the code :

bamf <- system.file("file.bam",package="rbamtools",idx=FALSE,verbose=0)
r1 <- bamReader(bamf)

the error:

Error in .local(.Object, ...) : [bam_reader_open] Opening bam_file "" failed! ```

It's not clear where your command is coming from; system.file() does not have arguments 'idx' or FALSE. Also, the return value of the function is

> system.file("file.bam",package="rbamtools",idx=FALSE,verbose=0)
[1] ""

so you are asking bamReader() to open a file called ""! bamReader() expects a path to a BAM file, for instance. Maybe if you used

bamf = file.choose()

to select one of your BAM fiiles, and then

rl = bamReader(bamf)

you would have more success?