Rsamtools problem

[efoss]

In trying to use the Bioconductor package VariantTools, I received an error complaining about open.BamFile, which is an Rsamtools function. In tracking down the error, I found that I couldn't open a sample bam file (from Bioconductor package LungCancerLines) that I know is indexed correctly:

> myb <- BamFile('H1993.analyzed.bam', index = 'H1993.analyzed.bam.bai')
> class(myb)
[1] "BamFile"
attr(,"package")
[1] "Rsamtools"
> open.BamFile(myb)
[bam_index_load] fail to load BAM index.
Error in open.BamFile(myb) : failed to load BAM index
  file: /home/efoss/sequencing/VariantTools/H1993.analyzed.bam.bai
> myb
class: BamFile 
path: /home/efoss/sequencing/VariantTools/H1993.analyzed.bam
index: /home/efoss/sequencing/VariantTools/H1993.analyzed.bam.bai
isOpen: FALSE 
yieldSize: NA

You can see that the objects are of the correct classes, but I can't open the file using Rsamtools' open.BamFile function. In trying to track down this problem, I talked with a colleague who is a developer and uses a developer's version of R. (I work at the Fred Hutchinson Cancer Research Center in Seattle, which is a bit of a hotbed of R - and especially Bioconductor - activity.) He could open these files fine using his developer's version of R, but couldn't open the same files from within my account. His version of Rsamtools is more up to date than mine, but I can''t upgrade to his version because it's part of the developer's version of R. Does anyone see a way around this or, better yet, see how I am somehow making a mistake?

Thank you.

Eric