NEWS.md

Known issues: https://github.com/PredictiveEcology/reproducible/issues

version 1.2.4

Bug fix

• typo in date

version 1.2.3

Bug fix

• minor url fix

version 1.2.2

New features

• removed several uses of rgeos
• moved paddedFloatToChar to reproducible from SpaDES.core.
• increased code coverage
• Pull in legacy %>% code from magrittr to allow the cached alternative, %C%. With new magrittr pipe now in compiled source code, more of the legacy code is required here.

Bug fixes

• several minor

version 1.2.1

New features

• harmonized message colours that are use adjustable via options: reproducible.messageColourPrepInputs for all prepInputs functions; reproducible.messageColourCache for all Cache functions; and reproducible.messageColourQuestion for questions that require user input. Defaults are cyan, blue and green respectively. These are user-visible colour changes.
• improved messaging for Cache cases where a file.link is used instead of saving.
• with improved messaging, now options(reproducible.verbose = 0) will turn off almost all messaging.
• postProcess and family now have filename2 = NULL as the default, so not saved to disk. This is a change.
• verbose is now an argument throughout, whose default is getOption(reproducible.verbose), which is set by default to 1. Thus, individual function calls can be more or less verbose, or the whole session via option.

Bug fixes

• RasterStack objects were not correctly saved to disk under some conditions in postProcess - fixed
• several minor

version 1.2.0

New features

• postProcess now uses a simpler single call to gdalwarp, if available, for RasterLayer class to accomplish cropInputs, projectInputs, maskInputs, and writeOutputs all at once. This should be faster, simpler and, perhaps, more stable. It will only be invoked if the RasterLayer is too large to fit into RAM. To force it to be used the user must set useGDAL = "force" in prepInputs or postProcess or globally with options("reproducible.useGDAL" = "force")
• postProcess when using the new gdalwarp, has better persistence of colour table, and NA values as these are kept with better reliability
• concurrent Cache now works as expected (e.g., with parallel processing, it will avoid collisions) with SQLite thanks to suggestion here: https://stackoverflow.com/a/44445010
• updated digesting of Raster class objects to account for more of the metadata (including the colortable). This will change the digest value of all Raster layers, causing re-run of Cache
• removed Require, pkgDep, trimVersionNumber, normPath, checkPath that were moved to Require package. For backwards compatibility, these are imported and reexported
• address permanently or temporarily new changes in GDAL>3 and PROJ>6 in the spatial packages.
• new function file.move used to rename/copy files across disks (a situation where file.rename would fail)
• all DBI type functions now have default cachePath of getOption("reproducible.cachePath")
• Cache(prepInputs, ... on a file-backed Raster* class object now gives the non-Cache repository folder as the filename(returnRaster). Previously, the return object would contain the cache repository as the folder for the file-backed Raster*

Dependency changes

• net reduction in number of packages that are imported from by 14. Removed completely: backports, memoise, quickPlot, R.utils, remotes, tools, and versions; moved to Suggests: fastdigest, gdalUtils, googledrive, httr, qs, rgdal, sf, testthat; added: Require. Now there are 12 non-base packages listed in Imports. This is down from 31 prior to Ver 1.0.0.

bug fixes

• fix over-wide tables in PDF manual (#144)
• use file.link not file.symlink for saveToCache. This would have resulted in C Stack overflow errors due to missing original file in the file.symlink
• use system call to unzip when extracting large (>= 4GB) files (#145, @tati-micheletti)
• several minor including projectInputs when converting to longlat projections, setMinMax for gdalwarp results
• Filenames now consistently returns a character vector (#149)
• improvements to file-backed Raster caching to accommodate a few more edge cases

version 1.1.1

New features

• none

Dependency changes

• none

bug fixes

• fix CRAN test failure when file.link does not succeed.

