Merge branch 'master' of github.com:Bioconductor/BiocParallel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71233 bc3139a8-67e5-0310-9ffc-ced21a209358
Add chunking options to pvec

This adds three options to pvec: "num.chunks", "chunk.size", and "mc.preschedule". These allow splitting of the job into more chunks than there are cores, which is sometimes appropriate.

This is facilitated by reimplementing "pvec" to use "mclapply" internally.

Needs documentation.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71234 bc3139a8-67e5-0310-9ffc-ced21a209358
Document new pvec chunking options

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71235 bc3139a8-67e5-0310-9ffc-ced21a209358
Modify windows pvec stub to accept chunking args

This modifies the pvec stub on windwos to accept the same chunking
arguments as the unix version. This is for compatibility only; the
chunking arguments are all ignored.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71236 bc3139a8-67e5-0310-9ffc-ced21a209358
documentation formatting

- no spill over 80 columns for text help

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71237 bc3139a8-67e5-0310-9ffc-ced21a209358
add pvectorize

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71238 bc3139a8-67e5-0310-9ffc-ced21a209358
update README and NEWS
correctly name 'tests' directory
Merge branch 'master' of github.com:Bioconductor/BiocParallel

Conflicts:
	inst/NEWS.Rd
standardize interface

- bpfun(X, FUN, ..., param) for bplapply, bpvec
- MulticoreParam, SnowParam, SerialParam
- register, registered
- bparallelize
code tidy

- zap trailing white space
- bparallelize,ANY,missing-method re-calls rather than re-implements
rename bparallelize bpvectorize
Merge branch 'master' of github.com:Bioconductor/BiocParallel

Conflicts:
	DESCRIPTION
	NAMESPACE
	README.md
	man/unix/pvec.Rd

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71569 bc3139a8-67e5-0310-9ffc-ced21a209358
Make SerialParam a singleton class
Add new BiocParallelParam class that uses foreach & %dopar%
minor changes to contributed patch

- return() is a function
- less nesting of function calls
- use explicit generic rather than callGeneric, for clarity
Make SerialParam a singleton class

From: Ryan C. Thompson <rct@thompsonclan.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71593 bc3139a8-67e5-0310-9ffc-ced21a209358
Add new BiocParallelParam class that uses foreach & %dopar%

From: Ryan C. Thompson <rct@thompsonclan.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71594 bc3139a8-67e5-0310-9ffc-ced21a209358
minor changes to contributed patch

- return() is a function
- less nesting of function calls
- use explicit generic rather than callGeneric, for clarity

From: Martin Morgan <mtmorgan@fhcrc.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocParallel@71595 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' of github.com:Bioconductor/BiocParallel