On Thu, Oct 25, 2012 at 2:44 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Thu, Oct 25, 2012 at 2:27 PM, Brent Pedersen <bpederse@gmail.com>wrote: > >> Hi, with a call like >> > getGEO("GSE15219", destdir="/tmp/", GSEMatrix=TRUE) >> I get: >> Found 1 file(s) >> GSE15219_series_matrix.txt.gz >> % Total % Received % Xferd Average Speed Time Time Time >> Current >> Dload Upload Total Spent Left >> Speed >> 100 762k 100 762k 0 0 313k 0 0:00:02 0:00:02 --:--:-- >> 330k >> 100 762k 100 762k 0 0 301k 0 0:00:02 0:00:02 >> --:--:-- 301kFile stored at: >> /tmp//GPL6255.soft >> Error in read.table(file = file, header = header, sep = sep, quote = >> quote, : >> no lines available in input >> >> >> Is there something I can do to get around this error? >> >> > Hi, Brent. > > Thanks for the report. This is due to a change in behavior of NCBI GEO > with regard to GEO platform records. I have contacted NCBI GEO staff to > see if this is a problem on their end or a permanent change in behavior. > I'll let you know as soon as I hear. > > Hi, Brent. There was a glitch at NCBI. Everything should be working again. Sean > Sean > > > >> >> > sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GEOquery_2.23.5 Biobase_2.16.0 BiocGenerics_0.2.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.95-1.1 XML_3.95-0.1 >> > >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]