[BioC] GEOquery error

[Sean Davis]

Hi, again, James.

NCBI is still checking into the issue (may have been a storm-related
issue), but your (simplified) example now works for me.

> gpl = getGEO('GPL90')
File stored at:
/var/folders/21/8t47kwys6vqb8606kdfn71780000gn/T//RtmpQXZfrr/GPL90.soft
> sessionInfo()
R version 3.0.2 Patched (2014-01-22 r64855)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GEOquery_2.28.0      Biobase_2.21.7       BiocGenerics_0.7.5
[4] BiocInstaller_1.12.0

loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.95-0.2


Sean

On Thu, May 1, 2014 at 1:11 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> Hi, James.
>
> Thanks for the report.  This is due to a change at NCBI.  I am
> checking with them to see if the change is meant to be permanent or is
> simply a transient issue.  I'll let everyone know as soon as I hear
> back from NCBI.
>
> Sean
>
>
> On Thu, May 1, 2014 at 9:19 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
>> Hi Sean,
>>
>>> geoq <- getGEO("GSE9514")
>> ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/
>> Found 1 file(s)
>> GSE9514_series_matrix.txt.gz
>>   % Total    % Received % Xferd  Average Speed   Time    Time Time  Current
>>                                  Dload  Upload   Total   Spent Left  Speed
>> 100  378k  100  378k    0     0   204k      0  0:00:01  0:00:01 --:--:--
>> 204k
>> File stored at:
>> /data3/tmp/RtmpkDXZzR/GPL90.soft
>> Error in xj[i] : only 0's may be mixed with negative subscripts
>>
>> And the error appears to come from this section in parseGPL():
>>
>> if (hasDataTable) {
>>         nLinesToRead <- NULL
>>         if (!is.null(n)) {
>>             nLinesToRead <- n - length(txt)
>>         }
>>         dat3 <- fastTabRead(con, n = nLinesToRead, quote = "")
>>         geoDataTable <- new("GEODataTable", columns = cols, table =
>> dat3[1:(nrow(dat3) -
>>             1), ])
>>     }
>>
>> Where there is no error trapping for the case that fastTabRead returns a
>> zero row data.frame:
>>
>> debug: dat3 <- fastTabRead(con, n = nLinesToRead, quote = "")
>> Browse[3]> dim(dat3)
>> [1]  0 17
>> Browse[3]> dat3
>>  [1] ID ORF
>>  [3] SPOT_ID                          Species Scientific Name
>>  [5] Annotation Date                  Sequence Type
>>  [7] Sequence Source                  Target Description
>>  [9] Representative Public ID         Gene Title
>> [11] Gene Symbol ENTREZ_GENE_ID
>> [13] RefSeq Transcript ID             SGD accession number
>> [15] Gene Ontology Biological Process Gene Ontology Cellular Component
>> [17] Gene Ontology Molecular Function
>> <0 rows> (or 0-length row.names)
>>
>> Best,
>>
>> Jim
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
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