[BioC] GEOquery getGEO error in read.table

[Dan Tenenbaum]

On Tue, Jan 8, 2013 at 1:37 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Tue, Jan 8, 2013 at 12:40 AM, Dave Tang <davetingpongtang at gmail.com> wrote:
>> Dear mailing list,
>>
>> I've been trying to use GEOquery to fetch microarray data from GEO but to no
>> avail. I've searched online and found several discussions about a similar
>> problem but the bug was solved for an older version.
>>
>> Here I've just tried to run the first couple of steps of the vignette:
>>
>> library(GEOquery)
>> Loading required package: Biobase
>> Loading required package: BiocGenerics
>>
>> Attaching package: 'BiocGenerics'
>>
>> The following object(s) are masked from 'package:stats':
>>
>>     xtabs
>>
>> The following object(s) are masked from 'package:base':
>>
>>     Filter, Find, Map, Position, Reduce, anyDuplicated, cbind,
>>     colnames, duplicated, eval, get, intersect, lapply, mapply, mget,
>>     order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int,
>>     rownames, sapply, setdiff, table, tapply, union, unique
>>
>> Welcome to Bioconductor
>>
>>     Vignettes contain introductory material; view with
>>     'browseVignettes()'. To cite Bioconductor, see
>>     'citation("Biobase")', and for packages 'citation("pkgname")'.
>>
>> Setting options('download.file.method.GEOquery'='curl')
>> #no issue here
>> gds <- getGEO("GDS507")
>> File stored at:
>> /tmp/RtmpqHbIvi/GDS507.soft.gz
>> #error here
>> gds <- getGEO("GSM11805")
>> File stored at:
>> /tmp/RtmpqHbIvi/GSM11805.soft
>> Error in read.table(file = file, header = header, sep = sep, quote = quote,
>> :
>>   no lines available in input
>
> Hi, Dave.
>
> I have not been able to reproduce your error on linux or mac, but that
> doesn't mean there is not a problem.  There have been intermittent
> problems in the past associated with NCBI servers that might cause
> truncated downloads, but that is hard to sort out.  In any case, could
> you try this again when you get a chance to see if the problem has
> resolved itself?

Several BioC packages that download data from GEO failed to build last
night, in a way that suggests GEO was at least partially down last
night.
I could reproduce the error earlier today but it works now.

Dan


>
> Thanks,
> Sean
>
>
>> I've tried this for several other microarray datasets and I get the same
>> error message.
>>
>> Here's my sessionInfo():
>>
>> sessionInfo()
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] GEOquery_2.24.0    Biobase_2.18.0     BiocGenerics_0.4.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.95-3 XML_3.95-0.1
>>
>> Cheers,
>>
>>
>> --
>> Dave
>>
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>
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