getGEO error
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Alyaa Mahmoud ▴ 440
@alyaa-mahmoud-4670
Last seen 4.7 years ago
Dear Group I am trying to download some datasets from GEO using package GEOquery. It worked fine for most of the datasets except for a couple of them, I get the following error: * * Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input * * This is the script line I use: GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]] I also tried to download the soft files and read these directly; GSE37830 = getGEO (filename = "GSE37830_family.soft.gz") but I still get the same error. Please advise Thanks a lot Alyaa Mahmoud R version 2.9.2 (2009-08-24) x86_64-pc-linux-gnu locale: LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_ MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_A DDRESS=C;LC_TELEPHONE=C;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_2.8.0 RCurl_1.95-3 bitops_1.0-5 Biobase_2.4.1 loaded via a namespace (and not attached): [1] tools_2.9.2 -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
GEOquery GEOquery • 1.7k views
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@vincent-j-carey-jr-4
Last seen 10 weeks ago
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On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud@gmail.com>wrote: > Dear Group > > I am trying to download some datasets from GEO using package GEOquery. It > worked fine for most of the datasets except for a couple of them, I get the > following error: > * > * > Error in read.table(file = file, header = header, sep = sep, quote = quote, > : > no lines available in input > * > * > This is the script line I use: > GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]] > > I also tried to download the soft files and read these directly; > GSE37830 = getGEO (filename = "GSE37830_family.soft.gz") > > but I still get the same error. > > Please advise > Thanks a lot > > Alyaa Mahmoud > your version of R is very old -- current is 2.15.2; GEOquery has current version 2.24.0. There are many changes that have occurred since 2009. Please update (first R, then your Bioconductor packages) and if further problems persist, file a new report. > > R version 2.9.2 (2009-08-24) > x86_64-pc-linux-gnu > > locale: > > LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;L C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC _ADDRESS=C;LC_TELEPHONE=C;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_2.8.0 RCurl_1.95-3 bitops_1.0-5 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] tools_2.9.2 > > -- > Alyaa Mahmoud > > "Love all, trust a few, do wrong to none"- Shakespeare > > [[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]]
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@sean-davis-490
Last seen 3 months ago
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On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud at="" gmail.com=""> wrote: > Dear Group > > I am trying to download some datasets from GEO using package GEOquery. It > worked fine for most of the datasets except for a couple of them, I get the > following error: > * > * > Error in read.table(file = file, header = header, sep = sep, quote = quote, > : > no lines available in input > * > * > This is the script line I use: > GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]] > > I also tried to download the soft files and read these directly; > GSE37830 = getGEO (filename = "GSE37830_family.soft.gz") > > but I still get the same error. Thanks, Alyaa, for the report. This is, indeed, a bug. It has been fixed in the current release and devel branches (versions 2.24.1 and 2.25.1, respectively) and should be available in the next couple of days for installation. Note that you will need to update to the current R version to get these changes. Sean > Please advise > Thanks a lot > > Alyaa Mahmoud > > R version 2.9.2 (2009-08-24) > x86_64-pc-linux-gnu > > locale: > LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;L C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC _ADDRESS=C;LC_TELEPHONE=C;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_2.8.0 RCurl_1.95-3 bitops_1.0-5 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] tools_2.9.2 > > -- > Alyaa Mahmoud > > "Love all, trust a few, do wrong to none"- Shakespeare > > [[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
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Thanks a lot for the replies. I updated to "R version 2.15.0 (2012-03-30" to but I still get the same error msg; test = getGEO ("GSE17221") Found 1 file(s) GSE17221_series_matrix.txt.gz Using locally cached version: /tmp/RtmpBQOrpt/GSE17221_series_matrix.txt.gz Using locally cached version of GPL8891 found here: /tmp/RtmpBQOrpt/GPL8891.soft Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input In addition: Warning message: closing unused connection 3 (/tmp/RtmpBQOrpt/GPL8891.soft) On Fri, Jan 25, 2013 at 4:35 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud@gmail.com> > wrote: > > Dear Group > > > > I am trying to download some datasets from GEO using package GEOquery. It > > worked fine for most of the datasets except for a couple of them, I get > the > > following error: > > * > > * > > Error in read.table(file = file, header = header, sep = sep, quote = > quote, > > : > > no lines available in input > > * > > * > > This is the script line I use: > > GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]] > > > > I also tried to download the soft files and read these directly; > > GSE37830 = getGEO (filename = "GSE37830_family.soft.gz") > > > > but I still get the same error. > > Thanks, Alyaa, for the report. > > This is, indeed, a bug. It has been fixed in the current release and > devel branches (versions 2.24.1 and 2.25.1, respectively) and should > be available in the next couple of days for installation. Note that > you will need to update to the current R version to get these changes. > > Sean > > > Please advise > > Thanks a lot > > > > Alyaa Mahmoud > > > > R version 2.9.2 (2009-08-24) > > x86_64-pc-linux-gnu > > > > locale: > > > LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;L C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC _ADDRESS=C;LC_TELEPHONE=C;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_2.8.0 RCurl_1.95-3 bitops_1.0-5 Biobase_2.4.1 > > > > loaded via a namespace (and not attached): > > [1] tools_2.9.2 > > > > -- > > Alyaa Mahmoud > > > > "Love all, trust a few, do wrong to none"- Shakespeare > > > > [[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 > -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
