I have some old code that's stopped working since I upgraded to R2.15 due to the unpackVcf method not being found. Is this still in the devel branch? or has it been deprecated completely?

Or does anyone know another workaround I can use? 

thanks

-s




>   vcfScan <- scanVcf(file_name)
There were 50 or more warnings (use warnings() to see the first 50)
>   scanVcfHeader(file_name)
class: VCFHeader 
samples(3): Fd03_high.vcf Fd03_low.vcf Fd03_zero.vcf
meta(2): fileformat samtoolsVersion
fixed(0):
info(21): DP DP4 ... AC AN
geno(7): DP4 GT ... SP PL
>   vcf <- unpackVcf(vcfScan, vcftab, info=TRUE, geno=TRUE)
Error: could not find function "unpackVcf"
>   sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
 [1] splines   stats4    grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] VariantAnnotation_1.4.7 GGtools_4.6.2           GGBase_3.20.0           snpStats_1.8.1          Matrix_1.0-10          
 [6] survival_2.37-2         ShortRead_1.16.3        latticeExtra_0.6-24     RColorBrewer_1.0-5      Rsamtools_1.10.2       
[11] lattice_0.20-13         Biostrings_2.26.3       gridExtra_0.9.1         zoo_1.7-9               plyr_1.8               
[16] rtracklayer_1.18.2      GenomicRanges_1.10.6    IRanges_1.16.4          BiocGenerics_0.4.0      ggbio_1.6.6            
[21] ggplot2_0.9.3           BiocInstaller_1.8.3    

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.20.3   BSgenome_1.26.1        Biobase_2.18.0         DBI_0.2-5              GenomicFeatures_1.10.1
 [6] Hmisc_3.10-1           MASS_7.3-23            RCurl_1.95-3           RSQLite_0.11.2         XML_3.95-0.1          
[11] annotate_1.36.0        biomaRt_2.14.0         biovizBase_1.6.2       bit_1.1-9              bitops_1.0-4.2        
[16] cluster_1.14.3         colorspace_1.2-1       dichromat_2.0-0        digest_0.6.1           ff_2.2-10             
[21] genefilter_1.40.0      gtable_0.1.2           hwriter_1.3            labeling_0.1           munsell_0.4           
[26] parallel_2.15.2        proto_0.3-10           reshape2_1.2.2         scales_0.2.3           stringr_0.6.2         
[31] tools_2.15.2           xtable_1.7-0           zlibbioc_1.4.0        


--
Seth Redmond
  Unité Génetique et Génomique des Insectes Vecteurs
  Institut Pasteur
  28,rue du Dr Roux
  75724 PARIS
seth.redmond@pasteur.fr


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