[BioC] GEOquery and GSE error

[Ovokeraye Achinike-Oduaran]

Thanks Sean.I got RCurl installed but GEOquery doesn't update with the
update.packages() or the specific update.packages("GEOquery") options.
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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>>
>