[BioC] VariantAnnotation development branch issue

[Hamid Bolouri]

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