On Sun, Sep 6, 2009 at 8:48 PM, [email protected] < [email protected]> wrote:
> Dear Bioc-sig-sequencing, > > I would like to learn about the rtracklayer package by working thru its > vignette using code in rtracklayer.R > > I have tried using both the stable and developer versions of R. There > appears to be an error when using the stable version. The developer version > comes to a point where I don't know how to proceed. A short description for > each attempt follows. > > P.Terry > [email protected] > > ########################################################################## > > 1. Stable version. > > Chunk 19 produces error message: > > > subTargetTrack <- targetTrack[1,] # get first feature > > view <- browserView(session, range(subTargetTrack) * -10, > + pack = "targets") > Error in resolveTrackIndex(x, i) : Unknown tracks:targets > > > > If skip forward to chunk 22 (2.2.4 A shortcut) > > > browseGenome(subTargetTrack) > A genome browser session of class 'UCSCSession' with 1 views and 206 tracks > > > > Produces new Foxfire browser page at ucsc browser, but with a window (box) > near top of the page with the error message: > > Error(s): > > * Sorry, couldn't locate chrchr1 in genome database > > My sessionInfo() is: > > > sessionInfo() > R version 2.9.2 (2009-08-24) > x86_64-pc-linux-gnu > > locale: > > LC_CTYPE=en_US.UTF-8;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_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] rtracklayer_1.4.1 RCurl_0.98-1 bitops_1.0-4.1 > [4] org.Hs.eg.db_2.2.11 microRNA_1.2.0 Rlibstree_0.3-2 > [7] Biostrings_2.12.8 IRanges_1.2.3 limma_2.18.3 > [10] genefilter_1.24.2 humanStemCell_0.2.2 hgu133plus2.db_2.2.11 > [13] RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.6.1 > [16] Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 BSgenome_1.12.3 splines_2.9.2 survival_2.35-5 > [5] tools_2.9.2 XML_2.5-1 xtable_1.5-5 > > > > > 2. Developer version (R-49517) > > At chunk 14: > > > track(session, "targets") <- targetTrack > Called from: FUN(X[[1L]], ...) > Browse[1]> > > My question is what to do at this point? > > Sorry, just checked in change (version 1.5.13) to remove a stray browser() command. Should be fixed in devel. Michael > Ctl^C won't return to R prompt ? > > My sessionInfo() is > > > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-09-01 r49517) > x86_64-unknown-linux-gnu > > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 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_1.5.12 RCurl_1.2-0 bitops_1.0-4.1 > [4] microRNA_1.3.1 Rlibstree_0.3-2 Biostrings_2.13.36 > [7] IRanges_1.3.66 limma_2.19.4 genefilter_1.25.7 > [10] humanStemCell_0.2.3 hgu133plus2.db_2.3.4 org.Hs.eg.db_2.3.4 > [13] RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.7.11 > [16] Biobase_2.5.6 > > loaded via a namespace (and not attached): > [1] annotate_1.23.1 BSgenome_1.13.11 splines_2.10.0 survival_2.35-5 > [5] tools_2.10.0 XML_2.6-0 xtable_1.5-5 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
