Building vignette `mapping.Rmd` fails.

The build process of Pbase fails on the Bioc servers: http://www.bioconductor.org/checkResults/devel/bioc-LATEST/Pbase/

Error message:

Quitting from lines 392-405 (mapping.Rmd) Error: processing vignette 'mapping.Rmd' failed with diagnostics: subscript contains NAs or out-of-bounds indices Execution halted

It seems that the start/end positions of the gene moved/changed in the ensembl database and were not updated in the TxDb.Hsapiens.UCSC.hg19.knownGene object?!

bm[1, c("start_position", "end_position")]
#  start_position end_position
#1       78065188     78129296
#  (were 77320685 and 77384793 before)

The changed start/end positions result in an empty (zero rows) GeneRegionTrack object because there is no overlap between the position in the txdb and the bm start/end positions.

library("TxDb.Hsapiens.UCSC.hg19.knownGene")
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
txTr <- GeneRegionTrack(txdb, chromosome = "chrX",
                        start = bm$start_position[1],
                        end = bm$end_position[1])

txTr
#GeneRegionTrack 'GeneRegionTrack'
#| genome: hg19
#| active chromosome: chrX
#| annotation features: 0

head(as(txTr, "data.frame"))
# [1] X.seqnames   X.start      X.end        X.width      X.strand     X.feature    X.exon
# [8] X.transcript X.gene       X.symbol     feature      exon         transcript   gene
#[15] symbol
#<0 rows> (or 0-length row.names)

lgatto / Pbase

Building vignette `mapping.Rmd` fails. #8