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
Merge branch 'master' of github.com:Bioconductor/BiocParallel
Merge branch 'master' of github.com:Bioconductor/BiocParallel
Add and use splitList function in bpvec

This makes it work correctly for non-fork-based parallel methods such
as SNOW and Dopar, not just fork-based ones like multicore.
Implement a default bpvec function that works for any param type

Now the default method for bpvec dispatches to bplapply, passing the
param object through to bplapply. So if this is the correct behavior
for a given param class, then there is no need to provide a specific
method just for that param class. The only reason to provide a bpvec
method specific to a given param class is if that param class can
provide a more efficient implementation than simply splitting the
input and dispatching to bplapply.

Hence, now the DoparParam and SnowParam methods of bpvec are now
replaced by the default method, and only MulticoreParam gets its own
bpvec method.
clean bpvec implementation

- split indicies rather than list for memory efficiency (?)
- splitIndicies works for 0 arguments; unit test
Merge branch 'master' of github.com:Bioconductor/BiocParallel
Make SnowParam work with type="FORK"

You can't do "makeForkCluster(0)" (it throws an error), so for
type="FORK", .nullCluster uses type="PSOCK" instead, which gives the
expected result because makeForkCluster returns an object of type
SOCKCluster anyway.
Add basic tests for bplapply, bpvec, bpvectorize
Fix typo in bpvec

It used splitIndex instead of splitIndices
Merge branch 'misc-fix' of https://github.com/DarwinAwardWinner/BiocParallel into improvs
clean up unit tests and bugs revealed by same

- tests belong in no-argument function calls
- export DoparParam class and constructor
- bpvec,ANY,ANY,BiocParallelParam bplapply cannot use X, FUN as arg names
- Use Suggests: DESCRIPTION tag for packages used in unit tests
further adjust bpvec to pass X, FUN