Merge branch 'release/0.8.1'

Author: HenrikBengtsson

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: future.batchtools
-Version: 0.8.0
+Version: 0.8.1
 Depends:
     R (>= 3.2.0),
-    future (>= 1.12.0)
+    future (>= 1.14.0)
 Imports:
     batchtools (>= 0.9.11)
 Suggests:

NEWS

@@ -1,6 +1,14 @@
 Package: future.batchtools
 ==========================
 
+Version: 0.8.1 [2019-09-30]
+
+BUG FIXES:
+
+ * print() for BatchtoolsFuture would produce an error if the underlying
+   batchtools Registry was incomplete.
+
+
 Version: 0.8.0 [2019-05-04]
 
 NEW FEATURES:

R/BatchtoolsFuture-class.R

@@ -133,9 +133,9 @@ print.BatchtoolsFuture <- function(x, ...) {
            class(reg))
   } else {
     printf("batchtools Registry:\n  ")
-    print(reg)
     printf("  File dir exists: %s\n", file_test("-d", reg$file.dir))
     printf("  Work dir exists: %s\n", file_test("-d", reg$work.dir))
+    try(print(reg))
   }
 
   invisible(x)
@@ -305,6 +305,7 @@ result.BatchtoolsFuture <- function(future, cleanup = TRUE, ...) {
   stop_if_not(inherits(result, "FutureResult"))
   future$result <- result
   future$state <- "finished"
+
   if (cleanup) delete(future)
 
   NextMethod()

R/future_cache_path.R

@@ -1,22 +1,23 @@
 #' @importFrom utils file_test sessionInfo
 future_cache_path <- local({
-  ## The path used for this session
-  path <- NULL
+  ## The subfolder used for this session
+  dir <- NULL
 
   function(root_path = Sys.getenv("R_FUTURE_CACHE_PATH", ".future"), absolute = TRUE, create = TRUE) {
-    if (is.null(path)) {
+    if (is.null(dir)) {
       id <- basename(tempdir())
       id <- gsub("Rtmp", "", id, fixed = TRUE)
       timestamp <- format(Sys.time(), format = "%Y%m%d_%H%M%S")
-      dir <- sprintf("%s-%s", timestamp, id)
-      path_tmp <- file.path(root_path, dir)
-      if (create && !file_test("-d", path_tmp)) {
-        dir.create(path_tmp, recursive = TRUE)
-        pathname_tmp <- file.path(path_tmp, "sessioninfo.txt")
-        writeLines(capture_output(print(sessionInfo())), con = pathname_tmp)
-      }
-      path <<- path_tmp
+      dir <<- sprintf("%s-%s", timestamp, id)
     }
+    
+    path <- file.path(root_path, dir)
+    if (create && !file_test("-d", path)) {
+      dir.create(path, recursive = TRUE)
+      pathname <- file.path(path, "sessioninfo.txt")
+      writeLines(capture_output(print(sessionInfo())), con = pathname)
+    }
+
     if (absolute) path <- normalizePath(path, mustWork = FALSE)
 
     path

R/resources_OP.R

@@ -24,7 +24,7 @@
   on.exit(plan(oplan, substitute = FALSE, .call = NULL))
 
   ## Tweak current strategy and apply
-  args <- list(plan(), resources = tweaks, penvir = envir)
+  args <- list(plan("next"), resources = tweaks, penvir = envir)
   strategy <- do.call(tweak, args = args)
   plan(strategy, substitute = FALSE, .call = NULL)
 

R/zzz.R

@@ -1,3 +1,10 @@
+.onLoad <- function(libname, pkgname) {
+  inRCmdCheck <- import_future("inRCmdCheck")
+  if (inRCmdCheck()) {
+    Sys.setenv("R_FUTURE_CACHE_PATH" = file.path(tempdir(), ".future"))
+  }
+}
+
 #' @importFrom utils file_test
 .onUnload <- function(libpath) {
   ## (a) Force finalizer of Future objects to run such

README.md

@@ -116,19 +116,30 @@ To configure batchtools for job schedulers we need to setup a `*.tmpl` template
 file that is used to generate the script used by the scheduler.
 This is what a template file for TORQUE / PBS may look like:
 ```sh
+#!/bin/bash
+
 ## Job name:
-#PBS -N <%= job.name %>
+#PBS -N <%= if (exists("job.name", mode = "character")) job.name else job.hash %>
+
+## Direct streams to logfile:
+#PBS -o <%= log.file %>
 
 ## Merge standard error and output:
 #PBS -j oe
 
-## Resource parameters:
-<% for (name in names(resources)) { %>
-#PBS -l <%= name %>=<%= resources[[name]] %>
+## Email on abort (a) and termination (e), but not when starting (b)
+#PBS -m ae
+
+## Resources needed:
+<% if (length(resources) > 0) {
+  opts <- unlist(resources, use.names = TRUE)
+  opts <- sprintf("%s=%s", names(opts), opts)
+  opts <- paste(opts, collapse = ",") %>
+#PBS -l <%= opts %>
 <% } %>
 
-## Run R:
-R CMD BATCH --no-save --no-restore "<%= rscript %>" /dev/stdout
+## Launch R and evaluated the batchtools R job
+Rscript -e 'batchtools::doJobCollection("<%= uri %>")'
 ```
 If this template is saved to file `batchtools.torque.tmpl` (without period)
 in the working directory or as `.batchtools.torque.tmpl` (with period) the

