* force add PATH to current user
* checkin docker setup script
* Update cluster_setup.sh
* install docker and start container on cluster setup
* WIP: Run task in container
* fix merge conflict
* run tasks and merge task from within container
* refactor code to proper docker commands and make a single R container per job
* refactor command line utils into its own file
* refactor job utilities into its own file
* move cluster setup script to inst folder
* remove unnecessary curl installs
* remove starting container from setup script
* check in WIP
* add apt_install file
* make required directories
* update cluster setup files as needed
* include libxml2 packages in apt installs
* working cluster create with cran and github dependencies
* update job prep to install apt-get and not each task
* use rocker containers instead of r-base
* remove unused & commented code
* remove unused install function
* address several lintr issues
* initial test dockerfile
* add spacing between commands
* temporarily point wget to feature branch
* update bioconductor install for non-jobPrep installs
* Delete Dockerfile
* minor changes to install bioc
* resolve merge conflicts
* update cluster to correctly install BioC packages using install_bioconductor
* fix issue where some packages were not getting installed
* add missing BioConductorCommand initializer
* remove print lines
* initial dockerfile implementations
* update docker files
* Only install packages if they are required
* Remove requirement on bioconductor installer script on start task
* remove duplicate environment variable entry
* update docs for container support
* update version to 0.6.0
* refactor changes updates
* remove poorly formatted whitespaces
* add full path to pacakges directory
* fix docker command line
* update file share sample
* update azure files cluster name
* update mandelbrot sample
* update package management sample
* update plyr samples
* make montecarlo sample more consistent
* update montecarlo sample
* remove plyr example
* fix bad environment pointer
* fix linter issues
* more linter fixes
* more linter issues
* use latest rAzureBatch version
* update resource files example
* remove reference to deleted sample
* pr feedback
* PR docs feedback
* Print errors from worker (#154)
* Fixed pool package command line lintr test
* Package installation tests fixed - too long lines
* Fixed json in customize cluster docs
* Fix: Typos in customize cluster docs
* Cleaning up files
* Feature/githubbiopackage (#150)
* install github package worked for foreach loop
* fix lintr error
* tests for github and bioc packages installation
* lintr fix
* add back lost code due to merge and update docs
* The Travis CI build failed for feature/githubbiopackage
* remove incorrect parameter for install_github
* Updated job prep task to have default command
* Use the latest version of rAzureBatch
* Updated description + Generate cluster config
* Fix: Bioconductor and Github packages installation (#155)
* Added multiple package install test and fix obj reading args
* Fixed naming for packages install
* Replaced validation exclusion for linter
* Fixed test validate test
* Fixing all interactive tests with skip
* Fixed renaming validation
* Removed default test - cannot be tested
* Removed in validation
* Added cluster package install tests (#156)
* Fixed worker and merger scripts
* Fixed verbose logs based on PR comments
* Added documentation on error handling
* Fixed header on table markdown
* Fixed based on PR comments
* Added set chunk size
* Added cluster configuration validation function (#30)
* Added pool config test validation
* Added a fix for validation
* Added if checks for null tests and more validation tests
* Install R packages at job run time (#29)
* Added cran/github installation scripts
* Added package installation tests
* Upgraded package version to 0.3.2
* Output file support (#40)
* Output files support
* Added createOutputFile method
* output files readme documentation
* added tests and find container sas
* Added more detailed variable names
* Enable/disable merge task (#39)
* Merge task pass params
* Fixed enableMerge cases
* Merge task documentation on README.md
* Fixed typo on merge task description
* Update doAzureParallel.R
* Changed enableMerge to enableCloudCombine
* Fix/backwards compatible (#68)
* Added backwards compatible in make cluster
* Added deprecated config validator
* Added mismatch label
* Added validation for quota limits and bad getPool requests in waitForNodesToComplete (#52)
* Added validation for quota limits and bad getPool requests
* Fixed based on PR
* Fixed progress bar layout to use switch statements instead of if statements
* Changed clusterId to poolId
* Added comments and fixed messages
* Added running state to the node status
* Reformatted lines for function
* Added end statement for node completion
* Feature/custom script and reduce (#70)
* Added custom scripts and removed dependencies parameter
* Updated roxygen tool version
* Added parallelThreads support
* Added test coverage
* Removed verbose message on command line
* Added Reduce function for group of tasks
* Fix build because of doc semantics mismatch with function
* Removed unused function
* Added command line arg
* Added docs for custom script
* Moved customize cluster to separate doc for future usage
* Fixed typo
* Bug - Waiting for tasks to completion function ends too early (#69)
* Moved wait for tasks to complete to doAzureParallel utility
* Removed unneeded variables and progress
* Fixed camel case for skiptoken
* Travis/lintr (#72)
* Added lintr config file
* Added travis github package installation
* Removed snake case rule
* Fixed documents on doAzureParallel
* Based on lintr default_settins docs, correctly added default rules
* Updated lintr package to use object_name_style
* Added package :: operator
* Reformatted after merge
* Fixed command line tests
* Upgraded roxygen to 6.0.1
* Cluster config docs
* Removed additional delete job
* Fixed warning descriptions in makeCluster
* Ramped up versions for DESCRIPTION
* Updated CHANGELOG to 0.4.0
* Fixed environmentSettings style from merge conflict
* Fixed cluster warning naming style
Brian Hoang
Pablo Selem