Merge branch 'release/0.4.0'

Author: HenrikBengtsson

.make/Makefile

@@ -56,6 +56,7 @@ R_NO_INIT := --no-init-file
 R_VERSION_STATUS := $(shell $(R_SCRIPT) -e "status <- tolower(R.version[['status']]); if (regexpr('unstable', status) != -1L) status <- 'devel'; cat(status)")
 R_VERSION_X_Y := $(shell $(R_SCRIPT) -e "cat(gsub('[.][0-9]+$$', '', getRversion()))")
 R_VERSION := $(shell $(R_SCRIPT) -e "cat(as.character(getRversion()))")
+R_VERSION_3_3_OR_NEWER := $(shell $(R_SCRIPT) -e "cat(getRversion() >= '3.3.0')")
 R_VERSION_FULL := $(R_VERSION)$(R_VERSION_STATUS)
 R_LIBS_USER_X := $(shell $(R_SCRIPT) -e "cat(.libPaths()[1])")
 R_INCLUDE := $(shell $(R_SCRIPT) -e "cat(R.home('include'))")
@@ -79,6 +80,16 @@ GIT_COMMIT := $(shell $(GIT) log -1 --format="%h")
 R_LIBS_BRANCH := $(CURDIR)/.R/$(GIT_BRANCH)
 
 
+# Asserts proper Windows toolchain in R (>= 3.3.0)
+ifeq ($(OS), Windows_NT)
+ifeq ($(R_VERSION_3_3_OR_NEWER), TRUE)
+ifndef BINPREF
+$(error R (>= 3.3.0) on Windows: BINPREF not set)
+endif
+endif
+endif
+
+
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # Main
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -123,6 +134,7 @@ debug:
 	@echo R_RD4PDF=\'$(R_RD4PDF)\'
 	@echo
 	@echo R_CRAN_OUTDIR=\'$(R_CRAN_OUTDIR)\'
+	@echo R_VERSION_3_3_OR_NEWER=\'$(R_VERSION_3_3_OR_NEWER)\'
 	@echo
 
 
@@ -326,6 +338,12 @@ $(R_OUTDIR)/vigns: install
 vignettes: $(R_OUTDIR)/vigns
 
 
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Static code validation etc
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+lint:
+	$(R_SCRIPT) -e "library(lintr); lint_package(linters = with_defaults(commented_code_linter = NULL, closed_curly_linter = closed_curly_linter(allow_single_line = TRUE), open_curly_linter = open_curly_linter(allow_single_line = TRUE)))"
+
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # Run package tests
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

.travis.yml

@@ -24,12 +24,6 @@ matrix:
       r: oldrel
     - os: linux
       r: release
-      r_github_packages:
-        - jimhester/covr
-      after_success:
-        - Rscript -e 'covr::codecov(quiet=FALSE)'
-      env:
-        - NB='w/ covr'  ## Just a label
     - os: linux
       r: devel
     - os: linux
@@ -38,14 +32,24 @@ matrix:
         - NB='w/ batchtools devel'  ## Just a label
     - os: osx
       r: oldrel
-      r_github_packages:
-        - HenrikBengtsson/globals
-        - HenrikBengtsson/future
     - os: osx
       r: release
+    - os: linux
+      r: release
       r_github_packages:
-        - HenrikBengtsson/globals
-        - HenrikBengtsson/future
+        - jimhester/covr
+      r_check_args: --no-codoc --no-examples --no-tests --ignore-vignettes
+      after_success:
+        - Rscript -e 'covr::codecov(quiet=FALSE)'
+      env: NB='w/ covr' ## Just a label
+    - os: linux
+      r: release
+      r_github_packages:
+        - jimhester/lintr
+      r_check_args: --no-codoc --no-examples --no-tests --ignore-vignettes
+      after_success:
+        - Rscript -e 'library(lintr); lint_package(linters = with_defaults(commented_code_linter = NULL, closed_curly_linter = closed_curly_linter(allow_single_line = TRUE), open_curly_linter = open_curly_linter(allow_single_line = TRUE)))'
+      env: NB='w/ lintr' ## Just a label
 
 before_install:
   - Rscript -e 'c(physical = parallel::detectCores(logical = FALSE), logical = parallel::detectCores())'

DESCRIPTION

@@ -1,11 +1,10 @@
 Package: future.batchtools
-Version: 0.3.0
+Version: 0.4.0
 Depends:
     R (>= 3.2.0),
     future (>= 1.4.0)
 Imports:
-    batchtools (>= 0.9.2),
-    R.utils
+    batchtools (>= 0.9.3)
 Suggests:
     listenv,
     markdown,

