version 0.2.1

DESCRIPTION

@@ -11,8 +11,8 @@ Description: Collection of high-level, robust, machine- and OS-independent tools
     Some features are still under active development.
 URL: http://reproducible.predictiveecology.org,
         https://github.com/PredictiveEcology/reproducible
-Date: 2018-06-15
-Version: 0.2.0
+Date: 2018-07-05
+Version: 0.2.1
 Authors@R: c(
     person("Eliot J B", "McIntire", email = "eliot.mcintire@canada.ca",
     role = c("aut", "cre")),
@@ -37,15 +37,16 @@ ByteCompile: yes
 RoxygenNote: 6.0.1
 Collate: 'RcppExports.R' 'cache-helpers.R' 'cache-tools.R'
         'robustDigest.R' 'cache.R' 'checksums.R' 'consistentPaths.R'
-        'download.R' 'gis.R' 'git.R' 'helpers.R' 'objectSize.R'
-        'packages.R' 'pipe.R' 'postProcess.R' 'preProcess.R'
-        'prepInputs.R' 'reproducible-package.R' 'search.R' 'zzz.R'
+        'convertPaths.R' 'download.R' 'gis.R' 'git.R' 'helpers.R'
+        'objectSize.R' 'packages.R' 'pipe.R' 'postProcess.R'
+        'preProcess.R' 'prepInputs.R' 'reproducible-package.R'
+        'search.R' 'zzz.R'
 NeedsCompilation: yes
-Packaged: 2018-06-15 16:23:35 UTC; achubaty
+Packaged: 2018-07-05 19:06:31 UTC; achubaty
 Author: Eliot J B McIntire [aut, cre],
   Alex M Chubaty [aut],
   Her Majesty the Queen in Right of Canada, as represented by the
     Minister of Natural Resources Canada [cph]
 Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
 Repository: CRAN
-Date/Publication: 2018-06-17 17:30:50 UTC
+Date/Publication: 2018-07-07 15:40:03 UTC

