[BioC] ArrayExpress error: unable to find an inherited method for function \"experimentData\", for signature \"try-error\"

Mikhail Spivakov spivakov at ebi.ac.uk
Sun Nov 27 23:41:10 CET 2011 

Thanks Vincent, I'm actually updating R as we speak - so thanks for
letting me know that I shouldn't expect this to work.
Please let me know if you stumble upon a possible cause.

Best,
Mikhail


On Sun, Nov 27, 2011 at 10:07 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> You really should update your R, but this is confirmed with current R 2.14
> -- I don't know what is happening, there are many possible causes, and I
> will investigate a little, but others closer to this package should have a
> look.
>
> Read 49 items
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "experimentData", for
> signature "try-error"
> Warning message:
> In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach experimentData
>>  sessionInfo()
> R version 2.14.0 Patched (2011-11-09 r57622)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.iso88591       LC_NUMERIC=C
>  [3] LC_TIME=en_US.iso88591        LC_COLLATE=en_US.iso88591
>  [5] LC_MONETARY=en_US.iso88591    LC_MESSAGES=en_US.iso88591
>  [7] LC_PAPER=C                    LC_NAME=C
>  [9] LC_ADDRESS=C                  LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  tools     utils     methods
> [8] base
>
> other attached packages:
> [1] ArrayExpress_1.14.0 Biobase_2.14.0      weaver_1.20.0
> [4] codetools_0.2-8     digest_0.5.1        BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] affy_1.32.0           affyio_1.22.0         limma_3.10.0
> [4] preprocessCore_1.16.0 XML_3.4-3             zlibbioc_1.0.0
>
>
> On Sun, Nov 27, 2011 at 6:07 AM, Mikhail Spivakov [guest]
> <guest at bioconductor.org> wrote:
>>
>> Hi everyone,
>>
>> I've tried importing two different datasets using ArrayExpress and
>> unfortunately I'm getting the same error: unable to find an inherited method
>> for function "experimentData", for signature "try-error".
>>
>> Could you please advice what might be causing the problem? The R output is
>> pasted below.
>>
>> Many thanks!
>> Mikhail
>>
>> > library(ArrayExpress)
>> > wang = ArrayExpress( input = "E-GEOD-3960") # also tried "E-GEOD-27608"
>> trying URL
>> 'http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-3960/index.html'
>> Content type 'text/html;charset=UTF-8' length unknown
>> opened URL
>> ........
>> downloaded 9082 bytes
>>
>> trying URL
>> 'http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-3960/E-GEOD-3960.raw.1.zip'
>> Content type 'application/zip' length 156512666 bytes (149.3 Mb)
>> opened URL
>> ================================================
>> downloaded 149.3 Mb
>>
>> Read 1 item
>> trying URL
>> 'http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-3960/E-GEOD-3960.sdrf.txt'
>> Content type 'text/plain' length 76290 bytes (74 Kb)
>> opened URL
>> ==================================================
>> downloaded 74 Kb
>>
>> trying URL
>> 'http://www.ebi.ac.uk/microarray-as/ae/files/A-AFFY-1/A-AFFY-1.adf.txt'
>> Content type 'text/plain' length 1547751 bytes (1.5 Mb)
>> opened URL
>> ==================================================
>> downloaded 1.5 Mb
>>
>> trying URL
>> 'http://www.ebi.ac.uk/microarray-as/ae/files/E-GEOD-3960/E-GEOD-3960.idf.txt'
>> Content type 'text/plain' length 4279 bytes
>> opened URL
>> ==================================================
>> downloaded 4279 bytes
>>
>> Error : the following are not valid files:
>>
>>  /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90393.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90378.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90405.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90387.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90356.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90334.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90361.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90368.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90332.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90327.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90314.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90392.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90320.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90360.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90333.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90389.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90357.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90337.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90401.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90379.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90399.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90315.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90309.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90347.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90308.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90375.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90380.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90344.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90321.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90394.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90348.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90328.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90403.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90388.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90346.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90383.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90310.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90335.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90395.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90365.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90364.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90331.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90339.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90325.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90374.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90367.CEL
>>
>> /net/isilon4/research/birney/birney4/spivakov/nb/E-GEOD-27608/GSM90382.CEL
>> Read 49 items
>> Error in function (classes, fdef, mtable)  :
>>  unable to find an inherited method for function "experimentData", for
>> signature "try-error"
>> Warning message:
>> In AB(i = 1, files, path, ph, adr, adf, idf) : Cannot attach
>> experimentData
>>
>>
>> --
>> Mikhail Spivakov, PhD
>> European Bioinformatics Institute
>>
>>  -- output of sessionInfo():
>>
>> R version 2.11.0 (2010-04-22)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
>>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] affy_1.25.3        ArrayExpress_1.8.0 Biobase_2.7.6
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.15.2        limma_3.3.21         preprocessCore_1.9.0
>> [4] XML_3.1-0
>>
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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