NAMESPACE

@@ -13,6 +13,7 @@ S3method(value,BatchtoolsFuture)
 export("%resources%")
 export(BatchtoolsFuture)
 export(BatchtoolsFutureError)
+export(batchtools_custom)
 export(batchtools_interactive)
 export(batchtools_local)
 export(batchtools_lsf)
@@ -26,11 +27,6 @@ export(loggedError)
 export(loggedOutput)
 export(status)
 export(value)
-importFrom(R.utils,isDirectory)
-importFrom(R.utils,isFile)
-importFrom(R.utils,mkdirs)
-importFrom(R.utils,removeDirectory)
-importFrom(R.utils,tempvar)
 importFrom(batchtools,batchExport)
 importFrom(batchtools,batchMap)
 importFrom(batchtools,clearRegistry)
@@ -41,6 +37,7 @@ importFrom(batchtools,loadResult)
 importFrom(batchtools,makeClusterFunctionsInteractive)
 importFrom(batchtools,makeClusterFunctionsLSF)
 importFrom(batchtools,makeClusterFunctionsMulticore)
+importFrom(batchtools,makeClusterFunctionsOpenLava)
 importFrom(batchtools,makeClusterFunctionsSGE)
 importFrom(batchtools,makeClusterFunctionsSlurm)
 importFrom(batchtools,makeClusterFunctionsTORQUE)

NEWS

@@ -1,32 +1,63 @@
 Package: future.batchtools
 ==========================
 
+Version: 0.4.0 [2017-05-16]
+
+NEW FEATURES:
+
+ o Added batchtools_custom() for specifying batchtools futures using any type
+   of batchtools cluster functions.
+   
+ o batchtools_template(pathname = NULL, type = <type>) now relies on the
+   batchtools package for locating the <type> template file.
+   
+ o nbrOfWorkers() for batchtools futures now defaults to +Inf unless the
+   evaluator's 'workers' or 'cluster.functions' specify something else.
+
+ o Renamed argument 'pathname' to 'template' for batchtools_<tmpl>() functions.
+
+BUG FIXES:
+   
+ o Under plan(batchjobs_*), when being created futures would produce an error
+   on "all(is.finite(workers)) is not TRUE" due to an outdated sanity check.
+
+SOFTWARE QUALITY:
+
+ o TESTS: Added test of future_lapply() for batchtools backends.
+
+ o TESTS: Added optional tests for batchjobs_* HPC schedulers listed in
+   environment variable 'R_FUTURE_TESTS_STRATEGIES'.
+
+CODE REFACTORING:
+
+ o CLEANUP: Package no longer depends on R.utils.
+
+ 
 Version: 0.3.0 [2017-03-19]
 
 NEW FEATURES:
 
  o The number of jobs one can add to the queues of HPC schedulers is in
-   principle unlimited, which is why the number of available workers for
-   such batchtools_* backends is reported as +Inf.  However, as the number
-   of workers is used by future_lapply() to decide how many futures should
-   be used to best partition the elements, this means that future_lapply()
-   will always use one future per element.  Because of this, it is now
-   possible to specify plan(batchtools_*, workers = n) where 'n' is the
-   target number of workers.
+   principle unlimited, which is why the number of available workers for such
+   batchtools_* backends is reported as +Inf.  However, as the number of
+   workers is used by future_lapply() to decide how many futures should be used
+   to best partition the elements, this means that future_lapply() will always
+   use one future per element.  Because of this, it is now possible to specify
+   plan(batchtools_*, workers = n) where 'n' is the target number of workers.
 
 
 Version: 0.2.0 [2017-02-23]
 
 GLOBALS:
 
- o batchtools (>= 0.9.2) now supports exporting objects with
-   any type of names (previously only possible if they mapped to
-   to strictly valid filenames).  This allowed me to avoid lots of
-   internal workaround code encoding and decoding globals.
+ o batchtools (>= 0.9.2) now supports exporting objects with any type of names
+   (previously only possible if they mapped to to strictly valid filenames).
+   This allowed me to avoid lots of internal workaround code encoding and
+   decoding globals.
 
 
 Version: 0.1.0 [2017-02-11]
 
- o Package created by porting the code of future.BatchJobs.
-   This version passes 'R CMD check --as-cran' with all OK
-   after a minimial amount of adjustments to the ported code.
+ o Package created by porting the code of future.BatchJobs. This version passes
+   'R CMD check --as-cran' with all OK after a minimial amount of adjustments
+   to the ported code.