version 1.2.6

DESCRIPTION

@@ -17,8 +17,8 @@ SystemRequirements: 'unrar' (Linux/macOS) or '7-Zip' (Windows) to work
         with '.rar' files.
 URL: https://reproducible.predictiveecology.org,
         https://github.com/PredictiveEcology/reproducible
-Date: 2020-12-03
-Version: 1.2.4
+Date: 2021-02-11
+Version: 1.2.6
 Authors@R: c(
     person("Eliot J B", "McIntire", email = "eliot.mcintire@canada.ca",
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6914-8316")),
@@ -39,7 +39,7 @@ Imports: data.table (>= 1.10.4), DBI, digest, fpCompare, glue,
         1.4-2), utils
 Suggests: covr, crayon, fastdigest, fasterize, future, gdalUtils,
         googledrive, httr, qs, knitr, parallel, RCurl (>= 1.95-4.8),
-        rgdal, rgeos, rmarkdown, sf, stats, testthat, TimeWarp
+        rgdal, rgeos, rmarkdown, sf, stats, testthat
 Encoding: UTF-8
 Language: en-CA
 License: GPL-3
@@ -55,7 +55,7 @@ Collate: 'DBI.R' 'cache-helpers.R' 'cache-internals.R' 'cache-tools.R'
         'reproducible-deprecated.R' 'reproducible-package.R' 'search.R'
         'spatialObjects-class.R' 'zzz.R'
 NeedsCompilation: no
-Packaged: 2020-12-03 18:03:06 UTC; emcintir
+Packaged: 2021-02-16 19:28:52 UTC; emcintir
 Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
   Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
   Tati Micheletti [ctb] (<https://orcid.org/0000-0003-4838-8342>),
@@ -65,4 +65,4 @@ Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
     Minister of Natural Resources Canada [cph]
 Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
 Repository: CRAN
-Date/Publication: 2020-12-07 15:50:02 UTC
+Date/Publication: 2021-02-17 17:20:02 UTC

