[BioC] zero-row result breaks select() on PolyPhen.Hsapiens.* and SIFT.Hsapiens.*

[Robert Castelo]

Dear list,

interrogating the TxDb.Hsapiens.UCSC.hg19.knownGene package with no 
result gives the following expected result:

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
select(TxDb.Hsapiens.UCSC.hg19.knownGene, keys="dummy", 
keytype="GENEID", cols="SYMBOL")
[1] GENEID
<0 rows> (or 0-length row.names)

however, when i try the same with the annotation packages 
PolyPhen.Hsapiens.dbSNP131 and SIFT.Hsapiens.dbSNP132, the select 
instruction breaks into an error:

library(SIFT.Hsapiens.dbSNP132)
library(PolyPhen.Hsapiens.dbSNP131)

select(SIFT.Hsapiens.dbSNP132, keys=c("dummy"))
Error in data.frame(RSID = unlist(rsid), PROTEINID = unlist(protein_id),  :
   arguments imply differing number of rows: 1, 0

select(PolyPhen.Hsapiens.dbSNP131, keys="dummy")
Error in `*tmp*`$RSID : $ operator is invalid for atomic vectors

i guess these two annotation packages should work analogously to 
TxDb.Hsapiens.UCSC.hg19.knownGene, and give just a 0-row data.frame 
object, right?

these errors reproduce also with the current devel version of BioC, 
please find below both sessionInfo() outputs.

cheers,
robert.

=====RELEASE====
R version 3.0.1 (2013-05-16)
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  stats     graphics  grDevices utils     datasets methods   
base

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 GenomicFeatures_1.12.3
  [3] AnnotationDbi_1.22.6 Biobase_2.20.1
  [5] PolyPhen.Hsapiens.dbSNP131_1.0.2 SIFT.Hsapiens.dbSNP132_1.0.2
  [7] RSQLite_0.11.4 DBI_0.2-7
  [9] VariantAnnotation_1.6.7 Rsamtools_1.12.4
[11] Biostrings_2.28.0 GenomicRanges_1.12.5
[13] IRanges_1.18.3 BiocGenerics_0.6.0
[15] vimcom_0.9-8 setwidth_1.0-3
[17] colorout_1.0-0

loaded via a namespace (and not attached):
[1] biomaRt_2.16.0     bitops_1.0-6       BSgenome_1.28.0 
RCurl_1.95-4.1     rtracklayer_1.20.4
[6] stats4_3.0.1       tools_3.0.1        XML_3.95-0.2 zlibbioc_1.6.0



=====DEVEL=====
R version 3.0.1 (2013-05-16)
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  stats     graphics  grDevices utils     datasets methods   
base

other attached packages:
  [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 GenomicFeatures_1.13.40
  [3] AnnotationDbi_1.23.23 Biobase_2.21.7
  [5] PolyPhen.Hsapiens.dbSNP131_1.0.2 SIFT.Hsapiens.dbSNP132_1.0.2
  [7] RSQLite_0.11.4 DBI_0.2-7
  [9] VariantAnnotation_1.7.46 Rsamtools_1.13.41
[11] Biostrings_2.29.19 GenomicRanges_1.13.44
[13] XVector_0.1.4 IRanges_1.19.37
[15] BiocGenerics_0.7.5 vimcom_0.9-8
[17] setwidth_1.0-3 colorout_1.0-0

loaded via a namespace (and not attached):
[1] biomaRt_2.17.3      bitops_1.0-6        BSgenome_1.29.1 
RCurl_1.95-4.1      rtracklayer_1.21.12
[6] stats4_3.0.1        tools_3.0.1         XML_3.95-0.2 zlibbioc_1.7.0