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

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