MD5

@@ -1,22 +1,23 @@
-46a44b68d9751c38991bfad09addd939 *DESCRIPTION
-054f9b77a847f334abd25924afa87196 *NAMESPACE
-b1922268dd8bb4576559c07275be18c9 *NEWS.md
+a8a8a561ed5c15dc818da52b228b175e *DESCRIPTION
+af189e78baa9c06cdd719b2d5be7e5cd *NAMESPACE
+3ca3f28c5362e5c0d82bea3ca763ca52 *NEWS.md
 40174c2abaa1ef103075c6f5fa492bd1 *R/RcppExports.R
-ff31db89064706c14e4d9d50db41e81e *R/cache-helpers.R
-5a1b4f0f0471b185301821293a86eebb *R/cache-tools.R
-848ae418515ece9ddd5b3243cbf5d8e7 *R/cache.R
+52ae4232d1ac47eb85af384a75b6dce6 *R/cache-helpers.R
+ec1bed2edd858aec11b02fb7ba8d0235 *R/cache-tools.R
+ddbc26f7204018a83e4e8a651270732f *R/cache.R
 9ae80b48ac39310a13ed032f979f5804 *R/checksums.R
 b5274cf125d7c9a9cb4e9172c99b69bc *R/consistentPaths.R
-aecd3ba1a72880631b7b593b5b058dda *R/download.R
-26cae2d4cbdeb309e6afb331c65efca9 *R/gis.R
+08d55ca57b2d87355895513ace92a968 *R/convertPaths.R
+8dd6801fde8e6d0815740a1eb0c05e69 *R/download.R
+0798a8dfcefa7cfc3674ab8d94df498c *R/gis.R
 eb657c85ba6ae9f894c93000e6d84d58 *R/git.R
 6f427a86e8a4734eaf21cca6addce860 *R/helpers.R
 6a1c54c7e248fc3ca5e481c5a25ba2ad *R/objectSize.R
 ee9e8200fa3b12a4a6c77af8d82a1669 *R/packages.R
 d1831a49980076e426ac9c94b4a49eaf *R/pipe.R
-1371260e93919d25dfc84225e33f7649 *R/postProcess.R
-4361a4ef7ed154a48069af2794149232 *R/preProcess.R
-62e8a70320ffaffc1c67461a9953f229 *R/prepInputs.R
+24fa7c9e3920991db876812eaa49ed31 *R/postProcess.R
+f868d8cf23e862818a391d3acf2b7c59 *R/preProcess.R
+cf956a37c99bfb2807bf80cf81263250 *R/prepInputs.R
 fbe7b2f823810b1735051964b95357c0 *R/reproducible-package.R
 b99c4587943a5835245abdfea2a83890 *R/robustDigest.R
 779b29ea2558cbc3755e2194c6a0e8ba *R/search.R
@@ -26,7 +27,7 @@ cb5e7af7f0121b3eb79b94b83d935dca *README.md
 ead02eff907f149c7ac855cb8fd748a4 *inst/WORDLIST
 99402fcbdae6aa4f874c7160ca6c32d7 *inst/doc/Intro-to-Cache.R
 a8f10d1ecf6af1a2f39bba4d1cc70d34 *inst/doc/Intro-to-Cache.Rmd
-9a59d4f89b7394fd33c72e13282fd51d *inst/doc/Intro-to-Cache.html
+9aa7d43f303953f5ef92da6445ca0bc7 *inst/doc/Intro-to-Cache.html
 0beca0a7a1defcb1730ed5b762653cd1 *inst/examples/example_Cache.R
 cde20f69f6baadbba47f1554eda344dd *inst/examples/example_checkPath.R
 6aa4ba6c2f7893e24e8bee6a30d01041 *inst/examples/example_postProcess.R
@@ -47,14 +48,15 @@ a5762391a4f6c7eea57c7829e179e8c9 *man/checkForAuxiliaryFiles.Rd
 4d97703ba1a199d5381ab481df960525 *man/checkoutVersion.Rd
 201b2d86398e3b9c5c54c48513fed3f5 *man/clearStubArtifacts.Rd
 ab4e525355fc31a0ff171c9795091897 *man/compareNA.Rd
+60d3246b814674b898012158b6e1bf7a *man/convertPaths.Rd
 49d2c93150cad2c6f8f5f4eff633c34e *man/copyFile.Rd
 a7f0bc18d33452db2c00792ea27ffbd8 *man/cropInputs.Rd
 18997c60b04a1a865bc66789f9e5e34d *man/debugCache.Rd
 42b14399cc3dd36520daa043fae4f7d2 *man/determineFilename.Rd
 94cc4b2e84b773e0a157a28d10d5b4fd *man/digest.Rd
 f12c47f4aeb33f32d5bd92f2c3b12bc3 *man/dlGeneric.Rd
 fedec3c792216d51f194baedb5c47ed3 *man/dlGoogle.Rd
-c69cf36de53a593526f4a0eff25f5961 *man/downloadFile.Rd
+dc226e1349b592ef52d0ac60ab596f94 *man/downloadFile.Rd
 a90591d3d02432fccc5fc80473771d5c *man/extractFromArchive.Rd
 22418b3c88cb6af101f2b8561a795b8a *man/fastMask.Rd
 f14b71099b9acc04c92230875be39fc1 *man/fixErrors.Rd
