Update parallel processing to BiocParallel

[sneumann]

Update parallel processing to BiocParallel

[jorainer]

Done that in 55817bd . For now I've just added additional functions/methods instead of replacing the original ones. If you find that acceptable (RUnit test confirms results are identical) I could go forward replacing the original ones, deprecating the old code (e.g. obsolete xcmsParallelSetup etc) and updating the documentation.

[jorainer]

Aah sorry; I pushed to the wrong remote, i.e. directly to the devel branch instead of the devel branch of my fork.

Since the changes I made (commit e81b590) are mainly related to the parallel processing (i.e. use BiocParallel bplapply for parallel processing instead of the old code) there should be no big problem.

In addition I fixed some minor stuff in the NAMESPACE to reduce the warnings on package load.
I hope you find my changes acceptable. In future I will definitely avoid pushing directly to devel.

[jorainer]

I think that issue can be closed; remains to bump the package version in DESCRIPTION and commit to Bioc svn.

[rietho]

To let you know: The manual of fillPeaks (xcms/man/fillPeaks.chrom-methods.Rd) does not show nSlaves as deprecated yet.

[jorainer]

Thanks for looking into that! I'll fix.