Merge pull request #3 from OHI-Science/master

including high seas and fixes in bbest repo
since problems with ohicore::Conf class not being found, ran build check and discovered errors with NAMESPACE unnecessarily calling stringr and sqldf. So removed dependencies (TODO: migrate sqldf() calls to dplyr), ran document() and trying with new NAMESPACE.
commented out Conf_write documentation and inserted blank line after export of classes
moved TODO comment at top to bottom, so starts with class name
cleaning up files based on check() messages
iterating over previous commits to find culprit to #80. strangely, now Conf.Rd and Conf-class.Rd showing up as new files. Added automated test to check for existence of key classes Conf and Layers.
updated rate limiting sleep and output of log.txt
export(Conf) export(Layers) added back to NAMESPACE since iterate_commits.R showing this as difference between the following most recent commit which didn't load Conf and the prior one which did.

committed: 2014-04-02T22:40:43Z
sha: 9733a842916547d74afc37a27a563896e04a4ac9
Conf exists: FALSE

----

committed: 2014-04-02T01:42:40Z
sha: 1d2d58c0cf2f5c8e3dd976c2d220d60a0678e05a
Conf exists: TRUE

hopefully this will do the trick for ohi-science/ohicore#80
added explicit @export and @exportClass to Conf and Layers fixing ohi-science/ohicore#80 by ensuring further devtools::document() calls include the needed export() in the NAMESPACE file. For more see

http://stackoverflow.com/questions/21532365/roxygen2-how-to-export-reference-class-generator
adding sqldf dependancy back for now to ensure AggreegateLayers.R and CalculatePressuresAll.R work.
Merge pull request #82 from bbest/master

getting Conf and Layers classes to load