makeTranscriptDbFromUCSC() fails to download table
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Burak Kutlu ▴ 140
@burak-kutlu-3941
Last seen 10.2 years ago
Hi For some reason I started getting error for the following call hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene") The curious thing is that it was working this morning, it does not seem to be a problem related to the goldenPath. Thanks in advance -burak > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2 IRanges_1.8.7 loaded via a namespace (and not attached): [1] Biobase_2.10.0 biomaRt_2.6.0 Biostrings_2.18.2 BSgenome_1.18.2 DBI_0.2-5 [6] RCurl_1.4-3 RSQLite_0.9-4 rtracklayer_1.10.6 XML_3.2-0 -- Burak Kutlu, PhD. Research Scientist Hood Lab Institute for Systems Biology
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@steve-lianoglou-2771
Last seen 21 months ago
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Hi, On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu <bkutlu at="" systemsbiology.org=""> wrote: > Hi > > For some reason I started getting error for the following call > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = > "knownGene") I'm not sure how we can shed some light on this without you providing the error that you're getting ;-) Can you paste that into a follow up email? Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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D'oh! Here it is > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "knownGene") Download the knownGene table ... Error in curlPerform(url = url, headerfunction = header$update, curl = curl, : transfer closed with outstanding read data remaining I also failed to mention this is about GenomicFeatures package. Thanks Steve! -burak On Thu, Dec 23, 2010 at 4:46 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu <bkutlu at="" systemsbiology.org=""> wrote: >> Hi >> >> For some reason I started getting error for the following call >> hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = >> "knownGene") > > I'm not sure how we can shed some light on this without you providing > the error that you're getting ;-) > > Can you paste that into a follow up email? > > Thanks, > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- Burak Kutlu, PhD. Research Scientist Hood Lab Institute for Systems Biology
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I just ran the code successfully with sessionInfo below. Could be transient network issue? > sessionInfo() R version 2.12.0 Patched (2010-11-28 r53696) Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices datasets tools utils methods [8] base other attached packages: [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2 IRanges_1.8.7 [4] weaver_1.16.0 codetools_0.2-6 digest_0.4.2 loaded via a namespace (and not attached): [1] BSgenome_1.18.2 Biobase_2.10.0 Biostrings_2.18.2 DBI_0.2-5 [5] RCurl_1.5-0 RSQLite_0.9-4 XML_3.2-0 biomaRt_2.6.0 [9] rtracklayer_1.10.6 On Thu, Dec 23, 2010 at 8:52 PM, Burak Kutlu <bkutlu@systemsbiology.org>wrote: > D'oh! > > Here it is > > > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = > "knownGene") > Download the knownGene table ... Error in curlPerform(url = url, > headerfunction = header$update, curl = curl, : > transfer closed with outstanding read data remaining > > I also failed to mention this is about GenomicFeatures package. > Thanks Steve! > -burak > > On Thu, Dec 23, 2010 at 4:46 PM, Steve Lianoglou > <mailinglist.honeypot@gmail.com> wrote: > > Hi, > > > > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu <bkutlu@systemsbiology.org> > wrote: > >> Hi > >> > >> For some reason I started getting error for the following call > >> hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = > >> "knownGene") > > > > I'm not sure how we can shed some light on this without you providing > > the error that you're getting ;-) > > > > Can you paste that into a follow up email? > > > > Thanks, > > > > -steve > > > > -- > > Steve Lianoglou > > Graduate Student: Computational Systems Biology > > | Memorial Sloan-Kettering Cancer Center > > | Weill Medical College of Cornell University > > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.ms="" kcc.org="" %7elianos="" contact=""> > > > > > > -- > Burak Kutlu, PhD. > Research Scientist > Hood Lab > Institute for Systems Biology > > _______________________________________________ > 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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Hello, I have a quick question about how this is working behind the scenes. Does the code access the Table Browser web interface at UCSC? I'm very interested in this .. it seems like a very convenient way to access a lot of data in various useful formats without having to manually download anything. Is there an easy way I can browse the source code on-line or check out just a portion of the Bioconductor repository so that I can see how this feature is working? Where does this code reside in the repository? (I'm looking at http://www.bioconductor.org/developers/source- control/) Sincerely, Ann Loraine On Thu, Dec 