MD5

@@ -1,43 +1,43 @@
-15dd03f7b0a0d2ef8795bf03d7ae72d7 *DESCRIPTION
+500cff4b96b1b35b5cf71c2195505b7a *DESCRIPTION
 ee416da1c063c110398b85c7f312d5fe *NAMESPACE
-402a5ed321b7980955fe68f59b3e2092 *NEWS.md
-ba3210bf10a360d01aa48093597f6826 *R/DBI.R
-4118c40c9469806fef1a4e7c6edde6d2 *R/cache-helpers.R
-fcb0dc0a56705b9ccbc5582f3563180f *R/cache-internals.R
+a1877485499e52a539e36325e8f376c2 *NEWS.md
+34e874dbe5015dedc5b939262315aa28 *R/DBI.R
+46ac15948d6aa2c7025ff22d0ab866f5 *R/cache-helpers.R
+c2c2cbbc214b0319ebd32ab5b3eab187 *R/cache-internals.R
 3c17b059b2aaffe9cdc9272e645dae67 *R/cache-tools.R
-403c6dc03fa05f375c113d14bea28a7d *R/cache.R
+e2e8a3b5cf895ed10f83308e23848685 *R/cache.R
 a65ee49bf6156f98d91cef9951ca1f61 *R/checksums.R
 f9f36edca546a1ee36c96f64dc78a815 *R/cloud.R
 69dc454d1283f2b62dafafdb4e73a15b *R/cloudOld.R
-9f5bda54a6a94fb5c71a57d48af21341 *R/convertPaths.R
+d5ac70723d708b98c771c14ece005e92 *R/convertPaths.R
 2f937b4e5e8673fdb4a46e2868ccc119 *R/copy.R
-220fc26c6566a3e768fdcbf56690f3d5 *R/download.R
-02fe8bd9c009376bc8a2dbdce0133c56 *R/gis.R
+bf64841f43cb6d8b5736f14ffe1c7a90 *R/download.R
+187f142136a839665cd0f2d043d09ecb *R/gis.R
 99d4b4384a36ad6c262a05e5013fe112 *R/git.R
-f601bfd1f63426ccedbbcea9c109d1a7 *R/helpers.R
+1f4366632b3c9667ac9a9133b370de8c *R/helpers.R
 34b498f0425ba3860a1880a530c498fa *R/objectSize.R
-d57c7782cb7c1d5c308c64e103044056 *R/options.R
+ad06c4f682ac89a30a8a8d9bb0a52cf4 *R/options.R
 5e87f73a860288b0788a30133320f286 *R/packages.R
 01b9a0199e834a9c6bd56ac07e3c21d5 *R/pipe.R
-130d7e04cb4098b2ad420682ea9509da *R/postProcess.R
-59f1bf1ff6c997392728b4dfd5988a00 *R/preProcess.R
-299bc8edad67acf117e9e49785061188 *R/prepInputs.R
+a7cce1ce1804f693fd26abd35aec81c7 *R/postProcess.R
+049fd09717f0ab68f57c62e43901b0c6 *R/preProcess.R
+5791d1761e71b3c7ea4bce205ff7d31d *R/prepInputs.R
 0124c1a6c6572ab64290ccf425136e50 *R/reexports.R
 d4248c1a08cd82c8cf7baa4c54cf28db *R/reproducible-deprecated.R
 85f0f3f02af340780ad0ab3f20796990 *R/reproducible-package.R
-8a89a0d05a16cc611d3f0a71304350b2 *R/robustDigest.R
+59b3c162fb3c1e631f961e0f9c964a94 *R/robustDigest.R
 009f050c7dc125f0705ed2faacdcf303 *R/search.R
 b3d76ff2a50040ab9f6c3b798867f241 *R/spatialObjects-class.R
 3a041dbf9652a96d8ec8c9aaae52fdb1 *R/zzz.R
 27ca6b085dd7653b805913b901a4869d *README.md
-f101f3b0a28f37186811733b3cc3d05f *build/vignette.rds
-729eb531ac94817469d4f9990ff62a0f *inst/WORDLIST
+10e3e223311822fbda2d965af9345bba *build/vignette.rds
+9548bc855a5b680854f6b975acfb6fa5 *inst/WORDLIST
 f9d8668f4dd4816449502a708cab90d4 *inst/doc/Cache-using-postgresql.R
 f18a3abeb46c0f11adeef45aeee2983c *inst/doc/Cache-using-postgresql.Rmd
-e3f7b8393b3a02655dbf638e4f35f1bc *inst/doc/Cache-using-postgresql.html
+f11782c941c2058cf6c6ec1733f7d3ea *inst/doc/Cache-using-postgresql.html
 2f4860e44a94deac77875ef282cbf670 *inst/doc/Intro-to-Cache.R
 03da70382bdfd9a3d0fa863264bb0d08 *inst/doc/Intro-to-Cache.Rmd
-e93eba9ff171c25582c5cc33b49db3aa *inst/doc/Intro-to-Cache.html
+916a5a1e3f325b42a34b3b64874d832b *inst/doc/Intro-to-Cache.html
 24ee977337f1f8aaa6eae358cd600644 *inst/examples/example_Cache.R
 d82b80339ca4b9b708132e90f5e08112 *inst/examples/example_assessDataType.R
 99f7dffe6c51ae928000edca93be4ff1 *inst/examples/example_assessDataTypeGDAL.R
@@ -117,16 +117,16 @@ f058441901e715abf7c4ba87a1152935 *man/pkgEnv.Rd
 7a381c2e3bee183434d07d8fac23582b *man/postProcess.Rd
 4ce5cb2d0316eef0c7bbb67bd5367fef *man/postProcessHelpers.Rd
 392088cb89180600f7278647a6e417fd *man/preDigestByClass.Rd
-93430a8b159b1d4248bffae8d53f4221 *man/preProcess.Rd
+9e4913828e48fe70313a92292ba0106c *man/preProcess.Rd
 f184e84f8df63a24bcb912bc583d7c89 *man/prefix.Rd
-872e1a7acff29570312586722f83a5d2 *man/prepInputs.Rd
+d23136c1cca5303ccc0f80756a46e233 *man/prepInputs.Rd
 1c017891eb8b8e070ecdb36159dbac77 *man/prepareFileBackedRaster.Rd
-6923ba414e1c837f7d960f09b23da55d *man/prepareOutput.Rd
+4066381ed59f0ec9c75faeeb08da4ba3 *man/prepareOutput.Rd
 ced085514f733031ed85304608981c22 *man/projectInputs.Rd
 5a1a4314604489908b7b04bbce4c406b *man/purge.Rd
 3b10e8900b8dea9fe84d04c9b1cf90b0 *man/reexports.Rd
