[Bioc-devel] AnnotationDbi and select function

Dear all,

I have an error using the select function from the AnnotationDbi package.
I try to convert some geneID into Symbol, but for some strange reasons it crashed.


library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
isActiveSeq(txdb)[seqlevels(txdb)] <- FALSE
isActiveSeq(txdb)[c("chr16","chr1")] <- TRUE
geneGR <- exonsBy(txdb, "gene")
library(Homo.sapiens)
symbol <- select(Homo.sapiens, keys = names(geneGR), keytype = "GENEID", columns = "SYMBOL")
Erreur dans head(select(Homo.sapiens, keys = names(geneGR)[1:1001], keytype = "GENEID",  :
   erreur d'?valuation de l'argument 'x' lors de la s?lection d'une m?thode pour la fonction 'head' : Erreur dans res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :

length(geneGR)

[1] 3269
## The first 1K work

symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1000], keytype = "GENEID", columns = "SYMBOL")

## The 1K+1 does not !

symbol <- select(Homo.sapiens, keys = names(geneGR)[1:1001], keytype = "GENEID", columns = "SYMBOL")

Erreur dans res[, .reverseColAbbreviations(x, cnames), drop = FALSE] :
   nombre de dimensions incorrect

It looks like I cannot convert more than 1K elements ?? Any reason for that ?
Thank you very much
Nicolas

sessionInfo()

R Under development (unstable) (2014-03-05 r65125)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8
  [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8
  [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
  [1] Homo.sapiens_1.1.2
  [2] org.Hs.eg.db_2.10.1
  [3] GO.db_2.10.1
  [4] RSQLite_0.11.4
  [5] DBI_0.2-7
  [6] OrganismDbi_1.5.3
  [7] XVector_0.3.7
  [8] TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
  [9] GenomicFeatures_1.15.9
[10] AnnotationDbi_1.25.14
[11] GenomeInfoDb_0.99.17
[12] Biobase_2.23.6
[13] GenomicRanges_1.15.32
[14] IRanges_1.21.32
[15] BiocGenerics_0.9.3
[16] RColorBrewer_1.0-5
[17] reshape2_1.2.2
[18] reshape_0.8.4
[19] plyr_1.8.1
[20] ggplot2_0.9.3.1
[21] Matrix_1.1-2-2

loaded via a namespace (and not attached):
  [1] BatchJobs_1.2             BBmisc_1.5
  [3] BiocParallel_0.5.16       biomaRt_2.19.3
  [5] Biostrings_2.31.14        bitops_1.0-6
  [7] brew_1.0-6                BSgenome_1.31.12
  [9] codetools_0.2-8           colorspace_1.2-4
[11] dichromat_2.0-0           digest_0.6.4
[13] fail_1.2                  foreach_1.4.1
[15] GenomicAlignments_0.99.29 graph_1.41.3
[17] grid_3.1.0                gtable_0.1.2
[19] iterators_1.0.6           labeling_0.2
[21] lattice_0.20-27           MASS_7.3-29
[23] munsell_0.4.2             proto_0.3-10
[25] RBGL_1.39.2               Rcpp_0.11.0
[27] RCurl_1.95-4.1            Rsamtools_1.15.32
[29] rtracklayer_1.23.15       scales_0.2.3
[31] sendmailR_1.1-2           stats4_3.1.0
[33] stringr_0.6.2             tools_3.1.0
[35] XML_3.98-1.1              zlibbioc_1.9.0

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