[Bioc-devel] cryptic error in VariantAnnotation::locateVariants()

[Robert Castelo]

hi Valerie,

i'm afraid i have hit another cryptic error in locateVariants() related 
to some recent update of the devel version of the package, could you 
take a look at it? (code below..)

thanks!!

robert.

==========================================

library(VariantAnnotation)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

gr <- GRanges("chrX", IRanges(start=128913961, width=1))

loc <- locateVariants(gr, txdb,
                       AllVariants(intergenic=IntergenicVariants(0, 0)))
Error in ans[order(meta$QUERYID, meta$TXID, meta$CDSID, meta$GENEID),  :
   error in evaluating the argument 'i' in selecting a method for 
function '[': Error in order(c(1L, 1L), c("76534", "76534"), 
list(integer(0), integer(0)),  :
   unimplemented type 'list' in 'listgreater'
4: ans[order(meta$QUERYID, meta$TXID, meta$CDSID, meta$GENEID),
        ]
3: .local(query, subject, region, ...)
2: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
        0)))
1: locateVariants(gr, txdb, AllVariants(intergenic = IntergenicVariants(0,
        0)))
sessionInfo()
R Under development (unstable) (2014-10-14 r66765)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF8       LC_NUMERIC=C 
LC_TIME=en_US.UTF8        LC_COLLATE=en_US.UTF8
  [5] LC_MONETARY=en_US.UTF8    LC_MESSAGES=en_US.UTF8 
LC_PAPER=en_US.UTF8       LC_NAME=C
  [9] LC_ADDRESS=C              LC_TELEPHONE=C 
LC_MEASUREMENT=en_US.UTF8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.0.0 GenomicFeatures_1.19.18 
               AnnotationDbi_1.29.17
  [4] Biobase_2.27.1                          VariantAnnotation_1.13.29 
               Rsamtools_1.19.27
  [7] Biostrings_2.35.8                       XVector_0.7.4 
               GenomicRanges_1.19.37
[10] GenomeInfoDb_1.3.13                     IRanges_2.1.38 
              S4Vectors_0.5.19
[13] BiocGenerics_0.13.4                     vimcom_1.0-0 
              setwidth_1.0-3
[16] colorout_1.0-3

loaded via a namespace (and not attached):
  [1] base64enc_0.1-2          BatchJobs_1.5            BBmisc_1.9 
          BiocParallel_1.1.13
  [5] biomaRt_2.23.5           bitops_1.0-6             brew_1.0-6 
          BSgenome_1.35.17
  [9] checkmate_1.5.1          codetools_0.2-10         DBI_0.3.1 
          digest_0.6.8
[13] fail_1.2                 foreach_1.4.2 
GenomicAlignments_1.3.27 iterators_1.0.7
[17] RCurl_1.95-4.5           RSQLite_1.0.0 
rtracklayer_1.27.7       sendmailR_1.2-1
[21] stringr_0.6.2            tools_3.2.0              XML_3.98-1.1 
         zlibbioc_1.13.1