batchtools 0.9.3

  • Running jobs now are also included while querying for status “started”. This affects findStarted(), findNotStarted and getStatus().
  • findExperiments() now performs an exact string match (instead of matching substrings) for patterns specified via prob.name and algo.name. For substring matching, use prob.pattern or algo.pattern, respectively.
  • Changed arguments for reduceResultsDataTable()
    • Removed fill, now is always TRUE
    • Introduced flatten to control if the result should be represented as a column of lists or flattened as separate columns. Defaults to a backward-compatible heuristic, similar to getJobPars.

batchtools 0.9.2

  • Full support for array jobs on Slurm and TORQUE.
  • Array jobs have been disabled for SGE and LSF (due to missing information about the output format) but will be re-enable in a future release. Note that the variable n.array.jobs has been removed from JobCollection in favor of the new variable array.jobs (logical).
  • findExperiments() now has two additional arguments to match using regular expressions. The possibility to prefix a string with “~” to enable regular expression matching has been removed.
  • New function batchReduce().
  • New function estimateRuntimes().
  • New function removeRegistry().
  • Missing result files are now handled more consistently, raising an exception in its defaults if the result is not available. The argument missing.val has been added to reduceResultsList() and reduceResultsDataTable() and removed from loadResult() and batchMapResults().
  • Timestamps are now stored with sub-second accuracy.
  • Renamed Torque to TORQUE. This especially affects the constructor makeClusterFunctionsTorque which now must be called via makeClusterFunctionsTORQUE()
  • chunkIds() has been deprecated. Use chunk(), lpt() or binpack() instead.
  • Fixed listing of jobs for ClusterFunctionsLSF and ClusterFunctionsOpenLava (thanks to @phaverty).
  • Job hashes are now prefixed with the literal string ‘job’ to ensure they start with a letter as required by some SGE systems.
  • Fixed handling of NULL results in reduceResultsList()
  • Fixed key lookup heuristic join functions.
  • Fixed a bug where getJobTable() returned difftimes with the wrong unit (e.g., in minutes instead of seconds).
  • Deactivated swap allocation for clusterFunctionsDocker().
  • The package is now more patient while communicating with the scheduler or file system by using a timeout-based approach. This should make the package more reliable and robust under heavy load.

batchtools 0.9.0

Initial CRAN release. See this vignette for a brief comparison with BatchJobs/BatchExperiments.