version 1.1.0

New features

• begin to accommodate changes in GDAL/PROJ and associated updates to other spatial packages. More updates are expected as other spatial packages (namely raster) are updated.
• can now change options('reproducible.cacheSaveFormat') on the fly; cache will look for the file by cacheId and write it using options('reproducible.cacheSaveFormat'). If it is in another format, Cache will load it and resave it with the new format. Experimental still.
• new Copy methods for refClass objects, SQLite and moved environment method into ANY as it would be dispatched for unknown classes that inherit from environment, of which there are many and this should be intercepted
• Require can now handle minimum version numbers, e.g., Require("bit (>=1.1-15.2)"); this can be worked into downstream tools. Still experimental.
• Cache will do file.link or file.symlink if an existing Cache entry with identical output exists and it is large (currently 1e6 bytes); this will save disk space.
• Cache database now has tags for elapsed time of "digest", "original call", and "subsequent recovery from file", elapsedTimeDigest, elapsedTimeFirstRun, and elapsedTimeLoad, respectively.
• Better management of temporary files in package and tests, e.g., during downloading (preProcess). Includes 2 new functions, tempdir2 and tempfile2 for use with reproducible package
• New option: reproducible.tempPath, which is used for the new control of temporary files. Defaults to file.path(tempdir(), "reproducible"). This feature was requested to help manage large amounts of temporary objects that were not being easily and automatically cleaned
• Copying or moving of Cache directories now works automatically if using default drv and conn; user may need to manually call movedCache if cache is not responding correctly. File-backed Rasters are automatically updated with new paths.
• Cache now treats file-backed Rasters as though they had a relative path instead of their absolute path. This means that Cache directories can be copied from one location to another and the file-backed Raster* will have their filenames updated on the fly during a Cache recovery. User doesn't need to do anything.
• postProcess now will perform simple tests and skip cropInputs and projectInputs with a message if it can, rather than using Cache to "skip". This should speed up postProcess in many cases.
• messaging with Cache has change. Now, cacheId is shown in all cases, making it easier to identify specific items in the cache.
• Automatically cleanup temporary (intermediate) raster files (with #110).

Dependency changes

• none

bug fixes

• Copy only creates a temporary directory for filebacked rasters; previously any Copy command was creating a temporary directory, regardless of whether it was needed
• cropInputs.spatialObjects had a bug when object was a large non-Raster class.
• cropInputs may have failed due to "self intersection" error when x was a SpatialPolygons* object; now catches error, runs fixErrors and retries crop. Great reprex by @tati-micheletti. Fixed in commit 89e652ef111af7de91a17a613c66312c1b848847 .
• Filenames bugfix related to RasterBrick
• prepInputs does a better job of keeping all temporary files in a temporary folder; and cleans up after itself better.
• prepInputs now will not show message that it is loading object into R if fun = NULL (#135).

version 1.0.0

New features

• This version is not backwards-compatible out of the box. To maintain backwards compatibility, set: options("reproducible.useDBI" = FALSE)
• A new backend was introduced that uses DBI package directly, without archivist. This has much improved speed.
• New option: options("reproducible.cacheSaveFormat"). This can be either rds (default) or qs. All cached objects will be saved with this format. Previously it was rda.
• Cache objects can now be saved with with qs::qsave. In many cases, this has much improved speed and file sizes compared to rds; however, testing across a wide range of conditions will occur before it becomes the default.
• Changed default behaviour for memoising ... because Cache is now much faster, the default is to turn memoising off, via options("reproducible.useMemoise" = FALSE). In cases of large objects, memoising should still be faster, so user can still activate it, setting the option to TRUE.
• Much better SQLite database handling for concurrent write attempts. Tested with dozens of write attempts per second by 3 cores with abundant locked database occurrences.
• postProcess arg useGDAL can now take "force" as the default behaviour is to not use GDAL if the problem can fit into RAM and sf or raster tools will be faster than GDAL tools
• useCloud argument in Cache and family has slightly modified functionality (see ?Cache new section useCloud) and now has more tests including edge cases, such as useCloud = TRUE, useCache = 'overwrite'. The cloud version now will also follow the "overwrite" command.

