Hi, Thanks for your answer, I'm gonna try that. One additional piece of information is that if I set GSEMatrix=F, then the error does not occur. I will try to upgrade R to see if it fixed the problem. Cheers Guillaume On Thu, Dec 2, 2010 at 14:12, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Thu, Dec 2, 2010 at 2:03 PM, Guillaume Mouron < > guillaume.mouron@gmail.com> wrote: > >> Hi, >> >> My problem might have to do with one previously sent today by Koray Kaya, >> but I was not yet member of the mailing list at that moment, so I don't >> know >> how to answer to that message, sorry for that. >> >> I also have a problem downloading GSE data. GSM and GDS downloads work. >> >> Here is the error I get : >> > test <- getGEO('GSE13481',destdir='./ >> test-geoquery') >> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, >> : >> line 1 did not have 6 elements >> >> > Hi, Guillaume. Could you upgrade to the latest versions of R and GEOquery > and see if that works for you? I am not able to reproduce the error with > the current version of GEOquery. > > Thanks, > Sean > > > >> The problem is not a proxy problem, as I already fixed this (by switching >> to >> wget for downloading with options("download.file.method"="wget"), and with >> the ftp_proxy correctly set in the environment variables (meaning defined >> as >> ftp_proxy="http://proxyname:proxyport), if that can help). >> >> When I try this : >> > download.file(' >> >> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE13481/GSE1348 1_family.soft.gz >> ',"test.soft.gz") >> >> The download of the GSE file works correctly. >> >> So the problem seems to be somewhere else ... >> >> Content of my sessioninfo() : >> > sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-redhat-linux-gnu >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] GEOquery_2.13.5 Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.5-0 XML_3.2-0 >> >> >> Thanks, >> Guillaume Mouron >> >> PS: I've already send an email but I was not subscribed yet, and I can't >> cancel it anymore, but it is not published yet though, sorry for the >> duplicate. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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]]