@@ -64,6 +66,8 @@ cb98497565ebfcf2c40473a460632f92 *man/guessAtTarget.Rd
 43cb3fea73f5096ecfe76182b14ef0de *man/installPackages.Rd
 e86843ce46f9ff759461979bba55173a *man/installVersions.Rd
 f6e1db089f36a340d4ac96c272d5fd5d *man/installedVersions.Rd
+587f63eeb07df0130e452fd7f8dd5ee1 *man/listFilesInArchive.Rd
+fede6d17622d165feff930cb9f5afb6c *man/makeMemoiseable.Rd
 500d359e4b1a5bfd5865cdf65ed9e5fe *man/maskInputs.Rd
 b2789a247b9c4ee7e715fe66eb061123 *man/mergeCache.Rd
 a4d9b422fc6f102012d6ddb876528ca9 *man/newLibPaths.Rd
@@ -78,13 +82,13 @@ f36d16a933e0a50876a2bc5cb7479104 *man/normPath.Rd
 e12e082b861d4c16fecc57a4394228d2 *man/postProcess.Rd
 a2faa99d60389027de12eca015e9cfdb *man/postProcessHelpers.Rd
 88421a31ccb0af22e173b9168cba6963 *man/preDigestByClass.Rd
-c388c138aa2807d8198bc24c20f0e3d5 *man/preProcess.Rd
+045bf582460b185fb1901415d3ee857d *man/preProcess.Rd
 4589dc3e67d3cc2a946ba31837456829 *man/prefix.Rd
-8503eb3e42d027226d4325106af623c4 *man/prepInputs.Rd
+32c8e8b85ec7c565b35133aa24097725 *man/prepInputs.Rd
 3578ab2ce38add8021bbfd338922475f *man/prepareFileBackedRaster.Rd
 0f2d347b88fac748c04804a92ef236b1 *man/prepareOutput.Rd
 794de11578838963fafd3d1e6e0c2e0f *man/projectInputs.Rd
-e338fa1b85c715fd9d94c0f7b292f838 *man/purge.Rd
+cdcbc786eb047427a37c3645ee1b38dc *man/purge.Rd
 975a4c6d1f4539cf6934b3317549329c *man/readLinesRcpp.Rd
 ddf718137b352e9f2b00d0e1d1d4b8fb *man/readLinesRcppInternal.Rd
 4f6a6de8bb0008631cab5f1a66f25d84 *man/reproducible-deprecated.Rd
@@ -93,22 +97,22 @@ b1027c658feb09ce6457ef04f5e141f4 *man/reproducible-package.Rd
 998a79f047c192826620dd9a966b6968 *man/search.Rd
 0c109d77c5dc51ed405b1c3531d4807f *man/sortDotsUnderscoreFirst.Rd
 9dfd2195f8fa7a706a7aa340b774d454 *man/tagsByClass.Rd
-e48215ecc8306d44a618f47d185772f3 *man/viewCache.Rd
+3773093d0c448c4dd6c7587de0d17c42 *man/viewCache.Rd
 6c5bc27b3b491c0a69aa9e3470c75268 *man/writeOutputs.Rd
 77901c8ef07a56401ea4d1e6ce73eb58 *src/RcppExports.cpp
 0d94c16cb0f946fc634ce5d954f683d1 *src/readLinesRcpp.cpp
 22c1619e69411c92fd520df0a53f8d8d *tests/test-all.R
 ee7da40fb42c327dc729a8ca916fe50b *tests/testthat/helper-allEqual.R
-9f99891f4f1bf5f877a3245af7c570c5 *tests/testthat/test-cache.R
+d4ef009df75e83779640cf48aa1fc96f *tests/testthat/test-cache.R
 0afd417ec47d98d5925c18f7628a3800 *tests/testthat/test-cacheArguments.R
 a203161f0e071bbb5f2d4735d2e65da7 *tests/testthat/test-checkPath.R
 cc6e7f6156b56b0f985ce4236c1a4d26 *tests/testthat/test-checksums.R
 ecf2b141db4c90d3b0e9a061123ae7de *tests/testthat/test-cluster.R
 4cf3c6c5d02d1de0e68f7ff7cc9512b6 *tests/testthat/test-copy.R
 aba94874678c78d6640c5002df0783b6 *tests/testthat/test-download.R
-c5276b306664da329c4ee47b6b01518a *tests/testthat/test-examples.R
+311b46d94fc9584d86d2232cf01145c2 *tests/testthat/test-examples.R
 0a49154131fd8c36f8c43ad8356ad1c1 *tests/testthat/test-gis.R
 bfccbf197ceda12a42313b75dc0e5bf8 *tests/testthat/test-git.R
 b3371355a60eca1f69debe841f5376ec *tests/testthat/test-packages.R
-6e3f28cf4d6430aaed521d9f3938cdbb *tests/testthat/test-prepInputs.R
+49c766548b260286099c0b444563d87c *tests/testthat/test-prepInputs.R
 a8f10d1ecf6af1a2f39bba4d1cc70d34 *vignettes/Intro-to-Cache.Rmd

