Thanks to Fenton for the report and Vince for looking into this. The problem as Vince indicated is that there are a huge number of tables for this track. You'll want to pass the table argument to select the one you actually want. By default, rtracklayer chooses the first table. There were some inefficiencies that caused the query to hang, and I've fixed those in devel. I've also made BED parsing more robust to empty inputs, which is what we get with the query range below. Michael On Wed, Sep 19, 2012 at 7:44 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > On Wed, Sep 19, 2012 at 8:54 AM, Fenton Christopher Graham < > christopher.fenton@uit.no> wrote: > > > Does anyone have a clue why the following code stalls. > > > > #Just testing functionality of the package > > > > >session <- browserSession("UCSC") > > >query <- ucscTableQuery(session, "wgEncodeSydhTfbs", > > GRangesForUCSCGenome("hg19","chr1", IRanges(100, 101))) > > > > >query > > > > """Get track 'wgEncodeSydhTfbs' within hg19:chr1:100-101""" > > > > getTable(query) > > > > 44 min and still running. > > This can't be right ? > > > > > > Anyone have a work around? > > > > > This is an interesting little debugging problem. If you run with something > like options(error=recover) and interrupt after a little while you'll see a > complicated traceback and you can poke around in the stack. > > Basically, the query you have issued involves 781 tables. A checking > operation is applied to each of them. If you really want this computation, > you may have to wait. > > > a little more detail > > Browse[3]> object > Get track 'wgEncodeSydhTfbs' within hg19:chr1:100-101 > > > Browse[3]> tableName(object) > NULL > > this sends us into > > 4: tableNames(object) > 5: tableNames(object) > 6: .local(object, ...) > 7: sapply(tables, checkOutput) > 8: sapply(tables, checkOutput) > 9: lapply(X = X, FUN = FUN, ...) > 10: FUN(c("wgEncodeSydhTfbsGm12878Bhlhe40cIggmusPk", > "wgEncodeSydhTfbsGm12878Bh > > with a vector of 781 tables to be checked. perhaps you can focus your > query, or retrieve the specific data you want for local import to R > > > > Chris > > > > R version 2.15.0 (2012-03-30) > > Platform: i686-pc-linux-gnu (32-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] rtracklayer_1.16.3 GenomicRanges_1.8.13 IRanges_1.14.4 > > [4] BiocGenerics_0.2.0 > > > > loaded via a namespace (and not attached): > > [1] Biostrings_2.24.1 bitops_1.0-4.1 BSgenome_1.24.0 RCurl_1.91-1 > > [5] Rsamtools_1.8.6 stats4_2.15.0 tools_2.15.0 XML_3.9-4 > > [9] zlibbioc_1.2.0 > > _______________________________________________ > > 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 > [[alternative HTML version deleted]]