[BioC] GEOquery and GSE error

[Sean Davis]

On Wed, Sep 21, 2011 at 3:13 AM, Ovokeraye Achinike-Oduaran
<ovokeraye at gmail.com> wrote:
> Thanks Sean.I got RCurl installed but GEOquery doesn't update with the
> update.packages() or the specific update.packages("GEOquery") options.

This should get the job done.

source('http://bioconductor.org/biocLite.R')
biocLite('GEOquery')

Sean


> So, I'm still having the same challenge.
>
> -Avoks
>
> On Tue, Sep 20, 2011 at 4:22 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>> On Tue, Sep 20, 2011 at 10:19 AM, Ovokeraye Achinike-Oduaran
>> <ovokeraye at gmail.com> wrote:
>>> Okay, thanks Sean. I used the update.packages() in the R window, and
>>> when I restarted R and tried loading the GEOquery library, this is
>>> what I got.
>>>
>>>> library(GEOquery)
>>> Loading required package: Biobase
>>>
>>> Welcome to Bioconductor
>>>
>>>  Vignettes contain introductory material. To view, type
>>>  'browseVignettes()'. To cite Bioconductor, see
>>>  'citation("Biobase")' and for packages 'citation("pkgname")'.
>>>
>>> Error in loadNamespace(i[[1L]], c(lib.loc, .libPaths())) :
>>>  there is no package called 'RCurl'
>>
>> Looks like you will need to install RCurl.
>>
>> Sean
>>
>>
>>> In addition: Warning message:
>>> '.readRDS' is deprecated.
>>> Use 'readRDS' instead.
>>> See help("Deprecated")
>>> Error: package/namespace load failed for 'GEOquery'
>>>
>>> Is it something I'm doing wrong at my end?
>>>
>>> Thanks again.
>>>
>>>
>>>
>>> On Tue, Sep 20, 2011 at 3:50 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>>> On Tue, Sep 20, 2011 at 9:44 AM, Ovokeraye Achinike-Oduaran
>>>> <ovokeraye at gmail.com> wrote:
>>>>> Hi Sean,
>>>>>
>>>>> Thanks. I'm thinking I have the latest version because I only very
>>>>> recently installed the package.
>>>>>
>>>>> [1] GEOquery_2.19.3 Biobase_2.12.2 .
>>>>>
>>>>> Is there a more recent one?
>>>>
>>>> Yes.  2.19.4 is the most recent version.
>>>>
>>>> Sean
>>>>
>>>>
>>>>> On Tue, Sep 20, 2011 at 3:37 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>>>>> Hi, Avoks.
>>>>>>
>>>>>> Without sessionInfo(), it is not possible to be sure what version of
>>>>>> GEOquery you are running, but I would suggest you upgrade to the
>>>>>> newest version of GEOquery.  I think that will fix the issue.
>>>>>>
>>>>>> Sorry for the inconvenience.
>>>>>>
>>>>>> Sean
>>>>>>
>>>>>>
>>>>>> On Tue, Sep 20, 2011 at 9:24 AM, Ovokeraye Achinike-Oduaran
>>>>>> <ovokeraye at gmail.com> wrote:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I am unable to access a series file even though I get a message that
>>>>>>> it saved to a local directory, albeit with an error message and a
>>>>>>> number of warnings, after retrieval with GEOquery. Any ideas as to
>>>>>>> what I may be doing wrong?
>>>>>>>
>>>>>>> Thanks.
>>>>>>>
>>>>>>> Avoks
>>>>>>>
>>>>>>>> gse9006 = getGEO("GSE9006", GSEMatrix = TRUE)
>>>>>>> Found 2 file(s)
>>>>>>> GSE9006-GPL96_series_matrix.txt.gz
>>>>>>> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE9006/GSE9006-GPL96_series_matrix.txt.gz'
>>>>>>> ftp data connection made, file length 5775933 bytes
>>>>>>> opened URL
>>>>>>> downloaded 5.5 Mb
>>>>>>>
>>>>>>> File stored at:
>>>>>>> C:\...\Temp\RtmpJM0ZOp/GPL96.soft
>>>>>>> Error in validObject(.Object) :
>>>>>>>  invalid class "ExpressionSet" object: featureNames differ between
>>>>>>> assayData and featureData
>>>>>>> In addition: Warning messages:
>>>>>>> 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>>>>>>>  seek on a gzfile connection returned an internal error
>>>>>>> 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
>>>>>>>  seek on a gzfile connection returned an internal error
>>>>>>> 3: In readLines(con, 1) :
>>>>>>>  seek on a gzfile connection returned an internal error
>>>>>>> 4: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>>>>>>  seek on a gzfile connection returned an internal error
>>>>>>> 5: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>>>>>>  seek on a gzfile connection returned an internal error
>>>>>>> 6: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>>>>>>  seek on a gzfile connection returned an internal error
>>>>>>> 7: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>>>>>>>  not all columns named in 'colClasses' exist
>>>>>>>
>>>>>>>> gse9006
>>>>>>> Error: object 'gse9006' not found
>>>>>>>
>>>>>>>> show(gse9006)
>>>>>>> Error in show(gse9006) :
>>>>>>>  error in evaluating the argument 'object' in selecting a method for
>>>>>>> function 'show': Error: object 'gse9006' not found
>>>>>>>
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>>>>>>
>>>>>
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>>>>
>>>
>>
>
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