23, 2010 at 11:18 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > I just ran the code successfully with sessionInfo below. ?Could be transient > network issue? > >> sessionInfo() > R version 2.12.0 Patched (2010-11-28 r53696) > Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats ? ? graphics ?grDevices datasets ?tools ? ? utils ? ? methods > [8] base > > other attached packages: > [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2 ? IRanges_1.8.7 > [4] weaver_1.16.0 ? ? ? ? codetools_0.2-6 ? ? ? digest_0.4.2 > > loaded via a namespace (and not attached): > [1] BSgenome_1.18.2 ? ?Biobase_2.10.0 ? ? Biostrings_2.18.2 > DBI_0.2-5 > [5] RCurl_1.5-0 ? ? ? ?RSQLite_0.9-4 ? ? ?XML_3.2-0 > biomaRt_2.6.0 > [9] rtracklayer_1.10.6 > > > On Thu, Dec 23, 2010 at 8:52 PM, Burak Kutlu <bkutlu at="" systemsbiology.org="">wrote: > >> D'oh! >> >> Here it is >> >> > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = >> "knownGene") >> Download the knownGene table ... Error in curlPerform(url = url, >> headerfunction = header$update, curl = curl, ?: >> ?transfer closed with outstanding read data remaining >> >> I also failed to mention this is about GenomicFeatures package. >> Thanks Steve! >> -burak >> >> On Thu, Dec 23, 2010 at 4:46 PM, Steve Lianoglou >> <mailinglist.honeypot at="" gmail.com=""> wrote: >> > Hi, >> > >> > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu <bkutlu at="" systemsbiology.org=""> >> wrote: >> >> Hi >> >> >> >> For some reason I started getting error for the following call >> >> hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = >> >> "knownGene") >> > >> > I'm not sure how we can shed some light on this without you providing >> > the error that you're getting ;-) >> > >> > Can you paste that into a follow up email? >> > >> > Thanks, >> > >> > -steve >> > >> > -- >> > Steve Lianoglou >> > Graduate Student: Computational Systems Biology >> > ?| Memorial Sloan-Kettering Cancer Center >> > ?| Weill Medical College of Cornell University >> > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio.m="" skcc.org="" %7elianos="" contact=""> >> > >> >> >> >> -- >> Burak Kutlu, PhD. >> Research Scientist >> Hood Lab >> Institute for Systems Biology >> >> _______________________________________________ >> 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 >> > > ? ? ? ?[[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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Hi Ann, On Sat, Dec 25, 2010 at 8:36 AM, Ann Loraine <aloraine@gmail.com> wrote: > Hello, > > I have a quick question about how this is working behind the scenes. > > Does the code access the Table Browser web interface at UCSC? > > I'm very interested in this .. it seems like a very convenient way to > access a lot of data in various useful formats without having to > manually download anything. > > Is there an easy way I can browse the source code on-line or check out > just a portion of the Bioconductor repository so that I can see how > this feature is working? > > Where does this code reside in the repository? > > (I'm looking at http://www.bioconductor.org/developers/source- control/) > > Sincerely, > > Ann Loraine > > > Probably the best way to see how this is done is to download the GenomicFeatures package. In R: source("http://bioconductor.org/biocLite.R") biocLite("GenomicFeatures") library(GenomicFeatures) Then you can not only see the source for any function: makeTranscriptDbFromUCSC You can also get documentation for the function: ?makeTranscriptDbFromUCSC If you still want to find the package in the repository, have a look at: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicFea tures/ That's the development version; the release version is: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rp acks/GenomicFeatures/ Dan > > On Thu, Dec 23, 2010 at 11:18 PM, Vincent Carey > <stvjc@channing.harvard.edu> wrote: > > I just ran the code successfully with sessionInfo below. Could be > transient > > network issue? > > > >> sessionInfo() > > R version 2.12.0 Patched (2010-11-28 r53696) > > Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) > > > > locale: > > [1] C > > > > attached base packages: > > [1] stats graphics grDevices datasets tools utils methods > > [8] base > > > > other attached packages: > > [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2 IRanges_1.8.7 > > [4] weaver_1.16.0 codetools_0.2-6 digest_0.4.2 > > > > loaded via a namespace (and not attached): > > [1] BSgenome_1.18.2 Biobase_2.10.0 Biostrings_2.18.2 > > DBI_0.2-5 > > [5] RCurl_1.5-0 RSQLite_0.9-4 XML_3.2-0 > > biomaRt_2.6.0 > > [9] rtracklayer_1.10.6 > > > > > > On Thu, Dec 23, 2010 at 8:52 PM, Burak Kutlu <bkutlu@systemsbiology.org> >wrote: > > > >> D'oh! > >> > >> Here it is > >> > >> > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = > >> "knownGene") > >> Download the knownGene table ... Error in curlPerform(url = url, > >> headerfunction = header$update, curl = curl, : > >> transfer closed with outstanding read data remaining > >> > >> I also failed to mention this is about GenomicFeatures package. > >> Thanks