Rcpp drop #17
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Rcpp drop #17
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…ts instead of Rsamtools (aka, changes from R 3.0.2 to 3.1)
…R CMD CHECK in 350 secs. Note that example('calculateStats', 'derfinder') leads to very small (-2e-12 to 2e-12) differences in calculated F-stats
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We are dropping the dependencies on Rcpp and RcppArmadillo because RcppArmadillo now requires a newer compiler than the one installed in our cluster. While our cluster will get upgraded, it could be possible that other users would have problems installing these dependencies.
As far as we have noticed, calculating the F-statistics with Rcpp and RcppArmadillo lead to a small reduction in memory used (specially with the largest chromosomes, like chromosome 1). Timing wise, there seems to be nearly no difference. Numerically wise, the observed differences are very small (in the order of +- 2e-12).
In the future, we might re-incorporate Rcpp and RcppArmadillo. But we will evaluate this at a later time.
PS If you know of a faster or less memory intensive way of calculating the F-statistics please let us know.