Changelog

Source: NEWS.md

version 0.2.0 Unreleased

New features

  • new functions:

    • prepInputs to aid in data downloading and preparation problems, solved in a reproducible, Cache-aware way.
    • postProcess which is a wrapper for sequences of several other new functions (cropInputs, fixErrors, projectInputs, maskInputs, writeOutputs, and determineFilename)
    • downloadFile can handle Google Drive and ftp/http(s) files
    • zipCache and mergeCache
    • compareNA does comparisons with NA as a possible value e.g., compareNA(c(1,NA), c(2, NA)) returns FALSE, TRUE

  • Cache – new features:

    • new arguments showSimilar, verbose which can help with debugging
    • new argument useCache which allows turning caching on and off at a high level (e.g., options(“useCache”))
    • new argument cacheId which allows user to hard code a result from a Cache
    • deprecated arguments: digestPathContent –> quick, compareRasterFileLength –> length
    • Cache arguments now propagate inward to nested Cache function calls, unless explicitly set on the inner functions
    • more precise messages provided upon each use
    • many more userTags added automatically to cache entries so much more powerful searching via showCache(userTags="something")
  • checksums now returns a data.table with the same columns whether write = TRUE or write = FALSE.
  • clearCache and showCache now give messages and require user intervention if request to clearCache would be large quantities of data deleted
  • memoise::memoise now used on 3rd run through an identical Cache call, dramatically speeding up in most cases
  • new options: reproducible.cachePath, reproducible.quick, reproducible.useMemoise, reproducible.useCache, reproducible.useragent, reproducible.verbose
  • asPath has a new argument indicating how deep should the path be considered when included in caching (only relevant when quick = TRUE)
  • New vignette on using Cache
  • Cache is parallel-safe, meaning there are tryCatch around every attempt at writing to SQLite database so it can be used safely on multi-threaded machines
  • bug fixes, unit tests, more imports for packages e.g., stats
  • updates for R 3.6.0 compact storage of sequence vectors
  • experimental pipes (%>%, %C%) and assign %<%

  • several performance enhancements

version 0.1.4 2018-01-25

  • mergeCache: a new function to merge two different Cache repositories
  • memoise::memoise is now used on loadFromLocalRepo, meaning that the 3rd time Cache() is run on the same arguments (and the 2nd time in a session), the returned Cache will be from a RAM object via memoise. To stop this behaviour and use only disk-based Caching, set options(reproducible.useMemoise = FALSE) .
  • Cache assign – %<% can be used instead of normal assign, equivalent to lhs <- Cache(rhs).
  • new option: reproducible.verbose, set to FALSE by default, but if set to true may help understand caching behaviour, especially for complex highly nested code.
  • all options now described in ?reproducible.
  • All Cache arguments other than FUN and … will now propagate to internal, nested Cache calls, if they are not specified explicitly in each of the inner Cache calls.
  • Cached pipe operator %C% – use to begin a pipe sequence, e.g., Cache() %C% ...
  • Cache arg sideEffect can now be a path
  • Cache arg digestPathContent default changed from FALSE (was for speed) to TRUE (for content accuracy)
  • New function, searchFull, which shows the full search path, known alternatively as “scope”, or “binding environments”. It is where R will search for a function when requested by a user.
  • Uses memoise::memoise for several functions (loadFromLocalRepo, pkgDep, package_dependencies, available.packages) for speed – will impact memory at the expense of speed.

  • New Require function

    • attempts to create a lighter weight package reproducibility chain. This function is usable in a reproducible workflow: it includes both installing and loading of packages, it can maintain version numbers, and uses smart caching for speed. In tests, it can evaluate whether 20 packages and their dependencies (~130 packages) are installed and loaded quickly (i.e., if all TRUE, ~0.1 seconds). This is much slower than running require on those 20 packages, but require does not check for dependencies and deal with them if missing: it just errors. This speed should be fast enough for many purposes.
    • can accept uncommented name, if length 1.
  • remove dplyr from Imports
  • Add RCurl to Imports

  • change name of digestRaster to .digestRaster

version 0.1.3 2017-08-10

  • fix R CMD check errors on Solaris that were not previously resolved

version 0.1.2 2017-08-09

  • fix R CMD check errors on Solaris
  • fix bug in digestRaster affecting in-memory rasters
  • move rgdal to Suggests

version 0.1.1 2017-08-05

  • cleanup examples and do run them (per CRAN)
  • add tests to ensure all exported (non-dot) functions have examples

version 0.1.0 Unreleased

  • A new package, which takes all caching utilities out of the SpaDES package.