Steve! > >> -burak > >> > >> On Thu, Dec 23, 2010 at 4:46 PM, Steve Lianoglou > >> <mailinglist.honeypot@gmail.com> wrote: > >> > Hi, > >> > > >> > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu < > bkutlu@systemsbiology.org> > >> wrote: > >> >> Hi > >> >> > >> >> For some reason I started getting error for the following call > >> >> hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename > = > >> >> "knownGene") > >> > > >> > I'm not sure how we can shed some light on this without you providing > >> > the error that you're getting ;-) > >> > > >> > Can you paste that into a follow up email? > >> > > >> > Thanks, > >> > > >> > -steve > >> > > >> > -- > >> > Steve Lianoglou > >> > Graduate Student: Computational Systems Biology > >> > | Memorial Sloan-Kettering Cancer Center > >> > | Weill Medical College of Cornell University > >> > Contact Info: http://cbio.mskcc.org/~lianos/contact< > http://cbio.mskcc.org/%7Elianos/contact> > >> > > >> > >> > >> > >> -- > >> Burak Kutlu, PhD. > >> Research Scientist > >> Hood Lab > >> Institute for Systems Biology > >> > >> _______________________________________________ > >> 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]] > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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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On Sat, Dec 25, 2010 at 8:36 AM, Ann Loraine <aloraine@gmail.com> wrote: > Hello, > > I have a quick question about how this is working behind the scenes. > > Does the code access the Table Browser web interface at UCSC? > > I'm very interested in this .. it seems like a very convenient way to > access a lot of data in various useful formats without having to > manually download anything. > > The rtracklayer package does the actual data access, and yes it's through the table browser. You can download any table you want through the low-level rtracklayer interface. > Is there an easy way I can browse the source code on-line or check out > just a portion of the Bioconductor repository so that I can see how > this feature is working? > > Where does this code reside in the repository? > > (I'm looking at http://www.bioconductor.org/developers/source- control/) > > Sincerely, > > Ann Loraine > > > > On Thu, Dec 23, 2010 at 11:18 PM, Vincent Carey > <stvjc@channing.harvard.edu> wrote: > > I just ran the code successfully with sessionInfo below. Could be > transient > > network issue? > > > >> sessionInfo() > > R version 2.12.0 Patched (2010-11-28 r53696) > > Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit) > > > > locale: > > [1] C > > > > attached base packages: > > [1] stats graphics grDevices datasets tools utils methods > > [8] base > > > > other attached packages: > > [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.2 IRanges_1.8.7 > > [4] weaver_1.16.0 codetools_0.2-6 digest_0.4.2 > > > > loaded via a namespace (and not attached): > > [1] BSgenome_1.18.2 Biobase_2.10.0 Biostrings_2.18.2 > > DBI_0.2-5 > > [5] RCurl_1.5-0 RSQLite_0.9-4 XML_3.2-0 > > biomaRt_2.6.0 > > [9] rtracklayer_1.10.6 > > > > > > On Thu, Dec 23, 2010 at 8:52 PM, Burak Kutlu <bkutlu@systemsbiology.org> >wrote: > > > >> D'oh! > >> > >> Here it is > >> > >> > hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = > >> "knownGene") > >> Download the knownGene table ... Error in curlPerform(url = url, > >> headerfunction = header$update, curl = curl, : > >> transfer closed with outstanding read data remaining > >> > >> I also failed to mention this is about GenomicFeatures package. > >> Thanks Steve! > >> -burak > >> > >> On Thu, Dec 23, 2010 at 4:46 PM, Steve Lianoglou > >> <mailinglist.honeypot@gmail.com> wrote: > >> > Hi, > >> > > >> > On Thu, Dec 23, 2010 at 7:38 PM, Burak Kutlu < > bkutlu@systemsbiology.org> > >> wrote: > >> >> Hi > >> >> > >> >> For some reason I started getting error for the following call > >> >> hg19KnownGene <- makeTranscriptDbFromUCSC(genome = "hg19", tablename > = > >> >> "knownGene") > >> > > >> > I'm not sure how we can shed some light on this without you providing > >> > the error that you're getting ;-) > >> > > >> > Can you paste that into a follow up email? > >> > > >> > Thanks, > >> > > >> > -steve > >> > > >> > -- > >> > Steve Lianoglou > >> > Graduate Student: Computational Systems Biology > >> > | Memorial Sloan-Kettering Cancer Center > >> > | Weill Medical College of Cornell University > >> > Contact Info: http://cbio.mskcc.org/~lianos/contact<http: cbio="" .mskcc.org="" %7elianos="" contact=""> > <http: cbio.mskcc.org="" %7elianos="" contact=""> > >> > > >> > >> > >> > >> -- > >> Burak Kutlu, PhD. > >> Research Scientist > >> Hood Lab > >> Institute for Systems Biology > >> > >> _______________________________________________ > >> 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]] > > > > _______________________________________________ > > 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 > > > > _______________________________________________ > 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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