[BioC] GEOquery error

[Sean Davis]

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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