[BioC] VariantAnnotation development branch issue
Hamid Bolouri
hbolouri at fhcrc.org
Tue Nov 6 03:42:38 CET 2012
hi : I am finding that the development version of R with VariantAnnotation_1.5.7 runs fine on one PC but not on another with very similar hardware and configuration:
> fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools",
+ mustWork=TRUE)
> tbx <- TabixFile(fl)
Error in eval(expr, envir, enclos) :
no slot of name "generator" for this object of class "refObjectGenerator"
>
> traceback()
7: eval(expr, envir, enclos)
6: eval(expr, p)
5: eval.parent(substitute(x at generator$name))
4: g$new
3: g$new
2: .RsamtoolsFile(.TabixFile, file, index, yieldSize = yieldSize,
...)
1: TabixFile(fl)
>
> sessionInfo()
R Under development (unstable) (2012-11-01 r61067)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.8.0 GenomicFeatures_1.11.1
[3] org.Hs.eg.db_2.8.0 RSQLite_0.11.2
[5] DBI_0.2-5 AnnotationDbi_1.21.4
[7] Biobase_2.19.0 VariantAnnotation_1.5.7
[9] Rsamtools_1.11.5 Biostrings_2.27.6
[11] GenomicRanges_1.11.8 IRanges_1.17.10
[13] BiocGenerics_0.5.1
loaded via a namespace (and not attached):
[1] biomaRt_2.15.0 bitops_1.0-4.1 BSgenome_1.27.1 RCurl_1.95-3 rtracklayer_1.19.2
[6] stats4_2.16.0 tools_2.16.0 XML_3.95-0.1 zlibbioc_1.5.0
Any thoughts?
Thanks!
Hamid
--
http://labs.fhcrc.org/bolouri
More information about the Bioconductor
mailing list