Hi Martin,
I'd really like to help, but from you code below I can't tell for which genome you are trying to do this (the value of 'gen'). I also have no idea how you came up with the 'track.name' vector.
In general, Gviz is using rtracklayer::tableNames to figure out which tables and tracks are available. So you should get the same results, assuming that you checked for the same chromosome.
Also please always include the output of sessionInfo() when asking for help in order for us to know which R and package version we are dealing with.
Florian

From: <Martin>, Tiphaine <tiphaine.martin@kcl.ac.uk<mailto:tiphaine.martin@kcl.ac.uk>>
Date: Thursday, February 13, 2014 11:18 PM
To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>>
Subject: Gviz problem to extract some track with UcscTrack like Broad ChromHMM

Dear Florian,

I am trying to use your package Gviz to visualise my data and some data from UCSC, for example: "Broad ChromHMM”. But I have a error message.
I don’t understand because I have checked with the package rtracklayer, whose your package inherits, the name of tracks and tables. Could you help me ?

Regards

Tiph
R Command used to find the name of track and table
>track.names["Broad ChromHMM"]
    Broad ChromHMM
“wgEncodeBroadHmm"

 >sapply(track, function(track) {
+     tableNames(ucscTableQuery(mySession, track=track))
+     })
      Broad ChromHMM
 [1,] "wgEncodeBroadHmmGm12878HMM"
 [2,] "wgEncodeBroadHmmH1hescHMM"
 [3,] "wgEncodeBroadHmmK562HMM"
 [4,] "wgEncodeBroadHmmHepg2HMM"
 [5,] "wgEncodeBroadHmmHuvecHMM"
 [6,] "wgEncodeBroadHmmHmecHMM"
 [7,] "wgEncodeBroadHmmHsmmHMM"
 [8,] "wgEncodeBroadHmmNhekHMM"
 [9,] "wgEncodeBroadHmmNhlfHMM"
> UcscTrack(genome = gen, chrom

My errors when I try to use  UcscTrack:
> UcscTrack(genome = gen, chromosome = chr, track = "Broad ChromHMM",
+           table="wgEncodeBroadHmmGm12878HMM",
+           from = start, to = end, trackType = "AnnotationTrack",
+           rstarts = "chromStart", rends = "chromEnd", gene = "name",
+           symbol = "name", strand = "strand",
+           fill = "itemRgb", name = "UCSC Genes”)

Error in match.arg(track, sort(c(availTracks, names(availTracks)))) :
  'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv


> UcscTrack(genome = gen, chromosome = chr, track = "wgEncodeBroadHmm",
+           table="wgEncodeBroadHmmGm12878HMM",
+           from = start, to = end, trackType = "AnnotationTrack",
+           rstarts = "chromStart", rends = "chromEnd", gene = "name",
+           symbol = "name", strand = "strand",
+           fill = "itemRgb", name = "UCSC Genes”)

Error in match.arg(track, sort(c(availTracks, names(availTracks)))) :
  'arg' should be one of “1000G Ph1 Accsbl”, “1000G Ph1 Vars”, “46-Way Cons”, “5% Lowest S”, “acembly”, “AceView Genes”, “Affy Exon Array”, “Affy GNF1H”, “Affy RNA Loc”, “Affy U133”, “Affy U133Plus2”, “Affy U95”, “affyExonArray”, “affyGnf1h”, “affyU133”, “affyU133Plus2”, “affyU95”, “All SNPs(132)”, “All SNPs(135)”, “All SNPs(137)”, “All SNPs(138)”, “Allen Brain”, “allenBrainAli”, “allHg19RS_BW”, “altSeqComposite10”, “Assembly”, “BAC End Pairs”, “bacEndPairs”, “Base Position”, “BU ORChID”, “Burge RNA-seq”, “burgeRnaSeqGemMapperAlign”, “CCDS”, “ccdsGene”, “CD34 DnaseI”, “CGAP SAGE”, “cgapSage”, “chainSelf”, “Chromosome Band”, “clinvar”, “ClinVar Variants”, “Common SNPs(132)”, “Common SNPs(135)”, “Common SNPs(137)”, “Common SNPs(138)”, “Cons Indels MmCf”, “cons100way”, “cons46way”, “Conserv

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