Hello, makeTranscriptDbFromUCSC isn't working for me. I can download R packages from CRAN and Bioconductor using install.packages or biocLite, so it's not a proxy issue. I can also paste the URL http://hgdownload.cse.ucsc.edu/goldenPath into a web browser and I get to the website fine. > tx19 <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene") Error in function (type, msg, asError = TRUE) : couldn't connect to host R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 [2] LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils [5] datasets methods base other attached packages: [1] GenomicFeatures_1.10.0 AnnotationDbi_1.20.2 [3] Biobase_2.18.0 GenomicRanges_1.10.1 [5] IRanges_1.16.2 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] biomaRt_2.12.0 Biostrings_2.26.1 [3] bitops_1.0-4.1 BSgenome_1.24.0 [5] DBI_0.2-5 parallel_2.15.1 [7] RCurl_1.95-1.1 Rsamtools_1.10.1 [9] RSQLite_0.11.1 rtracklayer_1.18.0 [11] stats4_2.15.1 tools_2.15.1 [13] XML_3.9-4.1 zlibbioc_1.2.0 -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia

Hi, On Sun, Oct 21, 2012 at 8:00 PM, Dario Strbenac <d.strbenac at="" garvan.org.au=""> wrote: > Hello, > > makeTranscriptDbFromUCSC isn't working for me. I can download R packages from CRAN and Bioconductor using install.packages or biocLite, so it's not a proxy issue. I can also paste the URL http://hgdownload.cse.ucsc.edu/goldenPath into a web browser and I get to the website fine. > >> tx19 <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene") > Error in function (type, msg, asError = TRUE) : couldn't connect to host This doesn't help you too much, but it's working for me -- my sessionInfo is the same as yours except for the fact that I'm not running windows. You say accessing the URL via your browser works, but does the following call to url.exists return `TRUE`? R> library(RCurl) R> url.exists("http://hgdownload.cse.ucsc.edu/goldenPaths") -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

I get FALSE, even after removing the typographical error on the end of your URL example. Must be something odd with the network here at university. ---- Original message ---- >Date: Sun, 21 Oct 2012 20:14:22 -0400 >From: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> >Subject: Re: [BioC] GenomicFeatures Transcripts Retrieval Fails >To: D.Strbenac at garvan.org.au >Cc: bioconductor at r-project.org > >Hi, > >On Sun, Oct 21, 2012 at 8:00 PM, Dario Strbenac ><d.strbenac at="" garvan.org.au=""> wrote: >> Hello, >> >> makeTranscriptDbFromUCSC isn't working for me. I can download R packages from CRAN and Bioconductor using install.packages or biocLite, so it's not a proxy issue. I can also paste the URL http://hgdownload.cse.ucsc.edu/goldenPath into a web browser and I get to the website fine. >> >>> tx19 <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene") >> Error in function (type, msg, asError = TRUE) : couldn't connect to host > >This doesn't help you too much, but it's working for me -- my >sessionInfo is the same as yours except for the fact that I'm not >running windows. > >You say accessing the URL via your browser works, but does the >following call to url.exists return `TRUE`? > >R> library(RCurl) >R> url.exists("http://hgdownload.cse.ucsc.edu/goldenPaths") > >-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

Turns out that setting was wrongly specified. ---- Original message ---- >Date: Sun, 21 Oct 2012 22:27:16 -0400 >From: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> >Subject: Re: [BioC] GenomicFeatures Transcripts Retrieval Fails >To: D.Strbenac at garvan.org.au >Cc: bioconductor at r-project.org > >On Sun, Oct 21, 2012 at 9:00 PM, Dario Strbenac ><d.strbenac at="" garvan.org.au=""> wrote: >> I get FALSE, even after removing the typographical error on the end of your URL example. > >Woops -- sorry about that, the URL I pasted was the one I used to see >what happens when you `url.exists` a phony URL. Good catch. > >> Must be something odd with the network here at university. > >Maybe -- but still might be a windows thing. Are you sure you're not >getting bit by something like this?: > >http://cran.r-project.org/bin/windows/base/rw-FAQ.html#The-Internet- download-functions-fail_002e > >-steve > >> >> ---- Original message ---- >>>Date: Sun, 21 Oct 2012 20:14:22 -0400 >>>From: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> >>>Subject: Re: [BioC] GenomicFeatures Transcripts Retrieval Fails >>>To: D.Strbenac at garvan.org.au >>>Cc: bioconductor at r-project.org >>> >>>Hi, >>> >>>On Sun, Oct 21, 2012 at 8:00 PM, Dario Strbenac >>><d.strbenac at="" garvan.org.au=""> wrote: >>>> Hello, >>>> >>>> makeTranscriptDbFromUCSC isn't working for me. I can download R packages from CRAN and Bioconductor using install.packages or biocLite, so it's not a proxy issue. I can also paste the URL http://hgdownload.cse.ucsc.edu/goldenPath into a web browser and I get to the website fine. >>>> >>>>> tx19 <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene") >>>> Error in function (type, msg, asError = TRUE) : couldn't connect to host >>> >>>This doesn't help you too much, but it's working for me -- my >>>sessionInfo is the same as yours except for the fact that I'm not >>>running windows. >>> >>>You say accessing the URL via your browser works, but does the >>>following call to url.exists return `TRUE`? >>> >>>R> library(RCurl) >>>R> url.exists("http://hgdownload.cse.ucsc.edu/goldenPaths") >>> >>>-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 > > > >-- >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