Maybe Jim and Simon have something different with their network configuration, e.g. routing through a proxy, or something. Michael On Fri, Jun 5, 2009 at 5:57 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Michael Lawrence wrote: > > >> >> On Thu, Jun 4, 2009 at 7:03 AM, James W. MacDonald <jmacdon@med.umich.edu<mailto:>> jmacdon@med.umich.edu>> wrote: >> >> Hi Michael, >> >> I get the same results as Simon. In fact, if I source() the vignette >> code and then run some of the chunks that are set to eval=false, I >> get errors: >> >> > source("c:/R-2.9.0/library/rtracklayer/doc/rtracklayer.R") >> Loading required package: hgu133plus2.db >> Loading required package: AnnotationDbi >> Loading required package: DBI >> Loading required package: Biostrings >> Loading required package: IRanges >> [snip] >> >> > session <- browserSession("UCSC") >> > track(session, "targets") <- targetTrack >> > targetTrack >> RangedData: 3063 ranges by 3 columns >> columns(3): strand name target >> sequences(23): chr1 chr10 chr11 chr12 chr13 ... chr7 chr8 chr9 chrX >> > view <- browserView(session, range(targetTrack)*-10, pack="targets") >> Error in validObject(x) : >> invalid class "IRanges" object: the widths must be non-NA integers >> In addition: Warning message: >> In numeric2integer(value) : NAs introduced by coercion >> Error in ucscForm(range) : >> error in evaluating the argument 'object' in selecting a method for >> function 'ucscForm' >> > view <- browserView(session, range(subTargetTrack) * -10,pack = >> "targets") >> Error in resolveTrackIndex(x, i) : Unknown tracks:targets >> >> If I export targetTrack as a bedfile and upload to UCSC I get no >> errors and can view the track without problems. >> >> >> I'm kind of at a loss here. I have your same sessionInfo on my machine >> (fresh R install, everything via biocLite) and yet it seems to work just >> fine. What's your curl version? Mine is 7.19.4. >> > > I am on Windows, and am using the binary from BioC, so the curl version is > whatever you guys are using to build the package with. I assume it is > relatively new? > > Jim > > > >> Michael >> >> >> On another subject, you might consider replacing the plot of the >> cpneTrack in the vignette with a .png rather than a .pdf. Trying to >> scroll through the vignette is a real drag when you get to that plot. >> >> >> Yes, good idea. >> >> >> >> > sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods >> [7] base >> >> other attached packages: >> [1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 >> [2] BSgenome_1.12.2 >> [3] rtracklayer_1.4.0 >> [4] RCurl_0.97-3 >> [5] bitops_1.0-4.1 >> [6] org.Hs.eg.db_2.2.11 >> [7] microRNA_1.2.0 >> [8] Rlibstree_0.3-2 >> [9] Biostrings_2.12.4 >> [10] IRanges_1.2.2 >> [11] genefilter_1.24.2 >> [12] humanStemCell_0.2.0 >> [13] hgu133plus2.db_2.2.11 >> [14] RSQLite_0.7-1 >> [15] DBI_0.2-4 >> [16] AnnotationDbi_1.6.0 >> [17] affy_1.22.0 >> [18] Biobase_2.4.1 >> [19] limma_2.18.1 >> [20] biomaRt_2.0.0 >> >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 annotate_1.22.0 preprocessCore_1.6.0 >> [4] splines_2.9.0 survival_2.35-4 tools_2.9.0 >> [7] XML_2.3-0 xtable_1.5-5 >> >> Best, >> >> Jim >> >> >> >> Michael Lawrence wrote: >> >> On Wed, Jun 3, 2009 at 3:22 AM, Simon Anders <anders@ebi.ac.uk>> <mailto:anders@ebi.ac.uk>> wrote: >> >> Hi Michael, >> >> I've just tried to use rtracklayer, following your vignette, >> and ran into >> two problems. >> >> >> 1. I cannot add any tracks to a session. >> >> I entered the code in the vignette to produce the "targets" >> track and >> exported it as "targets.bed". To make things easier to >> follow, let's say, I >> start from there with a fresh R session: >> >> library(rtracklayer) >> >> # Import the data >> targets <- import("targets.bed") >> # targets is now a RangedData object with 3052 ranges and >> # sequence names chr1 chr10 chr11 chr12 ... >> >> # Create a session >> session <- browserSession("UCSC") >> >> # Add the 'targets' track to the session: >> track(session, "MYTRACK") <- targets >> >> Is this last command correct? It does not produce an error, >> but it does not >> seem to do anything, either. If I list all the tracks in the >> session with >> trackNames(session) >> I get a list of 196 UCSC standard tracks, but "MYTRACK" is >> not mentioned. >> >> How do I correctly add a track? >> >> >> Well, I can say that this works for me. I need to look into >> parsing the >> error messages returned by UCSC. You can always try uploading >> to UCSC >> manually to see what went wrong. I know that back in December >> the BED output >> was mishandling the score values. >> >> >> >> 2. There is some mangling happening with the chromosome names. >> >> The man page for 'browserView' suggests to try: >> >> browserView(session, GenomicRanges(20000, 50000, "chr2")) >> >> Doing this asks my web browser to open the following URL: >> >> >> >> http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 >> < >> http://genome.ucsc.edu/cgi- bin/hgTracks?position=chrchr2%3a20000-50000&hgsid=133834314 >> > >> >> Note that it says "chrchr2", i.e., a superfluous "chr" got >> prefixed to the >> sequence name. Obviously, the UCSC page cannot deal with >> this and one gets >> an error message displayed by JavaScript that "chrchr2" is >> not known. >> >> I run into the same problem if I follow the vignette's code >> to demonstrate >> 'browserView'. >> >> If I try >> browserView(session, GenomicRanges(20000, 50000, "2")) >> I get the range chr2:20000-50000 correctly displayed in my >> web browser. >> There is, however, still now sight of "MYTRACK". >> >> What's going wrong here? >> >> >> Thanks for pointing this out. I've fixed this for version 1.5.3. >> >> Michael >> >> >> >> sessionInfo() >> >> R version 2.9.0 (2009-04-17) >> x86_64-unknown-linux-gnu >> >> locale: >> >> >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=e n_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID ENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets >> methods base >> >> other attached packages: >> [1] rtracklayer_1.4.0 RCurl_0.94-1 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.4.0 Biostrings_2.12.0 BSgenome_1.12.0 >> IRanges_1.2.0 >> [5] XML_2.3-0 >> >> >> Cheers >> Simon >> >> >> +--- >> | Dr. Simon Anders, Dipl. Phys. >> | European Bioinformatics Institute, Hinxton, Cambridgeshire, >> UK >> | office phone +44-1223-492680, mobile phone +44-7505-841692 >> | preferred (permanent) e-mail: sanders@fs.tum.de >> <mailto:sanders@fs.tum.de> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > [[alternative HTML version deleted]]