiocInstaller::biocValid()

>
> 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
>>>      ‘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
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


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