PredictiveEcology/reproducible: v0.2.2

Known issues: https://github.com/PredictiveEcology/reproducible/issues version 0.2.2 Dependency changes Add future to Suggests. New features new option on non-Windows OSs to use future for Cache saving to SQLite database, via options("reproducible.futurePlan"), if the future package is installed. This is FALSE by default. If a do.call function is Cached, previously, it would be labelled in the database as do.call. Now it attempts to extract the actual function being called by the do.call. Messaging is similarly changed. new option reproducible.ask, logical, indicating whether clearCache should ask for deletions when in an interactive session prepInputs, preProcess and downloadFile now have dlFun, to pass a custom function for downloading (e.g., "raster::getData") prepInputs will automatically use readRDS if the file is a .rds. prepInputs will return a list if fun = "base::load", with a message; can still pass an envir to obtain standard behaviour of base::load. clearCache - new argument ask. new function assessDataType, used in postProcess, to identify smallest datatype for Raster* objects, if user does not pass an explicity datatype in prepInputs or postProcess (#39, @CeresBarros). Bug fixes fix problems with tests introduced by recent git2r update (@stewid, #36). .prepareRasterBackedFile -- now will postpend an incremented numeric to a cached copy of a file-backed Raster object, if it already exists. This mirrors the behaviour of the .rda file. Previously, if two Cache events returned the same file name backing a Raster object, even if the content was different, it would allow the same file name. If either cached object was deleted, therefore, it would cause the other one to break as its file-backing would be missing. options were wrongly pointing to spades.XXX and should have been reproducible.XXX. copyFile did not perform correctly under all cases; now better handling of these cases, often sending to file.copy (slower, but more reliable) extractFromArchive needed a new Checksum function call under some circumstances several other minor bug fixes. extractFromArchive -- when dealing with nested zips, not all args were passed in recursively (#37, @CeresBarros) prepInputs -- arguments that were same as Cache were not being correctly passed internally to Cache, and if wrapped in Cache, it was not passed into prepInputs. Fixed. .prepareFileBackedRaster was failing in some cases (specifically if it was inside a do.call) (#40, @CeresBarros). Cache was failing under some cases of Cache(do.call, ...). Fixed. Cache -- when arguments to Cache were the same as the arguments in FUN, Cache would "take" them. Now, they are correctly passed to the FUN. preProcess -- writing to checksums may have produced a warning if CHECKSUMS.txt was not present. Now it does not. numerous other minor bugfixes Minor changes most tests now use a standardized approach to attaching libraries, creating objects, paths, enabling easier, error resistent test buildin