NAMESPACE

@@ -5,6 +5,7 @@ S3method(cropInputs,default)
 S3method(cropInputs,spatialObjects)
 S3method(fixErrors,SpatialPolygons)
 S3method(fixErrors,default)
+S3method(makeMemoiseable,default)
 S3method(maskInputs,Raster)
 S3method(maskInputs,Spatial)
 S3method(objSize,Path)
@@ -16,6 +17,7 @@ S3method(postProcess,spatialObjects)
 S3method(projectInputs,Raster)
 S3method(projectInputs,Spatial)
 S3method(projectInputs,sf)
+S3method(unmakeMemoiseable,default)
 export("%<%")
 export("%>%")
 export("%C%")
@@ -44,6 +46,8 @@ export(checkoutVersion)
 export(clearCache)
 export(clearStubArtifacts)
 export(compareNA)
+export(convertPaths)
+export(convertRasterPaths)
 export(copyFile)
 export(cropInputs)
 export(downloadFile)
@@ -52,6 +56,7 @@ export(fixErrors)
 export(getGDALVersion)
 export(installVersions)
 export(installedVersions)
+export(makeMemoiseable)
 export(maskInputs)
 export(newLibPaths)
 export(normPath)
@@ -66,6 +71,7 @@ export(readLinesRcpp)
 export(searchFull)
 export(searchFullEx)
 export(showCache)
+export(unmakeMemoiseable)
 export(writeOutputs)
 exportClasses(Path)
 exportMethods(.addTagsToOutput)

NEWS.md

@@ -1,5 +1,25 @@
 Known issues: https://github.com/PredictiveEcology/reproducible/issues
 
+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 additonal edge cases.
+* other minor bug fixes.
+
 version 0.2.0
 =============
 

R/cache-helpers.R

@@ -725,14 +725,14 @@ copyFile <- function(from = NULL, to = NULL, useRobocopy = TRUE,
     robocopyBin <- tryCatch(Sys.which("robocopy"), warning = function(w) NA_character_)
 
     robocopy <-  if (silent) {
-      paste0(robocopyBin, " /purge"[delDestination], " /ETA /XJ /XO /NDL /NFL /NJH /NJS ",  # nolint
-             normalizePath(dirname(from), mustWork = TRUE, winslash = "\\"), " ",
-             normalizePath(to, mustWork = FALSE, winslash = "\\"),  " ",
+      paste0(robocopyBin, " /purge"[delDestination], " /ETA /XJ /XO /NDL /NFL /NJH /NJS \"",  # nolint
+             normalizePath(dirname(from), mustWork = TRUE, winslash = "\\"), "\" \"",
+             normalizePath(to, mustWork = FALSE, winslash = "\\"),  "\" ",
              basename(from))
     } else {
-      paste0(robocopyBin, " /purge"[delDestination], " /ETA /XJ /XO ", # nolint
-             normalizePath(dirname(from), mustWork = TRUE, winslash = "\\"), " ",
-             normalizePath(to, mustWork = FALSE, winslash = "\\"), " ",
+      paste0(robocopyBin, " /purge"[delDestination], " /ETA /XJ /XO \"", # nolint
+             normalizePath(dirname(from), mustWork = TRUE, winslash = "\\"), "\" \"",
+             normalizePath(to, mustWork = FALSE, winslash = "\\"), "\" ",
              basename(from))
     }
 
@@ -741,6 +741,9 @@ copyFile <- function(from = NULL, to = NULL, useRobocopy = TRUE,
     } else {
       TRUE
     }
+    if (isTRUE(any(grepl("ERROR", useFileCopy)))) {
+      useFileCopy <- TRUE
+    }
   } else if ( (os == "linux") || (os == "darwin") ) { # nolint
     if (!dir.exists(to)) to <- dirname(to) # extract just the directory part
     rsyncBin <- tryCatch(Sys.which("rsync"), warning = function(w) NA_character_)