[BioC] Gviz UcscTrack error
Anna Sawicka [guest]
guest at bioconductor.org
Tue Jan 7 22:44:27 CET 2014
Dear All,
Gviz refuses to generate a UcscTrack. The code below worked in the middle of December:
genetrack=UcscTrack(track="RefSeq Genes", table="refGene",
trackType="GeneRegionTrack",chromosome="chr5", genome="mm9",
rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2",
transcript="name", strand="strand", name="RefSeq Genes", feature="name2",
showId=T, from=30334169, to=30349988, fill = "green")
But now it generates the following error:
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
line 1 did not have 2 elements
R as well as Bioconductor version is up-to-date. Does anyone know what the problem might be?
Thanks a lot!
Ania
-- output of sessionInfo():
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.22.0 GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0
[6] Gviz_1.6.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.24.0 Biobase_2.22.0 biomaRt_2.18.0 Biostrings_2.30.1
[5] biovizBase_1.10.7 bitops_1.0-6 BSgenome_1.30.0 cluster_1.14.4
[9] colorspace_1.2-4 DBI_0.2-7 dichromat_2.0-0 Formula_1.1-1
[13] GenomicFeatures_1.14.2 Hmisc_3.13-0 labeling_0.2 lattice_0.20-24
[17] latticeExtra_0.6-26 munsell_0.4.2 plyr_1.8 RColorBrewer_1.0-5
[21] RCurl_1.95-4.1 Rsamtools_1.14.2 RSQLite_0.11.4 scales_0.2.3
[25] splines_3.0.2 stats4_3.0.2 stringr_0.6.2 survival_2.37-4
[29] tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0
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