[BioC] warnings from getGeo() in Geoquery package

[Sean Davis]

On Sat, Sep 17, 2011 at 11:25 PM, Silav Bremos <silavb at yahoo.com> wrote:
> Hi
> I am trying to get GSE24080 from GEO using getGeo() function in Geoquery package and get several warnings.
>
> Can anyone please help me clear out the warnings and get successful download? I am using R version 2.13.1 (2011-07-08)
> on Windows XP. Thanks.--Silav
>

Hi, Silav.

The download worked fine and you should be able to proceed with your
analyses.  These are warnings, not errors.  I need to clean up the
warnings (which arise from some functions in base R and not in
GEOquery, directly), but in the meantime, you can ignore them.

Sean


>
>> Sys.getlocale()
> [1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252"
>
>
>> 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")'.
> Setting options('download.file.method.GEOquery'='curl')
> Warning message:
> '.readRDS' is deprecated.
> Use 'readRDS' instead.
> See help("Deprecated")
>
>> gse24080 <- getGEO("GSE24080")
> Found 3 file(s)
> GSE24080_series_matrix-1.txt.gz
> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/GSE24080_series_matrix-1.txt.gz'
> ftp data connection made, file length 38807310 bytes
> opened URL
> downloaded 37.0 Mb
>
> File stored at:
> C:\DOCUME~1\.......
> GSE24080_series_matrix-2.txt.gz
> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/GSE24080_series_matrix-2.txt.gz'
> ftp data connection made, file length 38738618 bytes
> opened URL
> downloaded 36.9 Mb
>
> Using locally cached version of GPL570 found here:
> C:\DOCUME~1\.........
> GSE24080_series_matrix-3.txt.gz
> trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/GSE24080_series_matrix-3.txt.gz'
> ftp data connection made, file length 7721111 bytes
> opened URL
> downloaded 7.4 Mb
>
> Using locally cached version of GPL570 found here:
> C:\DOCUME~1\........
> There were 15 warnings (use warnings() to see them)
>> warnings()
> 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,  ... :
>   seek on a gzfile connection returned an internal error
> 5: In read.table(file = file, header = header, sep = sep,  ... :
>   seek on a gzfile connection returned an internal error
> 6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>   seek on a gzfile connection returned an internal error
> 7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
>   seek on a gzfile connection returned an internal error
> 8: In readLines(con, 1) : seek on a gzfile connection returned an internal error
> 9: In read.table(file = file, header = header, sep = sep,  ... :
>   seek on a gzfile connection returned an internal error
> 10: In read.table(file = file, header = header, sep = sep,  ... :
>   seek on a gzfile connection returned an internal error
> 11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>   seek on a gzfile connection returned an internal error
> 12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :
>   seek on a gzfile connection returned an internal error
> 13: In readLines(con, 1) : seek on a gzfile connection returned an internal error
> 14: In read.table(file = file, header = header, sep = sep,  ... :
>   seek on a gzfile connection returned an internal error
> 15: In read.table(file = file, header = header, sep = sep,  ... :
>   seek on a gzfile connection returned an internal error
>>
>
>
> --Silav
>        [[alternative HTML version deleted]]
>
>
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