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Commits on Apr 6, 2018
  1. Change error message

    nturaga committed Apr 6, 2018
Commits on Mar 22, 2018
  1. suppressPackageStartupMessages when receiving data

    mtmorgan committed Mar 22, 2018
    - avoids messages when deserializing manager environment on worker
  2. implement remote error handling on bplapply,BatchtoolsParam

    mtmorgan committed Mar 22, 2018
    - bptry(), BPREDO, and more informative error messages
  3. Merge branch 'BatchToolsParam'

    mtmorgan committed Mar 22, 2018
    - Implements BatchtoolsParam() and bplapply,BatchtoolsParam-method
    - Closes #71
  4. R CMD check cleaneup

    mtmorgan committed Mar 22, 2018
    - document methods
    - document dots
  5. editorial changes to vignette

    mtmorgan committed Mar 22, 2018
    - template using system.file()
    - email address
    - number titles so sort OK on package landing page
    - a little more output; sessionInfo
    - minor formatting / syntax
  6. editorial changes to BatchtoolsParam-class.Rd

    mtmorgan committed Mar 22, 2018
    - documet batchtoolsRegistryargs()
Commits on Mar 21, 2018
  1. update test functions

    mtmorgan committed Mar 21, 2018
    - only evaluate when cluster type available
    - test windows-specific branches
  2. export batchtoolsTemplate()

    mtmorgan committed Mar 21, 2018
Commits on Mar 20, 2018
  1. clean up registry args

    mtmorgan committed Mar 20, 2018
    - add to show method
    - export batchtoolsRegistryargs
  2. .prettyPath() prints paths to fit width of screen

    mtmorgan committed Mar 20, 2018
    - used to print path to template
  3. remove public bptemplate()

    mtmorgan committed Mar 20, 2018
    - keep public API as 'clean' as possible
    - path to template already displayed as part of show()
  4. clean up DESCRIPTION

    mtmorgan committed Mar 20, 2018
  5. Add vigentte for BatchtoolsParam,

    nturaga committed Mar 20, 2018
    -- It has to be merged into the main BiocParallel vignette.
    
    -- Remove TODO items from class
  6. Remove 'bpstop()' as it is not needed

    nturaga committed Mar 20, 2018
    When bpstart is not called and bplapply is issued directly,
    bpstop fails. bplapply automatically calls bpstop.
  7. Add workers to cluster types using job schedulers

    nturaga committed Mar 20, 2018
    - SGE
    - slurm
    - lsf
    etc
    
    This fixes test cases
Commits on Mar 16, 2018
  1. Batchtools clean-up

    mtmorgan committed Mar 16, 2018
    - makeClusterFunctions in bpstart (socket workers are launched here)
    - specify default registry args, then allow user to modify
    - registryargs file.dir use tempfile in getwd()
    - on.exit(add = TRUE) in bpstart(), so all handlers run
  2. Add test cases for each cluster type

    nturaga committed Mar 16, 2018
    -- Add interactive cluster to type that returns NA for template
    -- Remove script Batchtools-biocParallel.R
Commits on Mar 15, 2018
  1. Add multiple cluster types

    nturaga committed Mar 15, 2018
    -- switch makeClusterFunctions from bpstart, to the class constructor
    -- batchtoolsRegistryargs takes in multiple arguments as a list
    to makeRegistry
    -- user can now add template file path, to the function.
    -- Modify batchtoolsTemplate
    -- remove setter for bptemplate
  2. Add bptemplate to NAMESPACE

    nturaga committed Mar 15, 2018
    bptemplate getter only
  3. Update unit tests to reflect new cluster types

    nturaga committed Mar 15, 2018
    -- Remove batchtools-sge.tmpl, this should be provided
    by the user if the template is different from the batchtools.
    
    BatchtoolsParam(template = "mytemplate.tmpl")
Commits on Mar 14, 2018
  1. Commit for additional clusters

    nturaga committed Mar 14, 2018
    - slurm
    - lsf
    - openlava
    - torque has issues
    
    batchtoolsTemplate has been modified to return files from the
    inst/templates folder in batchtools package.
Commits on Mar 13, 2018
  1. Remove torque, update template once it is selected

    nturaga committed Mar 13, 2018
    bpstart resets param$template to correct file
  2. Add multiple clusters to the BatchtoolsParam class

    nturaga committed Mar 13, 2018
    - SLURM
    - TORQUE
    - LSF
    - OPENLAVA
    
    these are untested cluster types
Commits on Mar 12, 2018
  1. Remove batchtools.Mutlicore-conf.R as it is not needed anymore

    Nitesh Turaga authored and nturaga committed Mar 12, 2018
    this file was needed before the batchtoolsTemplate was written,
    and bpstart looks up automatically