Commit made by the Bioconductor Git-SVN bridge.
Consists of 17 commit(s).

Commit information:

    Commit id: 32e1156db6c942933a120080aeff8151b497e2bd
    Commit message:
    merge from bioc devel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86310 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang <m.jiang at bc3139a8-67e5-0310-9ffc-ced21a209358>
    Commit date: 2014-02-10T16:19:28-08:00

    Commit id: 90457adbeed4d0d1b5e5f76d0fe1c409ad318972
    Commit message:
    Merge commit '32e1156db6c942933a120080aeff8151b497e2bd'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-10T16:37:46-08:00

    Commit id: 037faae02df966940ef80a3c08683f6ad335d13c
    Commit message:
    remove deprecated bitOps
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-11T14:10:02-08:00

    Commit id: 7f263ff6e91931c1aa7d36aa742b5a5e801c9cf5
    Commit message:
    add ellipsoidGate support for win/vX #142
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-11T16:19:54-08:00

    Commit id: a782297beb6d5698def88d194add792a10150da8
    Commit message:
    update
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-11T16:36:54-08:00

    Commit id: 6ae9f7a988e5adc5c82bce83491fb078a609a747
    Commit message:
    rm test.R
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-11T16:44:34-08:00

    Commit id: c926faa5562330ebb36db30f47fa66cfc73dc25d
    Commit message:
    Merge branch 'trunk' into EllipsoidGate
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-11T16:46:09-08:00

    Commit id: 067ae6ebde96fc20840cdb2bd093b13a38a91250
    Commit message:
    Merge branch 'trunk'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-11T16:46:24-08:00

    Commit id: 0ffc69c9a2a5060ca5c9e655edc1a33356b68cc1
    Commit message:
    add test-suites for flowJoWorkspace methods #133
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-12T11:53:33-08:00

    Commit id: dd23d681beea4ec3d4d80e67a480f0ea34f51ead
    Commit message:
    Merge branch 'trunk' into EllipsoidGate
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-12T13:57:45-08:00

    Commit id: f60c94a3eddd3fb57b2c9c7fba2691fb2182734a
    Commit message:
    add ellipsoidGate support on linear data space. #142
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-13T16:31:25-08:00

    Commit id: 4568c2b57cbe611143e5e54716ca48be5af3b341
    Commit message:
    add doc for #138. close #143
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-18T14:01:25-08:00

    Commit id: 9fc7ef69e0510b3734544e510bb15d632fdc59e1
    Commit message:
    resolve the archive backward compatibility issue. close #142
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-19T13:49:00-08:00

    Commit id: 65ef4bdc68afbbcc7514301e1829dd5713aec598
    Commit message:
    Merge branch 'EllipsoidGate' into trunk
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-19T13:49:32-08:00

    Commit id: 2fb7de8446e5e7af38801bb4961b7af955ab355d
    Commit message:
    bump version
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-19T13:54:03-08:00

    Commit id: 25c143f3536cf8eaf5d89be9f131a9fb32a8cc45
    Commit message:
    Merge branch 'trunk'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-19T13:56:05-08:00

    Commit id: d987ce167bc595514be6d6da393ffb7d8ad88d68
    Commit message:
    Merge branch 'master' of github.com:RGLab/flowWorkspace
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-19T13:56:28-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace@86596 bc3139a8-67e5-0310-9ffc-ced21a209358
merge from bioc-devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86598 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' of github.com:RGLab/flowWorkspace
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commit(s).

Commit information:

    Commit id: f17f9d0887c2162ac37df8a577880621ce9ba020
    Commit message:
    merge from bioc-devel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86313 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang <m.jiang at bc3139a8-67e5-0310-9ffc-ced21a209358>
    Commit date: 2014-02-10T16:38:25-08:00

    Commit id: fc9fa0c88c59cd22760b4e379bb06c70fc443076
    Commit message:
    Merge commit 'f17f9d0887c2162ac37df8a577880621ce9ba020'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-19T14:18:34-08:00

    Commit id: d8a82779bc71e58605369448624f504b9b17d891
    Commit message:
    update plotGate-methods.Rd
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-20T11:05:37-08:00

    Commit id: 373f169b703fadbc6fe34454becf3c7784dc4074
    Commit message:
    fix error in testSuite
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T09:58:28-08:00

    Commit id: f918d1424eb374294b3a339453b00dda6a05c736
    Commit message:
    Merge branch 'master' of github.com:RGLab/flowWorkspace
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T09:59:22-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace@86682 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge commit '12bd09f54d728b91ed65964e32699bd6dc9e1a00'
merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86683 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' of github.com:RGLab/flowWorkspace
Merge branch 'trunk'
Commit made by the Bioconductor Git-SVN bridge.
Consists of 10 commit(s).

