[BioC] problem in read in file with GEOquery library

[Sean Davis]

These are warnings, not errors.  You can safely ignore them.  I'll
work on silencing them as time permits.

Sean


On Wed, Aug 31, 2011 at 12:16 PM, zhliu.tju <zhliu.tju at gmail.com> wrote:
> Hi Bioconductor users,
>
> I encounter a problem in library GEOquery, I downloaded soft format gene
> expression profile from GEO database.
>
> whenever I run below lines, there appears a warning message though already
> read in the soft file.
>
>> setwd("C:\\work\\microarray\\Implementation")
>> GSE781<- getGEO(filename = "GSE781_family.soft.gz")
>
> There were 50 or more warnings (use warnings() to see the first 50)
>
> Warning messages:
> 1: In readLines(con, 1) : seek on a gzfile connection returned an internal
> error
> 2: In readLines(con, 1) : 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 readLines(con, 1) : seek on a gzfile connection returned an internal
> error
> 5: In readLines(con, 1) : seek on a gzfile connection returned an internal
> error
> 6: In readLines(con, 1) : seek on a gzfile connection returned an internal
> error
>
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] splines   stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
>  [1] annotate_1.30.0      affydata_1.11.11     affy_1.30.0
>  [4] flexmix_2.3-5        multcomp_1.2-7       survival_2.36-9
>  [7] mvtnorm_0.9-9991     modeltools_0.2-17    lattice_0.19-30
> [10] bioDist_1.24.1       KernSmooth_2.23-6    genefilter_1.34.0
> [13] hgu133a.db_2.5.0     org.Hs.eg.db_2.5.0   RSQLite_0.9-4
> [16] DBI_0.2-5            AnnotationDbi_1.14.1 reshape_0.8.4
> [19] plyr_1.6             GEOquery_2.19.3      Biobase_2.12.2
>
> loaded via a namespace (and not attached):
> [1] affyio_1.20.0         grid_2.13.1           preprocessCore_1.14.0
> [4] RCurl_1.6-7.1         tools_2.13.1          XML_3.4-2.2
> [7] xtable_1.5-6
>
> Anyone knows how to deal with the above problems, thanks a lot in advance!
>
> --
> Best Regards,
>
> Zhe Liu
>
>        [[alternative HTML version deleted]]
>
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