PredictiveEcology/reproducible: v1.2.7

Known issues: https://github.com/PredictiveEcology/reproducible/issues Version 1.2.7 reproducible will be slowly changing the defaults for vector GIS datasets from the sp package to the sf package. There is a large user-visible change that will come (in the next release), which will cause prepInputs to read .shp files with sf::st_read instead of raster::shapefile, as it is much faster. To change now, set options("reproducible.shapefileRead" = "sf::st_read") Enhancements default fun in prepInputs for shapefiles (.shp) is now sf::st_read if the system has sf installed. This can be overridden with options("reproducible.shapefileRead" = "raster::shapefile"), and this is indicated with a message at the moment this is occurring, as it will cause different behaviour. quick argument in Cache can now be a character vector, allowing individual character arguments to be digested as character vectors and others to be digested as files located at the specified path as represented by the character vector. objSize previously included objects in namespaces, baseenv and emptyenv, so it was generally too large. Now uses the same criteria as pryr::object_size improvements with messaging when unzip missing (thanks to C. Barros #202) while unzipping, will also search for 7z.exe on Windows if the object is larger than 2GB, if can't find unzip. fun argument in prepInputs and family can now be a quoted expression. archive argument in prepInputs can now be NA which means to treat the file downloaded not as an archive, even if it has a .zip file extension many minor improvements to functioning of esp. prepInputs speed improvements during postProcess especially for very large objects (>5GB tested). Previously, it was running many fixErrors calls; now only calls fixErrors on fail of the proximate call (e.g., st_crop or whatever) retry now has a new argument exprBetween to allow for doing something after the fail (for example, if an operation fails, e.g., st_crop, then run fixErrors, then return back to st_crop for the retry) Cache now has MUCH better nested levels detection, with messaging... and control of how deep the Caching goes seems good, via useCache = 2 will only Cache 2 levels in... archive argument in prepInputs family can now be NA ... meaning do not try to unzip even if it is a .zip file or other standard archive extension gdb.zip files (e.g., a file with a .zip extension, but that should not be opened with an unzip-type program) can now be opened with prepInputs(url = "whateverUrl", archive = NA, fun = "sf::st_read") fun argument in prepInputs can now be a quoted function call. preProcess now does a better job with large archives that can't be correctly handled with the default zip and unzip with R, by trying system2 calls to possible 7z.exe or other options on Linux-alikes. Bug fixees Copy generic no longer has fileBackedDir argument. It is now passed through with the .... This was creating a bug with some cases where fileBackedDir was not being correctly executed. fixErrors() now better handles sf polygons with mixed geometries that include points. inadvertent deleting of file-backed rasters in multi-filed stacks during Cache writeOutputs.Raster attempted to change datatype of Raster class objects using the setReplacement dataType<-, without subsequently writing to disk via writeRaster. This created bad values in the Raster* object. This now performs a writeRaster if there is a datatype passed to writeOutputs e.g., through prepInputs or postProcess. updateSlotFilename has many more tests. prepInputs(..., fun = NA) now is the correct specification for "do not load object into R". This essentially replicates preProcess with same arguments. several minor bugfixes Copy did not correctly copy RasterStacks when some of the RasterLayer objects were in memory, some on disk; raster::fromDisk returned FALSE in those cases, so Copy didn't occur on the file-backed layer files. Using Filenames instead to determine if there are any files that need copying