Hi all. Can someone advise on my issue below? I can't seem to grab the UCSC table 'knownGene', but it works for 'ensGene'. Is this a timeout error? 'knownGene' is only marginally larger (in rows) than 'ensGene'. Any solution? Thanks! Mark > library(rtracklayer) Loading required package: RCurl Loading required package: bitops > session <- browserSession("UCSC") > genome(session) <- "hg18" > q <- ucscTableQuery(session, "knownGene") > knownGene <- getTable(q) Error in curlPerform(url = url, headerfunction = header$update, curl = curl, : transfer closed with outstanding read data remaining > traceback() 11: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding, PACKAGE = "RCurl") 10: curlPerform(url = url, headerfunction = header$update, curl = curl, .opts = .opts) 9: getURLContent(uri, .opts = .opts, .encoding = .encoding, binary = binary, curl = curl) 8: getForm(url, .params = .form, .opts = list(..., useragent = "rtracklayer")) 7: httpGet(ucscURL(object, key), .form, ..., cookie = ucscCookie(object)) 6: ucscGet(browserSession(query), "tables", c(ucscForm(query, tracks = tracks), ...), .parse = .parse) 5: ucscTableGet(object, !is.null(followup), hgta_doTopSubmit = "get output", hgsid = hgsid) 4: ucscExport(object) 3: .local(object, ...) 2: getTable(q) 1: getTable(q) > q <- ucscTableQuery(session, "ensGene") > ensGene <- getTable(q) > > dim(ensGene) [1] 63280 16 > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.10.3 RCurl_1.5-0 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.0 [4] GenomicRanges_1.2.0 IRanges_1.8.0 XML_3.2-0 ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: mrobinson at wehi.edu.au e: m.robinson at garvan.org.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:6}}

Possibly a proxy issue? I don't think I've seen that particular error message. On Fri, Dec 3, 2010 at 9:51 PM, Mark Robinson <mrobinson@wehi.edu.au> wrote: > Hi all. > > Can someone advise on my issue below? I can't seem to grab the UCSC table > 'knownGene', but it works for 'ensGene'. Is this a timeout error? > 'knownGene' is only marginally larger (in rows) than 'ensGene'. Any > solution? > > Thanks! > Mark > > > library(rtracklayer) > Loading required package: RCurl > Loading required package: bitops > > session <- browserSession("UCSC") > > genome(session) <- "hg18" > > q <- ucscTableQuery(session, "knownGene") > > knownGene <- getTable(q) > Error in curlPerform(url = url, headerfunction = header$update, curl = > curl, : > transfer closed with outstanding read data remaining > > traceback() > 11: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding, > PACKAGE = "RCurl") > 10: curlPerform(url = url, headerfunction = header$update, curl = curl, > .opts = .opts) > 9: getURLContent(uri, .opts = .opts, .encoding = .encoding, binary = > binary, > curl = curl) > 8: getForm(url, .params = .form, .opts = list(..., useragent = > "rtracklayer")) > 7: httpGet(ucscURL(object, key), .form, ..., cookie = ucscCookie(object)) > 6: ucscGet(browserSession(query), "tables", c(ucscForm(query, tracks = > tracks), > ...), .parse = .parse) > 5: ucscTableGet(object, !is.null(followup), hgta_doTopSubmit = "get > output", > hgsid = hgsid) > 4: ucscExport(object) > 3: .local(object, ...) > 2: getTable(q) > 1: getTable(q) > > q <- ucscTableQuery(session, "ensGene") > > ensGene <- getTable(q) > > > > dim(ensGene) > [1] 63280 16 > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.10.3 RCurl_1.5-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.0 > [4] GenomicRanges_1.2.0 IRanges_1.8.0 XML_3.2-0 > > > ------------------------------ > Mark Robinson, PhD (Melb) > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: mrobinson@wehi.edu.au > e: m.robinson@garvan.org.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > ------------------------------ > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:13}}

Hi mark, I just tried your commands on my Windows box. Worked fine. I was actually distracted doing something else, but it had finished when I looked back 15 minutes later. knownGene had 66803 elements. I was wondering why you are using hg18 when hg19 is available. my sessionInfo is: R version 2.12.0 Patched (2010-11-26 r53670) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] rtracklayer_1.9.11 RCurl_1.4-4.1 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.9.2 Biostrings_2.17.48 BSgenome_1.17.7 [4] GenomicRanges_1.1.38 IRanges_1.7.40 XML_3.2-0.1 My R is the latest November release, not sure if that has had any effect or the fact that it was done at a different time (I did it at about 8:45pm (Australian EST = GMT+10) on Saturday Dec. 4 cheers, Keith ======================== Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria, Australia email:keith at wehi.edu.au ======================= Mark Robinson wrote: > Hi all. > > Can someone advise on my issue below? I can't seem to grab the UCSC table 'knownGene', but it works for 'ensGene'. Is this a timeout error? 'knownGene' is only marginally larger (in rows) than 'ensGene'. Any solution? > > Thanks! > Mark > > >> library(rtracklayer) >> > Loading required package: RCurl > Loading required package: bitops > >> session <- browserSession("UCSC") >> genome(session) <- "hg18" >> q <- ucscTableQuery(session, "knownGene") >> knownGene <- getTable(q) >> > Error in curlPerform(url = url, headerfunction = header$update, curl = curl, : > transfer closed with outstanding read data remaining > >> traceback() >> > 11: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding, > PACKAGE = "RCurl") > 10: curlPerform(url = url, headerfunction = header$update, curl = curl, > .opts = .opts) > 9: getURLContent(uri, .opts = .opts, .encoding = .encoding, binary = binary, > curl = curl) > 8: getForm(url, .params = .form, .opts = list(..., useragent = "rtracklayer")) > 7: httpGet(ucscURL(object, key), .form, ..., cookie = ucscCookie(object)) > 6: ucscGet(browserSession(query), "tables", c(ucscForm(query, tracks = tracks), > ...), .parse = .parse) > 5: ucscTableGet(object, !is.null(followup), hgta_doTopSubmit = "get output", > hgsid = hgsid) > 4: ucscExport(object) > 3: .local(object, ...) > 2: getTable(q) > 1: getTable(q) > >> q <- ucscTableQuery(session, "ensGene") >> ensGene <- getTable(q) >> >> dim(ensGene) >> > [1] 63280 16 > >> sessionInfo() >> > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.10.3 RCurl_1.5-0 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.0 > [4] GenomicRanges_1.2.0 IRanges_1.8.0 XML_3.2-0 > > > ------------------------------ > Mark Robinson, PhD (Melb) > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: mrobinson at wehi.edu.au > e: m.robinson at garvan.org.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > ------------------------------ > > > ______________________________________________________________________ > The information in this email is confidential and inte...{{dropped:14}}