Known issues: https://github.com/PredictiveEcology/reproducible/issues
gdalUtilities, gdalUtils, and
rgeos from Suggestsraster and
terra, because previous versions were causing
collisions.terra and
sf are used throughoutprepInputs can now take fun as a quoted
expression on x, the object loaded by dlFun in
preProcesspreProcess arg dlFun can now be a quoted
expressionobjSize; now is
primarily a wrapper around lobstr::obj_size, but has an
option to get more detail for lists and environments..robustDigest now deals explicitly with numerics, which
digest differently on different OSs. Namely, they get rounded prior to
digesting. Through trial and error, it was found that setting
options("reproducible.digestDigits" = 7) was sufficient for
all known cases. Rounding to deeper than 7 decimal places was
insufficient. There are also new methods for language,
integer, data.frame (which does each column
one at a time to address the numeric issue)postProcess called
postProcessTerra. This will eventually replace
postProcess as it is much faster in all cases and simpler
code base thanks to the fantastic work of Robert Hijmans
(terra) and all the upstream work that terra
relies onCache call. If there is a delay after this message, then it
is the code following the Cache call that is (silently)
slow.retry can now return a named list for the
exprBetween, which allows for more than one object to be
modified between retries..robustDigest was removing Cache attributes from
objects under many conditions, when it should have left them there. It
is unclear what the issues were, as this would likely not have impacted
Cache. Now these attributes are left on.data.table objects appear to not be recovered correctly
from disk (e.g., from Cache repository. We have added
data.table::copy when recovering from Cache repositoryclearCache and cc did not correctly remove
file-backed raster files (when not clearing whole CacheRepo); this may
have resulted in a proliferation of files, each a filename with an
underscore and a new higher number. This fix should eliminate this
problem.getGDALVersion() (#239)maskInputs() when not passing
rasterToMatch.isna.SpatialFix when using
postProcess.quosurelwgeom now a suggested packageterra class objects can now be correctly saved and
recovered by CachefixErrors can now distinguish
testValidity = NA meaning don’t fix errors and
testValidity = FALSE run buffering which fixes many errors,
but don’t test whether there are any invalid polygons first (maybe
slow), or testValidity = TRUE meaning test for validity,
then if some are invalid, then run buffer.reproducible.useNewDigestAlgorithm = 2 which will have user
visible changes. To keep old behaviour, set
options(reproducible.useNewDigestAlgorithm = 1)options(reproducible.showSimilar) is set. It is now more
compact e.g., 3 lines instead of 5.sf methods to studyAreaNameCache returns; i.e., a 2nd time through a Cache would
return a cached copy, when some of the arguments were different. It
occurred for when the differences were in unnamed arguments only.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")
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_sizeunzip missing (thanks
to @CeresBarros
#202)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 extensionprepInputspostProcess 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 extensiongdb.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.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.CachewriteOutputs.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.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.options("reproducible.useNewDigestAlgorithm" = 2)options("reproducible.polygonShortcut" = FALSE) as there
were still too many edge cases that were not covered.RasterStack objects with a single file (thus acting
like a RasterBrick) are now handled correctly by
Cache and prepInputs families, especially with
new options("reproducible.useNewDigestAlgorithm" = 2),
though in tests, it worked with default alsoRSQLite now uses a RNG during dbAppend;
this affected 2 tests (#185).rgeospaddedFloatToChar to reproducible from
SpaDES.core.%>% 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.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.Cache cases where a
file.link is used instead of saving.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.RasterStack objects were not correctly saved to disk
under some conditions in postProcess - fixedpostProcess 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 reliabilityCache now works as expected (e.g., with
parallel processing, it will avoid collisions) with SQLite thanks to
suggestion here: https://stackoverflow.com/a/44445010Raster 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
CacheRequire, pkgDep,
trimVersionNumber, normPath,
checkPath that were moved to Require package.
For backwards compatibility, these are imported and reexportedfile.move used to rename/copy files across
disks (a situation where file.rename would fail)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*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.file.link not file.symlink for
saveToCache. This would have resulted in C Stack overflow
errors due to missing original file in the
file.symlinkunzip when extracting large (>=
4GB) files (#145, @tati-micheletti)projectInputs when converting
to longlat projections, setMinMax for gdalwarp
resultsFilenames now consistently returns a character vector
(#149)file.link does not
succeed.raster) are updated.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.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 interceptedRequire can now handle minimum version numbers, e.g.,
Require("bit (>=1.1-15.2)"); this can be worked into
downstream tools. Still experimental.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.elapsedTimeDigest, elapsedTimeFirstRun, and
elapsedTimeLoad, respectively.preProcess). Includes 2 new functions,
tempdir2 and tempfile2 for use with
reproducible packagereproducible.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 cleaneddrv and conn; user may need to
manually call movedCache if cache is not responding
correctly. File-backed Rasters are automatically updated with new
paths.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.Cache has change. Now,
cacheId is shown in all cases, making it easier to identify
specific items in the cache.Copy only creates a temporary directory for filebacked
rasters; previously any Copy command was creating a
temporary directory, regardless of whether it was neededcropInputs.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
RasterBrickprepInputs 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).options("reproducible.useDBI" = FALSE)DBI package
directly, without archivist. This has much improved
speed.options("reproducible.cacheSaveFormat").