appveyor.yml

@@ -20,7 +20,7 @@ environment:
 init:
   ps: |
         $ErrorActionPreference = "Stop"
-        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+        Invoke-WebRequest https://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
         Import-Module '..\appveyor-tool.ps1'
 
 install:

cran-comments.md

@@ -1,10 +1,10 @@
-# CRAN submission future.batchtools 0.8.0
+# CRAN submission future.batchtools 0.8.1
 
-on 2019-05-04
+on 2019-09-30
 
 I've verified that this submission causes no issues for any of the 3 reverse package dependencies available on CRAN.
 
-Thanks in advance
+Thanks in advance.
 
 
 ## Notes not sent to CRAN
@@ -14,47 +14,35 @@ Thanks in advance
 The package has been verified using `R CMD check --as-cran` on:
 
 * Platform x86_64-apple-darwin15.6.0 (64-bit) [Travis CI]:
-  - R version 3.5.3 (2019-03-11)
-  - R version 3.6.0 (2019-04-26)
+  - R version 3.5.3 (2017-01-27)
+  - R version 3.6.1 (2019-07-05)
 
 * Platform x86_64-unknown-linux-gnu (64-bit) [Travis CI]:
-  - R version 3.5.3 (2017-01-27) [sic!]
-  - R version 3.6.0 (2019-04-26)
-  - R Under development (unstable) (2019-05-04 r76458)
+  - R version 3.5.3 (2017-01-27)
+  - R version 3.6.1 (2019-07-05)
+  - R Under development (unstable) (2019-09-27 r77229)
 
+* Platform x86_64-pc-linux-gnu (64-bit) [r-hub]:
+  - R version 3.6.1 (2019-07-05)
+  
 * Platform x86_64-pc-linux-gnu (64-bit):
-  - R version 3.2.0 (2015-04-16) w/ Torque/PBS scheduler
-  - R version 3.3.0 (2016-05-03) w/ Torque/PBS scheduler
-  - R version 3.4.0 (2017-04-21) w/ Torque/PBS scheduler
-  - R version 3.5.0 (2018-04-23) w/ SGE scheduler
-  - R version 3.6.0 (2019-04-26) w/ Torque/PBS scheduler
-  - R version 3.6.0 (2019-04-26) w/ SGE scheduler
-  - R version 3.6.0 (2019-04-26)
+  - R version 3.2.0 (2015-04-16)
+  - R version 3.6.1 (2019-07-05) w/ Torque/PBS scheduler
+  - R version 3.6.1 Patched (2019-09-12 r77183)
 
-* Platform x86_64-pc-linux-gnu (64-bit) [r-hub]:
+* Platform i386-pc-solaris2.10 (32-bit):
   - R version 3.6.0 (2019-04-26)
-  - R Under development (unstable) (2019-05-02 r76453)
-
-* Platform i686-pc-linux-gnu (32-bit):
-  - R version 3.4.4 (2018-03-15)
 
 * Platform i386-w64-mingw32 (32-bit) [Appveyor CI]:
-  - R version 3.6.0 (2019-04-26)
+  - R Under development (unstable) (2019-09-27 r77229)
 
-* Platform x86_64-w64-mingw32/x64 (64-bit) [Appveyor CI]:
-  - R version 3.6.0 (2019-04-26)
-  - R Under development (unstable) (2019-05-03 r76456)
-    
 * Platform x86_64-w64-mingw32 (64-bit) [r-hub]:
-  - R Under development (unstable) (2019-04-26 r76431)
-
-* Platform x86_64-w64-mingw32/x64 (64-bit) [win-builder]:
-  - R version 3.6.0 (2019-04-26)
-  - R Under development (unstable) (2019-05-02 r76454)
+  - R Under development (unstable) (2019-09-18 r77193)
 
+* Platform x86_64-w64-mingw32/x64 (64-bit) [Appveyor CI]:
+  - R version 3.6.1 (2019-07-05)
+  - R Under development (unstable) (2019-09-27 r77229)
 