 295972dc114c8593aa646609792119a3 *man/reproducible-package.Rd
-653935618942d2ebb911c99553289117 *man/reproducibleOptions.Rd
+43c3753f6b455467bc703dbf500ebe87 *man/reproducibleOptions.Rd
 cdfeb1a68785781f84c024013b6c2a75 *man/retry.Rd
 b6cabe46389bc30ebbb85f2094a46f78 *man/robustDigest.Rd
 371961e5747d502ef8c7df0652539df4 *man/search.Rd
@@ -141,29 +141,29 @@ d07b63c452e126ff84539623f0e14192 *man/unrarPath.Rd
 7258369161953385dfb6c15e0370cd48 *man/writeFuture.Rd
 6f98d2537369c2856d6d8a8a746c9ef2 *man/writeOutputs.Rd
 7225156ce4ec949d6a52364b25ea5c1b *tests/test-all.R
-b3483e55f435945644e5218ee0b25593 *tests/testthat/helper-allEqual.R
-507c2e23e4fc1a88fe8cf0729eb52884 *tests/testthat/test-cache.R
+2cb403c9ba2b56da5337eba8397cfff3 *tests/testthat/helper-allEqual.R
+698784e6012b4d0d19b449a88195e67a *tests/testthat/test-cache.R
 6781c0de3df7cf0cf64c8f2ebb7c919c *tests/testthat/test-cacheArguments.R
 37401dc8d2e5e8d2295be22bb4d632bf *tests/testthat/test-cacheHelpers.R
 72a5aba6ff747c415281fe039aa63ace *tests/testthat/test-checkPath.R
 effc5d05171b541446e1c62e2a34493a *tests/testthat/test-checksums.R
 70764bc5d54385428dc30c5bbad07a4f *tests/testthat/test-cloud.R
 af59957743439bcd9d8bff1c9f300528 *tests/testthat/test-cluster.R
 08092914afec28463d4b00e8bf4451c4 *tests/testthat/test-copy.R
-e2afa27a5ce5c019c08be3d612ddcb1a *tests/testthat/test-devMode.R
+654a5aad84d91b08da28af6e06a51401 *tests/testthat/test-devMode.R
 48691a6e0746f40465a0402e54675d8c *tests/testthat/test-download.R
 b1d00640307969f5da4e0e862c394873 *tests/testthat/test-examples.R
 7aed58fa77960aa2e1edd65252f7127c *tests/testthat/test-filesMissingExtension.R
 ffe5b203d856fc0e7e9481276476f9c4 *tests/testthat/test-gdal.R
 8809cd03698d7cbe9a7bc1ef321a6def *tests/testthat/test-gis.R
-c80a17d0856370e315ca9299c217d7e5 *tests/testthat/test-misc.R
-880f74ddcce486ea3a60d22df8b8c964 *tests/testthat/test-multipleCacheRepo.R
-5484a5f54501b1467951bec269e0455c *tests/testthat/test-postProcess.R
+575af6d552d63f6d678b0bc6de48c859 *tests/testthat/test-misc.R
+e2628fe5e033a41417a0e279c141bb8f *tests/testthat/test-multipleCacheRepo.R
+5290f4c8bc537183608ad041047e6182 *tests/testthat/test-postProcess.R
 fa23d3ab73e178be54c9751cb3548f3f *tests/testthat/test-preProcessDoesntWork.R
-a2cd37f864537925ee0c7f9590a86efa *tests/testthat/test-preProcessWorks.R
+3f911c41f494e367d862529c27f8ee52 *tests/testthat/test-preProcessWorks.R
 144f447ef0e4c5c3fb5b2e8eb59115b9 *tests/testthat/test-prepInputs-large-files.R
-317ff61115a00c7768aa74fccd2d4fc4 *tests/testthat/test-prepInputs.R
-bc722faecec368537a92ba681c0fe74d *tests/testthat/test-prepInputsInNestedArchives.R
+b6a3e187b90a308821b13c9806e452ea *tests/testthat/test-prepInputs.R
+d63da6d72e6f5f7a1bfa027fc9026857 *tests/testthat/test-prepInputsInNestedArchives.R
 d6766f69428ae86380e98d71695bc8dc *tests/testthat/test-reproducibleVerbose.R
 bd38c62fa4dd94a7fc567c62b19203e6 *tests/testthat/test-robustDigest.R
 f18a3abeb46c0f11adeef45aeee2983c *vignettes/Cache-using-postgresql.Rmd

NEWS.md

@@ -1,5 +1,17 @@
 Known issues: https://github.com/PredictiveEcology/reproducible/issues
 
+
+version 1.2.5
+==============
+
+## Enhancements
+* Optional (and may be default soon) -- An update to the internal digesting for file-backed Rasters that should be substantially faster, and smaller disk footprint. Set using `options("reproducible.useNewDigestAlgorithm" = 2)`
+* changed default of `options("reproducible.polygonShortcut" = FALSE)` as there were still too many edge cases that were not covered.
+
+## Bug fix
+* `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 also
+* Fix issue #185, RSQLite now uses a RNG during dbAppend; this affected 2 tests.
+
 version 1.2.4
 ==============
 

R/DBI.R

@@ -77,6 +77,7 @@ saveToCache <- function(cachePath = getOption("reproducible.cachePath"),
   # TRY link first, if there is a linkToCacheId, but some cases will fail; not sure what these cases are
   if (!is.null(linkToCacheId)) {
     ftL <- CacheStoredFile(cachePath, linkToCacheId)
+    if (exists("._saveToCache_1")) browser()
     suppressWarnings({
       out <- try(file.link(from = ftL, to = fts), silent = TRUE)
     })