merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@86108 bc3139a8-67e5-0310-9ffc-ced21a209358
merge from bioc-devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/openCyto@86314 bc3139a8-67e5-0310-9ffc-ced21a209358
conflicts resolved while setting up Git-SVN bridge

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@86322 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'trunk'
Commit made by the Bioconductor Git-SVN bridge.
Consists of 16 commit(s).

Commit information:

    Commit id: df68916178432cd28dadbc97832e6c87c0ddaf56
    Commit message:
    1. clean up documentation of  gating method 2. fix a bug in parallel gating using cluster #33
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-26T14:30:50-08:00

    Commit id: 2cfb0af27b8034acdeda5b12ce8c89abb64684e2
    Commit message:
    1. set alwasyLoadData to TRUE for recompute non-bool gates to avoid the overhead from checking the gate type. 2. add error handling for parallel gating. RGLab/flowWorkspace#139 #37
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-26T15:41:06-08:00

    Commit id: 1d47f77ecb4def451e0599e20f3f44dde7cd3234
    Commit message:
    add test data and test cases for template parsing.#74
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-05T15:35:46-08:00

    Commit id: 137ce73fbda0f13c5378c4c1f2f7cc0983194218
    Commit message:
    wrap the logic of expansion for each row into .preprocess_row routine #74
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-05T16:05:08-08:00

    Commit id: 7779159318829a63c6a3b0686ddcaa91c0c583b8
    Commit message:
    replace data.frame with data.table in csv preprocessing. #74
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-06T17:45:25-08:00

    Commit id: 059aa3fd64999cfccdc71c1d732250e062408f6a
    Commit message:
    fix the default plus sign to pop name
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-07T10:24:31-08:00

    Commit id: f6dff297cf3b2238b9cccbf6625c8ff34078c92b
    Commit message:
    replace double quote with single quote in ITN_Newell csv template
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-07T10:42:58-08:00

    Commit id: 96ec7c748ca3abf9ea8f5633dd61c85541095ab6
    Commit message:
    add R/csvTemplate-parser.R
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-07T11:00:38-08:00

    Commit id: 93531513ddfaf8d4838eecd46c7011945ed8224d
    Commit message:
    add test cases for plugin framework. #74
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-07T13:49:29-08:00

    Commit id: b875340e15e5b35c32ab7736266c3a68a8285fb8
    Commit message:
    add test-pluginFramework.R #74
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-07T13:51:07-08:00

    Commit id: 6312a174549bec4afdeeacdf8ad15bb4e360dac6
    Commit message:
    add registeration of preprocessing methods. #72
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-07T15:51:34-08:00

    Commit id: 34ebfab2a7d534a7dee12ae70a07cbf63f10da93
    Commit message:
    fix Rd files. #72
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-07T16:15:13-08:00

    Commit id: c157e4554fd4ebb6c07d4bc607abc01bedf49b0e
    Commit message:
    1.fix namespace issue 2. remove filterId from the required argument list of plugin gating functions. #72
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-10T15:25:08-07:00

    Commit id: 2cebc71a54299d11b36d7273c43ee58dc201be81
    Commit message:
    add internal gating test suite. #74
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-10T16:27:31-07:00

    Commit id: af79e7c65f5ddc347bebf01b36a571986424699e
    Commit message:
    fix file path in vignette
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-10T16:45:39-07:00

    Commit id: 612d01f5013c73f9663192c29ae15e74809952b2
    Commit message:
    Merge branch 'trunk'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-10T16:57:43-07:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@87287 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'trunk'
Merge branch 'master' of github.com:RGLab/openCyto
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commit(s).

Commit information:

    Commit id: af79e7c65f5ddc347bebf01b36a571986424699e
    Commit message:
    fix file path in vignette
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-10T16:45:39-07:00

    Commit id: c584b30a4b5e65d8a15fa7f8e472cbaa22e523fc
    Commit message:
    fix vignette
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-03-10T17:26:24-07:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@87289 bc3139a8-67e5-0310-9ffc-ced21a209358
close #75
Merge branch 'trunk'
Merge branch 'trunk'
Merge commit '4bb6de18f49d1274cb63dfce8fd8a1f7aee8be66'
merge from biocdevel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/openCyto@87340 bc3139a8-67e5-0310-9ffc-ced21a209358
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: db54bc2853862544c8c853943cf40bcec4cfa682
    Commit message:
    merge from biocdevel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/openCyto@87340 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang <m.jiang at bc3139a8-67e5-0310-9ffc-ced21a209358>
    Commit date: 2014-03-11T23:19:40Z

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@87341 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'trunk'
Merge branch 'master' of github.com:RGLab/openCyto
Merge commit 'db54bc2853862544c8c853943cf40bcec4cfa682'
Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit(s).

Commit information:

    Commit id: a7de8f13f973c99d046d0af0e68636cb91368590
    Commit message:
    merge from bioc-devel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/openCyto@87342 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang <m.jiang at bc3139a8-67e5-0310-9ffc-ced21a209358>
    Commit date: 2014-03-11T23:37:05Z

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/openCyto@87343 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'trunk'
Merge branch 'master' of github.com:RGLab/openCyto