Question: recourse for errors with GEOquery::getGEO
0
gravatar for Brent Pedersen
6.6 years ago by
United States
Brent Pedersen90 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? > 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 >
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ADD COMMENTlink modified 6.6 years ago by Sean Davis21k • written 6.6 years ago by Brent Pedersen90
Answer: recourse for errors with GEOquery::getGEO
0
gravatar for Sean Davis
6.6 years ago by
Sean Davis21k
United States
Sean Davis21k 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. 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]]
ADD COMMENTlink written 6.6 years ago by Sean Davis21k
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]]
ADD REPLYlink written 6.6 years ago by Sean Davis21k
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