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On Sat, Jan 26, 2013 at 4:35 AM, Alyaa Mahmoud <alyamahmoud at="" gmail.com=""> wrote: > Thanks a lot for the replies. > > I updated to "R version 2.15.0 (2012-03-30" to but I still get the same > error msg; > > test = getGEO ("GSE17221") > Found 1 file(s) > GSE17221_series_matrix.txt.gz > Using locally cached version: /tmp/RtmpBQOrpt/GSE17221_series_matrix.txt.gz > Using locally cached version of GPL8891 found here: > /tmp/RtmpBQOrpt/GPL8891.soft > Error in read.table(file = file, header = header, sep = sep, quote = quote, > : > no lines available in input Hi, Alyaa. The version of GEOquery with the bug fixed (I hope) is not quite available. It should probably be available in about 12 hours--the build system takes a while to do its magic. You'll want to re-install GEOquery using biocLite('GEOquery') and then make sure that the version of GEOquery that gets installed is 2.24.1. If you still have problems after that, definitely let us know and be sure to include the output of sessionInfo() in your email. Thanks for your patience, Sean > > > On Fri, Jan 25, 2013 at 4:35 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud at="" gmail.com=""> >> wrote: >> > Dear Group >> > >> > I am trying to download some datasets from GEO using package GEOquery. It >> > worked fine for most of the datasets except for a couple of them, I get >> the >> > following error: >> > * >> > * >> > Error in read.table(file = file, header = header, sep = sep, quote = >> quote, >> > : >> > no lines available in input >> > * >> > * >> > This is the script line I use: >> > GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]] >> > >> > I also tried to download the soft files and read these directly; >> > GSE37830 = getGEO (filename = "GSE37830_family.soft.gz") >> > >> > but I still get the same error. >> >> Thanks, Alyaa, for the report. >> >> This is, indeed, a bug. It has been fixed in the current release and >> devel branches (versions 2.24.1 and 2.25.1, respectively) and should >> be available in the next couple of days for installation. Note that >> you will need to update to the current R version to get these changes. >> >> Sean >> >> > Please advise >> > Thanks a lot >> > >> > Alyaa Mahmoud >> > >> > R version 2.9.2 (2009-08-24) >> > x86_64-pc-linux-gnu >> > >> > locale: >> > >> LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8; LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;L C_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATIO N=C >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > other attached packages: >> > [1] GEOquery_2.8.0 RCurl_1.95-3 bitops_1.0-5 Biobase_2.4.1 >> > >> > loaded via a namespace (and not attached): >> > [1] tools_2.9.2 >> > >> > -- >> > Alyaa Mahmoud >> > >> > "Love all, trust a few, do wrong to none"- Shakespeare >> > >> > [[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 >> > > > > -- > Alyaa Mahmoud > > "Love all, trust a few, do wrong to none"- Shakespeare > > [[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
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Dear Sean It worked perfectly fine. Thank you very much for all your efforts. Kindest regards, Alyaa On Sat, Jan 26, 2013 at 3:45 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Sat, Jan 26, 2013 at 4:35 AM, Alyaa Mahmoud <alyamahmoud@gmail.com> > wrote: > > Thanks a lot for the replies. > > > > I updated to "R version 2.15.0 (2012-03-30" to but I still get the same > > error msg; > > > > test = getGEO ("GSE17221") > > Found 1 file(s) > > GSE17221_series_matrix.txt.gz > > Using locally cached version: > /tmp/RtmpBQOrpt/GSE17221_series_matrix.txt.gz > > Using locally cached version of GPL8891 found here: > > /tmp/RtmpBQOrpt/GPL8891.soft > > Error in read.table(file = file, header = header, sep = sep, quote = > quote, > > : > > no lines available in input > > Hi, Alyaa. > > The version of GEOquery with the bug fixed (I hope) is not quite > available. It should probably be available in about 12 hours--the > build system takes a while to do its magic. You'll want to re- install > GEOquery using biocLite('GEOquery') and then make sure that the > version of GEOquery that gets installed is 2.24.1. If you still have > problems after that, definitely let us know and be sure to include the > output of sessionInfo() in your email. > > Thanks for your patience, > Sean > > > > > > > > On Fri, Jan 25, 2013 at 4:35 PM, Sean Davis <sdavis2@mail.nih.gov> > wrote: > > > >> On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud@gmail.com> > >> wrote: > >> > Dear Group > >> > > >> > I am trying to download some datasets from GEO using package > GEOquery. It > >> > worked fine for most of the datasets except for a couple of them, I > get > >> the > >> > following error: > >> > * > >> > * > >> > Error in read.table(file = file, header = header, sep = sep, quote = > >> quote, > >> > : > >> > no lines available in input > >> > * > >> > * > >> > This is the script line I use: > >> > GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]] > >> > > >> > I also tried to download the soft files and read these directly; > >> > GSE37830 = getGEO (filename = "GSE37830_family.soft.gz") > >> > > >> > but I still get the same error. > >> > >> Thanks, Alyaa, for the report. > >> > >> This is, indeed, a bug. It has been fixed in the current release and > >> devel branches (versions 2.24.1 and 2.25.1, respectively) and should > >> be available in the next couple of days for installation. Note that > >> you will need to update to the current R version to get these changes. > >> > >> Sean > >> > >> > Please advise > >> > Thanks a lot > >> > > >> > Alyaa Mahmoud > >> > > >> > R version 2.9.2 (2009-08-24) > >> > x86_64-pc-linux-gnu > >> > > >> > locale: > >> > > >> > LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;L C_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC _ADDRESS=C;LC_TELEPHONE=C;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_2.8.0 RCurl_1.95-3 bitops_1.0-5 Biobase_2.4.1 > >> > > >> > loaded via a namespace (and not attached): > >> > [1] tools_2.9.2 > >> > > >> > -- > >> > Alyaa Mahmoud > >> > > >> > "Love all, trust a few, do wrong to none"- Shakespeare > >> > > >> > [[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 > >> > > > > > > > > -- > > Alyaa Mahmoud > > > > "Love all, trust a few, do wrong to none"- Shakespeare > > > > [[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 > -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
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