Hi, Cherif.

You didn't include the output of sessionInfo(), so I am not sure what
version of GEOquery you are using.  I suspect that you are using an
outdated version and need to upgrade.  In any case, I am not able to
reproduce your problem, so let me know if you have problems after upgrading.

Sean


> gds1257 = getGEO('GDS1257')
File stored at:
/var/folders/21/8t47kwys6vqb8606kdfn71780000gn/T//RtmpFgWQxT/GDS1257.soft.gz
> eset = GDS2eSet(gds1257)
File stored at:
/var/folders/21/8t47kwys6vqb8606kdfn71780000gn/T//RtmpFgWQxT/GPL96.annot.gz
There were 30 warnings (use warnings() to see them)
> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22283 features, 33 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM32620 GSM32621 ... GSM32651 (33 total)
  varLabels: sample disease.state description
  varMetadata: labelDescription
featureData
  featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total)
  fvarLabels: ID Gene title ... GO:Component ID (21 total)
  fvarMetadata: Column labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 15741505
Annotation:
> 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


On Mon, Mar 31, 2014 at 10:59 AM, BEN HAMDA Cherif <cherifbenhamda@gmail.com
> wrote:

> Hello,
> I need help ,
> I have a problem with (GEOquery) package a
> first of all, I can't download and this the warning message
>
> >library(GEOquery)
> Setting options('download.file.method.GEOquery'='curl')
>
> > gds1257 <- getGEO('GDS858', destdir=".")
> File stored at:
> ./GDS1257.soft.gz
> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>   invalid 'nlines' argument
> > gds1257
> Error: object 'gds1257' not found
>
> The second problem is :
>
> If i download the gds file manually with "wget" and after that we use
> the GDS2eSet i have this message :
>
> gds <- getGEO(filename='GDS1257.soft.gz')
> eset <- GDS2eSet(gds, do.log2=TRUE)
> File stored at:
> /tmp/RtmpY4ZgWQ/GPL96.annot.gz
> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>   invalid 'nlines' argument
> > eset
> Error: object 'eset' not found
>
> waiting response  , thank you very much
>
>
> Best
> Cherif
>
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