This can be either rds (default) or qs. All
cached objects will be saved with this format. Previously it was
rda.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.... 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.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 toolsuseCloud 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.archivist; moved to Suggests.bitops, dplyr,
fasterize, flock, git2r,
lubridate, RcppArmadillo, RCurl
and tidyselect. Some of these went to Suggests.postProcess calls that use GDAL made more robust
(including #93).dplyr as a direct dependency. It is still an
indirect dependency through DiagrammeRreproducible.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 cachingoptions("reproducible.futurePlan") to something other than
FALSE, then it will show download progress if the file is
“large”.googledrive v 1.0.0 (#119)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 ?CachepkgDep 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"))retry to use exponential backoff when
attempting to access online resources (#121)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.Cache, i.e.,
useCache and cloudFolderIDdownloadData from Google Drive now protects against
HTTP2 error by capturing error and retrying. This is a curl issue for
interrupted connections.rcnst errors on R-devel, tested using
devtools::check(env_vars = list("R_COMPILE_PKGS"=1, "R_JIT_STRATEGY"=4, "R_CHECK_CONSTANTS"=5))cacheRepo: getArtifact,
getCacheId, getUserTagsretry, 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.Rcpp functionality as the functions were no
longer faster than their R base alternatives.prepInputs was not correctly passing
useCachecropInputs 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)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
cacheIdpostProcess family for
sf class objectscloudCache bugfixes for more casestibble from Imports as it’s no longer being
used%>% pipe that was long ago deprecated. User
should use %C% if they want a pipe that is Cache-aware. See
examples.options descriptions now in
reproducible, see ?reproducibleOptionscacheRepo 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.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.options("reproducible.useNewDigestAlgorithm" = FALSE).
There is a message of this change on package load.cloud* functions, especially
cloudCache which allows sharing of Cache among
collaborators. Currently only works with googledriveassessDataType to consolidate
assessDataTypeGDAL and assessDataType into
single function (#71, @ianmseddy)cc: new function – a shortcut for some commonly used
options for clearCache()prepInputs to handle
.rar archives, on systems with correct binaries to deal
with them (#86, @tati-micheletti)fastdigest::fastdigest as it is not return the
identical hash across operating systemsprepInputs on GIS objects that don’t use
raster::raster to load object were skipping
postProcess. Fixed.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.gdalwarp from prostProcess now
correctly matches extent (#73, @tati-micheletti)preProcess (#92, @tati-micheletti)remotes to Imports and removed
devtoolsNew 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
Raster objects,
enact gdalwarp system call if
raster::canProcessInMemory(x,4) = FALSE for faster and
memory-safe processingRaster
objects, including factor rastersextractFromArchive 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.raster::getData issues.Cache() when deeply nested, due to
grep(sys.calls(), ...) that would take long and hang.preProcess(url = NULL) (#65, @tati-micheletti)clearCache (#67),
especially for large Raster objects that are stored as
binary R files (i.e., .rda)raster package changes in development
version of raster packageraster::projectRaster.robustDigest now does not include
Cache-added attributespreProcess() (#68, @tati-micheletti)future to Suggests.future for
Cache saving to SQLite database, via
options("reproducible.futurePlan"), if the
future package is installed. This is FALSE by
default.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.reproducible.ask, logical, indicating
whether clearCache should ask for deletions when in an
interactive sessionprepInputs, 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.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).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.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 circumstancesextractFromArchive – 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.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).postProcess altogether if no
studyArea or rasterToMatch. Previously, this
would invoke Cache even if there was nothing to
postProcess.copyFile correctly handles directory names containing
spaces.makeMemoisable fixed to handle additional edge
cases.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)
fileszipCache and mergeCachecompareNA does comparisons with NA as a possible value
e.g., compareNA(c(1,NA), c(2, NA)) returns
FALSE, TRUECache – new features:
showSimilar, verbose which
can help with debugginguseCache which allows turning caching on
and off at a high level (e.g., options(“useCache”))cacheId which allows user to hard code a
result from a CachedigestPathContent –>
quick, compareRasterFileLength –>
lengthCache
function calls, unless explicitly set on the inner functionsuserTags 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
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
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.remove dplyr from Imports
Add RCurl to Imports
change name of digestRaster to
.digestRaster
digestRaster affecting in-memory
rastersrgdal to SuggestsSpaDES package.