[BioC] Error in assign while calling the vmatchPattern function

[mattia pelizzola]

Hi,

I have a recurrent but not reproducible error.. If I run the same
piece of code twice the error will disappear, but it will likely shop
up the day after.
This is the error message:

Error in assign(".defined", method at defined, envir = envir) :
  formal argument "envir" matched by multiple actual arguments
Calls: vmatchPattern ... lapply -> FUN -> loadMethod -> loadMethod -> assign

this is the code where the error show up calling the vmatchPattern
function for one chromosome. The code is actually repeated several
times for all the chromosomes during the same R session:

chrseq=Hsapiens$chr1
Gviews = Views(chrseq, starts, ends)    #  where length(starts)> 20000
Gset = DNAStringSet(Gviews)
querySeq=DNAString('ATTH')
a = startIndex(vmatchPattern(querySeq, Gset, fixed=F))



and finally this is my sessionInfo:

R version 2.8.1 (2008-12-22)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg18_1.3.11 BSgenome_1.10.3
[3] Biostrings_2.10.15                 IRanges_1.0.11

loaded via a namespace (and not attached):
[1] grid_2.8.1         lattice_0.17-17    Matrix_0.999375-20



thanks,

mattia