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

[Ludwig Geistlinger]

Thx Martin, but that means that the Docker image is outdated, isn't it?


> 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
>>>>
>>>
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> --
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>
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>


-- 
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