Cast integer objects to numeric type to handle large integers

[ycl6]

This PR cast some R objects that store integer values to numeric type, so to avoid errors/warnings when the calculation of FASTQs reads/bases numbers are larger than .Machine$integer.max. Specifically,

• The NREADS and NBASES are changed to numeric type, to allow learnErrors() to run. "NAs produced by integer overflow" when running learnErrors #1747
• The rval matrix is changed to numeric type, to avoid NAs produced by integer overflow warning when running dada(). Integer overflow #1074