Dependency changes

• deprecating archivist; moved to Suggests.
• removed imports for bitops, dplyr, fasterize, flock, git2r, lubridate, RcppArmadillo, RCurl and tidyselect. Some of these went to Suggests.

bug fixes

• postProcess calls that use GDAL made more robust (including #93).
• Several minor, edge cases were detected and fixed.

version 0.2.11

Dependency changes

• remove dplyr as a direct dependency. It is still an indirect dependency through DiagrammeR

New features

• new option: reproducible.showSimilarDepth allows for a deeper assessment of nested lists for differences between the nearest cached object and the present object. This greater depth may allow more fine tuned understanding of why an object is not correctly caching
• for downloading large files from GoogleDrive (currently only implemented), if user has set options("reproducible.futurePlan") to something other than FALSE, then it will show download progress if the file is "large".

bug fixes

• Several minor, edge cases were detected and fixed.

version 0.2.10

Dependency changes

• made compatible with googledrive v 1.0.0 (#119)

New features

• pkgDep2, a new convenience function to get the dependencies of the "first order" dependencies.
• useCache, used in many functions (incl Cache, postProcess) can now be numeric, a qualitative indicator of "how deep" nested Cache calls should set useCache = TRUE -- implemented as 1 or 2 in postProcess currently. See ?Cache

bug fixes

• pkgDep was becoming unreliable for unknown reasons. It has been reimplemented, much faster, without memoising. The speed gains should be immediately noticeable (6 second to 0.1 second for pkgDep("reproducible"))
• improved retry to use exponential backoff when attempting to access online resources (#121)

version 0.2.9

New features

• Cache has 2 new arguments, useCloud and cloudFolderID. This is a new approach to cloud caching. It has been tested with file backed RasterLayer, RasterStack and RasterBrick and all normal R objects. It will not work for any other class of disk-backed files, e.g., ff or bigmatrix, nor is it likely to work for R6 class objects.
• Slowly deprecating cloudCache and family of functions in favour of a new approach using arguments to Cache, i.e., useCache and cloudFolderID
• downloadData from Google Drive now protects against HTTP2 error by capturing error and retrying. This is a curl issue for interrupted connections.

Bug fixes

• fixes for rcnst errors on R-devel, tested using devtools::check(env_vars = list("R_COMPILE_PKGS"=1, "R_JIT_STRATEGY"=4, "R_CHECK_CONSTANTS"=5))
• other minor improvements, including fixes for #115

version 0.2.8

New features

• new functions for accessing specific items from the cacheRepo: getArtifact, getCacheId, getUserTags
• retry, a new function, wraps try with an explicit attempt to retry the same code upon error. Useful for flaky functions, such as googldrive::drive_download which sometimes fails due to curl HTTP2 error.
• removed all Rcpp functionality as the functions were no longer faster than their R base alternatives.

Bug fixes

• prepInputs was not correctly passing useCache
• cropInputs was reprojecting extent of y as a time saving approach, but this was incorrect if studyArea is a SpatialPolygon that is not close to filling the extent. It now reprojects studyArea directly which will be slower, but correct. (#93)
• other minor improvements

version 0.2.7

New features

• CHECKSUMS.txt should now be ordered consistently across operating systems (note: base::order will not succeed in doing this --> now using .orderDotsUnderscoreFirst)
• cloudSyncCache has a new argument: cacheIds. Now user can control entries by cacheId, so can delete/upload individual objects by cacheId
• Experimental support within the postProcess family for sf class objects

bug fixes

• mostly minor
• cloudCache bugfixes for more cases

version 0.2.6

Dependency changes

• remove tibble from Imports as it's no longer being used

New features

• remove %>% pipe that was long ago deprecated. User should use %C% if they want a pipe that is Cache-aware. See examples.
• Full rewrite of all options descriptions now in reproducible, see ?reproducibleOptions
• now cacheRepo and options("reproducible.cachePath") can take a vector of paths. Similar to how .libPaths() works for libraries, Cache will search first in the first entry in the cacheRepo, then the second etc. until it finds an entry. It will only write to the first entry.
• new value for the option: options("reproducible.useCache" = "devMode"). The point of this mode is to facilitate using the Cache when functions and datasets are continually in flux, and old Cache entries are likely stale very often. In devMode, the cache mechanism will work as normal if the Cache call is the first time for a function OR if it successfully finds a copy in the cache based on the normal Cache mechanism. It differs from the normal Cache if the Cache call does not find a copy in the cacheRepo, but it does find an entry that matches based on userTags. In this case, it will delete the old entry in the cacheRepo (identified based on matching userTags), then continue with normal Cache. For this to work correctly, userTags must be unique for each function call. This should be used with caution as it is still experimental.
• change to how hashes are calculated. This will cause existing caches to not work correctly. To allow a user to keep old behaviour (during a transition period), the "old" algorithm can be used, with options("reproducible.useNewDigestAlgorithm" = FALSE). There is a message of this change on package load.
• add experimental cloud* functions, especially cloudCache which allows sharing of Cache among collaborators. Currently only works with googledrive
• updated assessDataType to consolidate assessDataTypeGDAL and assessDataType into single function (#71, @ianmseddy)
• cc: new function -- a shortcut for some commonly used options for clearCache()
• added experimental capacity for prepInputs to handle .rar archives, on systems with correct binaries to deal with them (#86, @tati-micheletti)
• remove fastdigest::fastdigest as it is not return the identical hash across operating systems