Commit information:

    Commit id: 12bd09f54d728b91ed65964e32699bd6dc9e1a00
    Commit message:
    merge from bioc-devel

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86598 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang <m.jiang at bc3139a8-67e5-0310-9ffc-ced21a209358>
    Commit date: 2014-02-19T14:19:50-08:00

    Commit id: f398c4b5071c321339b379ed9abbaf3ba24029cf
    Commit message:
    remove legacy APIs for flowJoWorkspace. (like getTransformations, getCompensationMatrices) to eliminate the need of parsing different type of flowJo within R (which is better taken care of by the c++ polymorphism)
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-20T11:44:19-08:00

    Commit id: 3319432da797a20f0452f9d200fdc9daef03adee
    Commit message:
    remove the hardcoded xpaths from all the flowJoWorkspace R methods. #144
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-20T16:19:51-08:00

    Commit id: 89397190e3ca9bedd609add0a63f689224258a12
    Commit message:
    modify c++ code to handle new workspace. #144
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-20T17:16:44-08:00

    Commit id: 054e24f3c39a91e74e185dab6bac765713d3bf99
    Commit message:
    Merge commit '12bd09f54d728b91ed65964e32699bd6dc9e1a00'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T10:00:05-08:00

    Commit id: a62c2a82c7255f3d9d33549104a09cdc2f778911
    Commit message:
    merge from trunk
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T10:02:53-08:00

    Commit id: acf73b893a520040935bf9c787ef9eed315774b5
    Commit message:
    remove the redudant message
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:11:20-08:00

    Commit id: 0e37d224a6e9773f8de333d35fe49545967360cf
    Commit message:
    bump version
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:13:47-08:00

    Commit id: 8b87abd5878d8a58b0e79e904dd3957b4f6a2494
    Commit message:
    Merge branch 'master' of github.com:RGLab/flowWorkspace
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:15:47-08:00

    Commit id: fdd7cd0b92ec0c18da49387a45789244792267b8
    Commit message:
    Merge branch 'trunk'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:15:57-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace@86691 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge commit '2b058c5296f3d9bfcbda752a18efd89ec9d998cc'
merge from git

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86692 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' of github.com:RGLab/flowWorkspace
Merge branch 'trunk'
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commit(s).

Commit information:

    Commit id: 2b058c5296f3d9bfcbda752a18efd89ec9d998cc
    Commit message:
    merge from git

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86683 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang <m.jiang at bc3139a8-67e5-0310-9ffc-ced21a209358>
    Commit date: 2014-02-21T10:00:43-08:00

    Commit id: 270e65606b7452bd4c7a57091ca45436621c37de
    Commit message:
    Merge commit '2b058c5296f3d9bfcbda752a18efd89ec9d998cc'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:16:43-08:00

    Commit id: b55d81c7249e86024d56b5514325780bec5c6063
    Commit message:
    fix a typo
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:32:40-08:00

    Commit id: d4c0507e9f64b01d96c5ceb76cd44affa0bd30d3
    Commit message:
    Merge branch 'master' of github.com:RGLab/flowWorkspace
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:33:04-08:00

    Commit id: e4bbcd265df92e4d4a2fa0cef245cdac06b95299
    Commit message:
    Merge branch 'trunk'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:33:08-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace@86694 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge commit '744d4a8e8d6325b8b1259b37332c003e663210e2'
fix a typo

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86695 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' of github.com:RGLab/flowWorkspace
Merge branch 'trunk'
Commit made by the Bioconductor Git-SVN bridge.
Consists of 5 commit(s).

Commit information:

    Commit id: 744d4a8e8d6325b8b1259b37332c003e663210e2
    Commit message:
    merge from git

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/flowWorkspace@86692 bc3139a8-67e5-0310-9ffc-ced21a209358
    Committed by m.jiang <m.jiang at bc3139a8-67e5-0310-9ffc-ced21a209358>
    Commit date: 2014-02-21T15:17:33-08:00

    Commit id: 1e1e8c13725c5fe0a60e68db7ed2502d3d09616f
    Commit message:
    Merge commit '744d4a8e8d6325b8b1259b37332c003e663210e2'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T15:34:01-08:00

    Commit id: 0eb6f485ee6cc4b08a1417b7e8ae534d9d69dc8f
    Commit message:
    fix vignette
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T16:46:14-08:00

    Commit id: cef4a03c733280a178b7de85e0fca5ddebacbcc2
    Commit message:
    Merge branch 'master' of github.com:RGLab/flowWorkspace
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T16:50:28-08:00

    Commit id: fb2b3d068540a47e56200b4ff5bb582e7f6427bc
    Commit message:
    Merge branch 'trunk'
    Committed by mikejiang <wjiang2 at fhcrc.org>
    Commit date: 2014-02-21T16:50:31-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/flowWorkspace@86699 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge commit '9590081e2d7b4cd04dd33a68c97ceb3ec9d5ee2f'