[BioC] troubles with GEOquery

[Sean Davis]

2008/5/11 Pascal Barbry <barbry at ipmc.cnrs.fr>:
> Hello Sean,
> I tried again after having clean a lot my disk, and reinstalling everything.
> This time, it worked!...
> I did not succeed with the GSEmatrix option turned to TRUE.

So, if you don't mind, what do you mean by "did not succeed"?  Did you
receive an error?  If so, what was it?  It really helps me to know
these things so that if there is a bug, I can fix it.

> Here is the script and message from the console:
>
>>> Sys.time()
>>
>> [1] "2008-05-11 17:14:19 CEST"
>>>
>>> GSE7216 <- getGEO("GSE7216", GSEMatrix = FALSE)
>>
>> essai de l'URL
>> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE7216/GSE7216_family.soft.gz'
>> ftp data connection made, file length 13316485 bytes
>> URL ouverte
>> downloaded 12.7 Mb
>>
>> File stored at: C:\DOCUME~1\Pascal\LOCALS~1\Temp\RtmpiH1ZtG/GSE7216.soft
>> Parsing....
>> ^PLATFORM = GPL570
>> ^SAMPLE = GSM173533
>> ^SAMPLE = GSM173534
>> ^SAMPLE = GSM173535
>> ^SAMPLE = GSM173536
>> ^SAMPLE = GSM173537
>> ^SAMPLE = GSM173538
>> ^SAMPLE = GSM173539
>> ^SAMPLE = GSM173540
>> ^SAMPLE = GSM173541
>> ^SAMPLE = GSM173542
>> ^SAMPLE = GSM173543
>> ^SAMPLE = GSM173544
>> ^SAMPLE = GSM173545
>> ^SAMPLE = GSM173546
>> ^SAMPLE = GSM173547
>> ^SAMPLE = GSM173548
>> ^SAMPLE = GSM173549
>> ^SAMPLE = GSM173550
>> ^SAMPLE = GSM173551
>> ^SAMPLE = GSM173552
>> ^SAMPLE = GSM173553
>> ^SAMPLE = GSM173554
>> ^SAMPLE = GSM173555
>> ^SAMPLE = GSM173556
>>>
>>> Sys.time()
>>
>> [1] "2008-05-11 17:49:20 CEST"
>>>
>>>
>
> As you can notice, it took about 35 minutes to download (around 5 minutes),
> then parse the file (30 minutes).

Yes, the files are large and the parsing is slow.

Sean

> Pascal
>
>
> Sean Davis a écrit :
>>
>> On Fri, May 9, 2008 at 6:34 PM, Pascal Barbry <barbry at ipmc.cnrs.fr> wrote:
>>>
>>> Hi all,
>>> I have troubles trying to download GSE files from GEO:
>>> library(GEOquery)
>>> GSE6281 <- getGEO("GSE6281", GSEMatrix = FALSE).
>>>
>>> Surprisingly, the example found in the help file is working nicely:
>>> gse <- getGEO("GSE462", GSEMatrix = FALSE)
>>>
>>> ?????!!!.............
>>>
>>> My troubles started after switching to the new version of Bioconductor.
>>> As I
>>> am using a Windows OS and that some of the getGEO options are not
>>> windows-proof, I was wondering if any others had experienced a similar
>>> situation? Any idea (outside swtching to Linux) would be appreciated.
>>
>> Hi, Pascal.  What problems are you having?  You didn't give a report
>> of the errors that you received.
>>
>> Sean
>>
>>
>>>> sessionInfo()
>>>
>>> R version 2.7.0 (2008-04-22)
>>> i386-pc-mingw32
>>>
>>> locale:
>>>
>>> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
>>>
>>> attached base packages:
>>> [1] tools     stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] GEOquery_2.4.0 RCurl_0.9-2    Biobase_2.0.1
>>>
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>