-The following setups were skipped due to non-availability:
-
-* Platform i386-pc-solaris2.10 (32-bit) [r-hub]:
-  - R version 3.5.0 Patched (2018-04-30 r74674)
-    REASON: Package required but not available: ‘batchtools’
+* Platform x86_64-w64-mingw32/x64 (64-bit) [win-builder]:
+  - R version 3.6.1 (2019-07-05)
+  - R Under development (unstable) (2019-09-30 r77236)

revdep/README.md

@@ -1,54 +1,59 @@
 # Platform
 
-|field    |value                        |
-|:--------|:----------------------------|
-|version  |R version 3.6.0 (2019-04-26) |
-|os       |Ubuntu 18.04.2 LTS           |
-|system   |x86_64, linux-gnu            |
-|ui       |X11                          |
-|language |en                           |
-|collate  |en_US.UTF-8                  |
-|ctype    |en_US.UTF-8                  |
-|tz       |America/Los_Angeles          |
-|date     |2019-05-04                   |
+|field    |value                                       |
+|:--------|:-------------------------------------------|
+|version  |R version 3.6.1 Patched (2019-09-12 r77183) |
+|os       |Ubuntu 18.04.3 LTS                          |
+|system   |x86_64, linux-gnu                           |
+|ui       |X11                                         |
+|language |en                                          |
+|collate  |en_US.UTF-8                                 |
+|ctype    |en_US.UTF-8                                 |
+|tz       |America/Los_Angeles                         |
+|date     |2019-09-30                                  |
 
 # Dependencies
 
 |package           |old    |new        |Δ  |
 |:-----------------|:------|:----------|:--|
-|future.batchtools |0.7.2  |0.7.2-9000 |*  |
+|future.batchtools |0.8.0  |0.8.0-9000 |*  |
 |assertthat        |0.2.1  |0.2.1      |   |
 |backports         |1.1.4  |1.1.4      |   |
 |base64url         |1.4    |1.4        |   |
 |batchtools        |0.9.11 |0.9.11     |   |
 |brew              |1.0-6  |1.0-6      |   |
-|checkmate         |1.9.3  |1.9.3      |   |
+|checkmate         |1.9.4  |1.9.4      |   |
+|codetools         |0.2-16 |0.2-16     |   |
 |crayon            |1.3.4  |1.3.4      |   |
 |data.table        |1.12.2 |1.12.2     |   |
-|digest            |0.6.18 |0.6.18     |   |
-|fs                |1.3.0  |1.3.0      |   |
-|future            |1.12.0 |1.12.0     |   |
+|digest            |0.6.21 |0.6.21     |   |
+|ellipsis          |0.3.0  |0.3.0      |   |
+|fs                |1.3.1  |1.3.1      |   |
+|future            |1.14.0 |1.14.0     |   |
 |globals           |0.12.4 |0.12.4     |   |
-|hms               |0.4.2  |0.4.2      |   |
+|glue              |1.3.1  |1.3.1      |   |
+|hms               |0.5.1  |0.5.1      |   |
 |listenv           |0.7.0  |0.7.0      |   |
 |magrittr          |1.5    |1.5        |   |
-|pkgconfig         |2.0.2  |2.0.2      |   |
+|pkgconfig         |2.0.3  |2.0.3      |   |
 |prettyunits       |1.0.2  |1.0.2      |   |
-|progress          |1.2.0  |1.2.0      |   |
+|progress          |1.2.2  |1.2.2      |   |
 |R6                |2.4.0  |2.4.0      |   |
 |rappdirs          |0.3.1  |0.3.1      |   |
-|Rcpp              |1.0.1  |1.0.1      |   |
-|rlang             |0.3.4  |0.3.4      |   |
+|Rcpp              |1.0.2  |1.0.2      |   |
+|rlang             |0.4.0  |0.4.0      |   |
 |stringi           |1.4.3  |1.4.3      |   |
+|vctrs             |0.2.0  |0.2.0      |   |
 |withr             |2.1.2  |2.1.2      |   |
+|zeallot           |0.1.0  |0.1.0      |   |
 
 # Revdeps
 
 ## All (3)
 
-|package                              |version |error |warning |note |
-|:------------------------------------|:-------|:-----|:-------|:----|
-|[batchtools](problems.md#batchtools) |0.9.11  |      |        |1    |
-|[drtmle](problems.md#drtmle)         |1.0.4   |      |        |1    |
-|[FAMoS](problems.md#famos)           |0.1.0   |      |        |1    |
+|package    |version |error |warning |note |
+|:----------|:-------|:-----|:-------|:----|
+|batchtools |0.9.11  |      |        |     |
+|drtmle     |1.0.4   |      |        |     |
+|FAMoS      |0.2.0   |      |        |     |