Bug fixes

• prepInputs on GIS objects that don't use raster::raster to load object were skipping postProcess. Fixed.
• under some circumstances, the prepInputs would cause virtually all entries in CHECKSUMS.txt to be deleted. 2 cases where this happened were identified and corrected.
• data.table class objects would give an error sometimes due to use of attr(DT). Internally, attributes are now added with data.table::setattr to deal with this.
• calling gdalwarp from prostProcess now correctly matches extent (#73, @tati-micheletti)
• files from url that have unknown extension are now guessed with by preProcess (#92, @tati-micheletti)

version 0.2.5

Dependency changes

• Added remotes to Imports and removed devtools

New features

• New value possible for options(reproducible.useCache = 'overwrite'), which allows use of Cache in cases where the function call has an entry in the cacheRepo, will purge it and add the output of the current call instead.

• New option reproducible.inputPaths (default NULL) and reproducible.inputPathsRecursive (default FALSE), which will be used in prepInputs as possible directory sources (searched recursively or not) for files being downloaded/extracted/prepared. This allows the using of local copies of files in (an)other location(s) instead of downloading them. If local location does not have the required files, it will proceed to download so there is little cost in setting this option. If files do exist on local system, the function will attempt to use a hardlink before making a copy.

• dlGoogle() now sets options(httr_oob_default = TRUE) if using Rstudio Server.

• Files in CHECKSUMS now sorted alphabetically.

• Checksums can now have a CHECKSUMS.txt file located in a different place than the destinationPath

• Attempt to select raster resampling method based on raster type if no method supplied (#63, @ianmseddy)

• projectInputs

• new function assessDataTypeGDAL, used in postProcess, to identify smallest datatype for large Raster* objects passed to GDAL system call

  • when masking and reprojecting large Raster objects, enact gdalwarp system call if raster::canProcessInMemory(x,4) = FALSE for faster and memory-safe processing
  • better handling of various data types in Raster objects, including factor rasters

Bug fixes

• Work around internally inside extractFromArchive for large (>2GB) zip files. In the R help manual, unzip fails for zip files >2GB. This uses a system call if the zip file is too large and fails using base::unzip.
• Work around for raster::getData issues.
• Speed up of Cache() when deeply nested, due to grep(sys.calls(), ...) that would take long and hang.
• Bugfix for preProcess(url = NULL) (#65, @tati-micheletti)
• Improved memory performance of clearCache (#67), especially for large Raster objects that are stored as binary R files (i.e., .rda)
• Other minor bugfixes

Other changes

• Deal with new raster package changes in development version of raster package
• Added checks for float point number issues in raster resolutions produced by raster::projectRaster
• .robustDigest now does not include Cache-added attributes
• Additional tests for preProcess() (#68, @tati-micheletti)
• Many new unit tests written, which caught several minor bugs

version 0.2.3

• fix and skip downloading test on CRAN

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 explicit 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

Other changes

• most tests now use a standardized approach to attaching libraries, creating objects, paths, enabling easier, error resistant test building

version 0.2.1

New features

• new functions:

  • convertPaths and convertRasterPaths to assist with renaming moved files.

• prepInputs -- new features

  • alsoExtract now has more options (NULL, NA, "similar") and defaults to extracting all files in an archive (NULL).
  • skips postProcess altogether if no studyArea or rasterToMatch. Previously, this would invoke Cache even if there was nothing to postProcess.

Bug fixes

• copyFile correctly handles directory names containing spaces.
• makeMemoisable fixed to handle additional edge cases.
• other minor bug fixes.

version 0.2.0

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

• 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

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

version 0.1.2

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

version 0.1.1

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

version 0.1.0

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