Hi all I'm having a problem with the getGEO(...) function of the package GEOquery. I've looked through the previous responses to this problem but the fixes aren't working for me. I'm working on a mac and have R 3.0.1. and I have a good internet connection. When I open R, I enter >library(GEOquery) >options('download.file.method.GEOquery' = 'curl') >getGEO("GDS1") and get this curl: (7) Failed to connect to 2607:f220:41e:250::11: No route to host File stored at: /var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS10.sof t.gz Error in gzfile(fname, open = "rt") : cannot open the connection In addition: Warning messages: 1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : download had nonzero exit status 2: In gzfile(fname, open = "rt") : cannot open compressed file '/var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS10.so ft.gz', probable reason 'No such file or directory' ------------------------------ Leaving out the 'options' method gives me this: Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : cannot open URL ' ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDSnnn/GDS10/soft/GDS10.soft.g z' -------------------------------- I have had issues downloading from GEO files from the internet before, so this may be an issue with my security settings. However my firewall is not turned on and I am not sure what else could cause problems like this. Any input would be really helpful, thanks for you time Nick [[alternative HTML version deleted]]

On Tue, Jul 23, 2013 at 3:40 PM, Nick Goelz <nickgoelz at="" gmail.com=""> wrote: > Hi all > > I'm having a problem with the getGEO(...) function of the package GEOquery. > I've looked through the previous responses to this problem but the fixes > aren't working for me. I'm working on a mac and have R 3.0.1. and I have a > good internet connection. When I open R, I enter > >>library(GEOquery) >>options('download.file.method.GEOquery' = 'curl') >>getGEO("GDS1") > > and get this > > curl: (7) Failed to connect to 2607:f220:41e:250::11: No route to host > File stored at: > /var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS10.s oft.gz > Error in gzfile(fname, open = "rt") : cannot open the connection > In addition: Warning messages: > 1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = > getOption("download.file.method.GEOquery")) : > download had nonzero exit status > 2: In gzfile(fname, open = "rt") : > cannot open compressed file > '/var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS10. soft.gz', > probable reason 'No such file or directory' > ------------------------------ > Leaving out the 'options' method gives me this: > > Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = > getOption("download.file.method.GEOquery")) : > cannot open URL ' > ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDSnnn/GDS10/soft/GDS10.soft .gz' > -------------------------------- > I have had issues downloading from GEO files from the internet before, so > this may be an issue with my security settings. However my firewall is not > turned on and I am not sure what else could cause problems like this. > > Any input would be really helpful, thanks for you time > It may be that there is no GDS1 dataset. It doesn't work for me either, but I am able to do this: getGEO("GDS10") Dan > Nick > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

On Tue, Jul 23, 2013 at 3:49 PM, Goelz, Nicholas <nicholas_goelz at="" brown.edu=""> wrote: > Shoot, that's just a typo by me. I used GDS10 and still got the error. Could be a firewall or proxy setting at your institution. Are you able to download the file by pasting this url into your web browser? ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDSnnn/GDS10/soft/GDS10.soft.g z Dan > Thanks for your quick response though > > > On Tue, Jul 23, 2013 at 3:48 PM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> On Tue, Jul 23, 2013 at 3:40 PM, Nick Goelz <nickgoelz at="" gmail.com=""> wrote: >> > Hi all >> > >> > I'm having a problem with the getGEO(...) function of the package >> > GEOquery. >> > I've looked through the previous responses to this problem but the >> > fixes >> > aren't working for me. I'm working on a mac and have R 3.0.1. and I >> > have a >> > good internet connection. When I open R, I enter >> > >> >>library(GEOquery) >> >>options('download.file.method.GEOquery' = 'curl') >> >>getGEO("GDS1") >> > >> > and get this >> > >> > curl: (7) Failed to connect to 2607:f220:41e:250::11: No route to host >> > File stored at: >> > >> > /var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS1 0.soft.gz >> > Error in gzfile(fname, open = "rt") : cannot open the connection >> > In addition: Warning messages: >> > 1: In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = >> > getOption("download.file.method.GEOquery")) : >> > download had nonzero exit status >> > 2: In gzfile(fname, open = "rt") : >> > cannot open compressed file >> > >> > '/var/folders/00/162s57712tngn2shq_1mxg5c0000gn/T//Rtmp3xusrK/GDS 10.soft.gz', >> > probable reason 'No such file or directory' >> > ------------------------------ >> > Leaving out the 'options' method gives me this: >> > >> > Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, >> > method = >> > getOption("download.file.method.GEOquery")) : >> > cannot open URL ' >> > ftp://ftp.ncbi.nlm.nih.gov/geo/datasets/GDSnnn/GDS10/soft/GDS10.s oft.gz' >> > -------------------------------- >> > I have had issues downloading from GEO files from the internet before, >> > so >> > this may be an issue with my security settings. However my firewall is >> > not >> > turned on and I am not sure what else could cause problems like this. >> > >> > Any input would be really helpful, thanks for you time >> > >> >> It may be that there is no GDS1 dataset. >> >> It doesn't work for me either, but I am able to do this: >> >> getGEO("GDS10") >> >> Dan >> >> >> > Nick >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >