[BioC] GEOquery and GSE error

[Sean Davis]

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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>