Dear mailing list, I've been trying to use GEOquery to fetch microarray data from GEO but to no avail. I've searched online and found several discussions about a similar problem but the bug was solved for an older version. Here I've just tried to run the first couple of steps of the vignette: library(GEOquery) Loading required package: Biobase Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object(s) are masked from 'package:stats': xtabs The following object(s) are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, colnames, duplicated, eval, get, intersect, lapply, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Setting options('download.file.method.GEOquery'='curl') #no issue here gds <- getGEO("GDS507") File stored at: /tmp/RtmpqHbIvi/GDS507.soft.gz #error here gds <- getGEO("GSM11805") File stored at: /tmp/RtmpqHbIvi/GSM11805.soft Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input I've tried this for several other microarray datasets and I get the same error message. Here's my sessionInfo(): sessionInfo() R version 2.15.2 (2012-10-26) 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_2.24.0 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] RCurl_1.95-3 XML_3.95-0.1 Cheers, -- Dave

On Tue, Jan 8, 2013 at 1:37 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > On Tue, Jan 8, 2013 at 12:40 AM, Dave Tang <davetingpongtang at="" gmail.com=""> wrote: >> Dear mailing list, >> >> I've been trying to use GEOquery to fetch microarray data from GEO but to no >> avail. I've searched online and found several discussions about a similar >> problem but the bug was solved for an older version. >> >> Here I've just tried to run the first couple of steps of the vignette: >> >> library(GEOquery) >> Loading required package: Biobase >> Loading required package: BiocGenerics >> >> Attaching package: 'BiocGenerics' >> >> The following object(s) are masked from 'package:stats': >> >> xtabs >> >> The following object(s) are masked from 'package:base': >> >> Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, >> colnames, duplicated, eval, get, intersect, lapply, mapply, mget, >> order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, >> rownames, sapply, setdiff, table, tapply, union, unique >> >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >> Setting options('download.file.method.GEOquery'='curl') >> #no issue here >> gds <- getGEO("GDS507") >> File stored at: >> /tmp/RtmpqHbIvi/GDS507.soft.gz >> #error here >> gds <- getGEO("GSM11805") >> File stored at: >> /tmp/RtmpqHbIvi/GSM11805.soft >> Error in read.table(file = file, header = header, sep = sep, quote = quote, >> : >> no lines available in input > > Hi, Dave. > > I have not been able to reproduce your error on linux or mac, but that > doesn't mean there is not a problem. There have been intermittent > problems in the past associated with NCBI servers that might cause > truncated downloads, but that is hard to sort out. In any case, could > you try this again when you get a chance to see if the problem has > resolved itself? Several BioC packages that download data from GEO failed to build last night, in a way that suggests GEO was at least partially down last night. I could reproduce the error earlier today but it works now. Dan > > Thanks, > Sean > > >> I've tried this for several other microarray datasets and I get the same >> error message. >> >> Here's my sessionInfo(): >> >> sessionInfo() >> R version 2.15.2 (2012-10-26) >> 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_2.24.0 Biobase_2.18.0 BiocGenerics_0.4.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.95-3 XML_3.95-0.1 >> >> Cheers, >> >> >> -- >> Dave >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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, Jan 8, 2013 at 12:40 AM, Dave Tang <davetingpongtang at="" gmail.com=""> wrote: > Dear mailing list, > > I've been trying to use GEOquery to fetch microarray data from GEO but to no > avail. I've searched online and found several discussions about a similar > problem but the bug was solved for an older version. > > Here I've just tried to run the first couple of steps of the vignette: > > library(GEOquery) > Loading required package: Biobase > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, > colnames, duplicated, eval, get, intersect, lapply, mapply, mget, > order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, > rownames, sapply, setdiff, table, tapply, union, unique > > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > Setting options('download.file.method.GEOquery'='curl') > #no issue here > gds <- getGEO("GDS507") > File stored at: > /tmp/RtmpqHbIvi/GDS507.soft.gz > #error here > gds <- getGEO("GSM11805") > File stored at: > /tmp/RtmpqHbIvi/GSM11805.soft > Error in read.table(file = file, header = header, sep = sep, quote = quote, > : > no lines available in input Hi, Dave. I have not been able to reproduce your error on linux or mac, but that doesn't mean there is not a problem. There have been intermittent problems in the past associated with NCBI servers that might cause truncated downloads, but that is hard to sort out. In any case, could you try this again when you get a chance to see if the problem has resolved itself? Thanks, Sean > I've tried this for several other microarray datasets and I get the same > error message. > > Here's my sessionInfo(): > > sessionInfo() > R version 2.15.2 (2012-10-26) > 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_2.24.0 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-3 XML_3.95-0.1 > > Cheers, > > > -- > Dave > > _______________________________________________ > 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

Hi Dave, I could not reproduce your error with R2.15.2 and GEOQuery 2.23.1 I updated to GEOQuery 2.24 as you and i also worked without error ? Are you sure you have Curl and XML libs (outside R) installed properly ? Julien On 08/01/2013 06:40, Dave Tang wrote: > Dear mailing list, > > I've been trying to use GEOquery to fetch microarray data from GEO but > to no avail. I've searched online and found several discussions about > a similar problem but the bug was solved for an older version. > > Here I've just tried to run the first couple of steps of the vignette: > > library(GEOquery) > Loading required package: Biobase > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, > colnames, duplicated, eval, get, intersect, lapply, mapply, mget, > order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, > rownames, sapply, setdiff, table, tapply, union, unique > > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > Setting options('download.file.method.GEOquery'='curl') > #no issue here > gds <- getGEO("GDS507") > File stored at: > /tmp/RtmpqHbIvi/GDS507.soft.gz > #error here > gds <- getGEO("GSM11805") > File stored at: > /tmp/RtmpqHbIvi/GSM11805.soft > Error in read.table(file = file, header = header, sep = sep, quote = > quote, : > no lines available in input > > I've tried this for several other microarray datasets and I get the > same error message. > > Here's my sessionInfo(): > > sessionInfo() > R version 2.15.2 (2012-10-26) > 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_2.24.0 Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-3 XML_3.95-0.1 > > Cheers, > >