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Improve consistency among message, warnings, and errors #28

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Improve consistency among message, warnings, and errors #28

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Commits on Oct 15, 2011

  1. adds sva to the repos. 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59266 bc3139a8-67e5-0310-9ffc-ced21a209358
    m.carlson committed Oct 15, 2011
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  2. adds sva to the repos. 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59266 bc3139a8-67e5-0310-9ffc-ced21a209358
    Marc Carlson committed Oct 15, 2011
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Commits on Oct 26, 2011

  1. (1) Added ComBat to sva, (2) updated vignette with ComBat section, (3… 

    …) added man files for ComBat

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59673 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Oct 26, 2011
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  2. (1) Added ComBat to sva, (2) updated vignette with ComBat section, (3… 

    …) added man files for ComBat

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59673 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Oct 26, 2011
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Commits on Oct 27, 2011

  1. added ComBat.Rd 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59716 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Oct 27, 2011
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  2. added ComBat.Rd 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59716 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Oct 27, 2011
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  3. removed svadat.Rd 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59717 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Oct 27, 2011
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  4. removed svadat.Rd 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59717 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Oct 27, 2011
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Commits on Oct 31, 2011

  1. bumped package version numbers prior to creating 2.9 branch 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Oct 31, 2011
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  2. bumped package version numbers prior to creating 2.9 branch 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Oct 31, 2011
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  3. version bump for start of 2.10 development cycle 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Oct 31, 2011
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  4. version bump for start of 2.10 development cycle 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Oct 31, 2011
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Commits on Nov 30, 2011

  1. Set default method to be for num svs in sva package. Gave users optio… 

    …n of setting num.sv method in sva. Fixed a bug in Combat so only an intercept term can be included

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@60980 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Nov 30, 2011
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  2. Set default method to be for num svs in sva package. Gave users optio… 

    …n of setting num.sv method in sva. Fixed a bug in Combat so only an intercept term can be included

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@60980 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Nov 30, 2011
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Commits on Dec 5, 2011

  1. Fixed num.sv documentation to put method be first, updated vignette t… 

    …o use method leek

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@61130 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Dec 5, 2011
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  2. Fixed num.sv documentation to put method be first, updated vignette t… 

    …o use method leek

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@61130 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Dec 5, 2011
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Commits on Mar 10, 2012

  1. Fixed Combat bug so that numerical covariates can appear anywhere in … 

    …the list, updated fsva to include the new fast method as well as the original method

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@63723 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Mar 10, 2012
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  2. Fixed Combat bug so that numerical covariates can appear anywhere in … 

    …the list, updated fsva to include the new fast method as well as the original method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@63723 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Mar 10, 2012
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Commits on Mar 30, 2012

  1. first version bump prior to creating 2.10 branch 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Mar 30, 2012
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  2. first version bump prior to creating 2.10 branch 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Mar 30, 2012
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  3. bumped version numbers after creating 2.10 branch 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Mar 30, 2012
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  4. bumped version numbers after creating 2.10 branch 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Mar 30, 2012
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Commits on Apr 25, 2012

  1. fixed bug in the sweave document that was preventing windows binary f… 

    …rom being built. removed bug in fsva where svs where being normalized incorrectly for the exact case.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@65411 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Apr 25, 2012
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  2. fixed bug in the sweave document that was preventing windows binary f… 

    …rom being built. removed bug in fsva where svs where being normalized incorrectly for the exact case.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@65411 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Apr 25, 2012
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Commits on Sep 24, 2012

  1. update Imports: 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@69763 bc3139a8-67e5-0310-9ffc-ced21a209358
    mtmorgan@fhcrc.org committed Sep 24, 2012
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  2. update Imports: 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@69763 bc3139a8-67e5-0310-9ffc-ced21a209358
    Martin Morgan committed Sep 24, 2012
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Commits on Oct 1, 2012

  1. Bump all packages before creating 2.11 branch. 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Oct 1, 2012
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  2. Bump all packages before creating 2.11 branch. 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Oct 1, 2012
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  3. bump package versions after creating 2.11 branch 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Oct 1, 2012
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  4. bump package versions after creating 2.11 branch 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Oct 1, 2012
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Commits on Apr 3, 2013

  1. bump y of x.y.z version number for BioC 2.12 release 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Apr 3, 2013
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  2. bump y of x.y.z version number for BioC 2.12 release 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Apr 3, 2013
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  3. Bump y in version x.y.z to odd number in devel 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Apr 3, 2013
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  4. Bump y in version x.y.z to odd number in devel 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Apr 3, 2013
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Commits on Oct 14, 2013

  1. bump versions prior to creating BioC 2.13 branch 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Oct 14, 2013
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  2. bump versions prior to creating BioC 2.13 branch 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Oct 14, 2013
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  3. bump version after release branch has been created 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Oct 14, 2013
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  4. bump version after release branch has been created 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
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    dtenenba committed Oct 14, 2013
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Commits on Nov 1, 2013

  1. rename inst/doc to vignettes and bump version 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@82688 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Nov 1, 2013
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  2. rename inst/doc to vignettes and bump version 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@82688 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Nov 1, 2013
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Commits on Mar 4, 2014

  1. modify to new biocViews to DESCRIPTION file 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@87035 bc3139a8-67e5-0310-9ffc-ced21a209358
    s.arora committed Mar 4, 2014
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  2. modify to new biocViews to DESCRIPTION file 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@87035 bc3139a8-67e5-0310-9ffc-ced21a209358
    @sonali-bioc
    sonali-bioc committed Mar 4, 2014
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Commits on Apr 11, 2014

  1. First version bump prior to creating 2.14 branch. 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@88838 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Apr 11, 2014
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  2. First version bump prior to creating 2.14 branch. 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@88838 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Apr 11, 2014
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  3. Second version bump after creating 2.14 release branch. 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@88840 bc3139a8-67e5-0310-9ffc-ced21a209358
    d.tenenbaum committed Apr 11, 2014
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  4. Second version bump after creating 2.14 release branch. 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@88840 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
    dtenenba committed Apr 11, 2014
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Commits on Jun 5, 2014

  1. setting up git-svn bridge 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@91009 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Jun 5, 2014
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  2. setting up git-svn bridge 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@91009 bc3139a8-67e5-0310-9ffc-ced21a209358
    @jtleek
    jtleek committed Jun 5, 2014
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  3. Commit made by the Bioconductor Git-SVN bridge. 

    Consists of 1 commit.

Commit information:

Commit id: c39bfae
Commit message: fixed sva docs bug
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-04 23:53:35 -0400
Author date: 2014-06-04 23:53:35 -0400



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@91011 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Jun 5, 2014
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  4. Commit made by the Bioconductor Git-SVN bridge. 

    Consists of 1 commit.

Commit information:

Commit id: c39bfae
Commit message: fixed sva docs bug
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-04 23:53:35 -0400
Author date: 2014-06-04 23:53:35 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@91011 bc3139a8-67e5-0310-9ffc-ced21a209358
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Commits on Jun 13, 2014

  1. Commit made by the Bioconductor Git-SVN bridge. 

    Consists of 2 commits.

Commit information:

Commit id: 055e3a6
Commit message: Merge branch 'master' of https://github.com/jtleek/sva-devel
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-13 10:41:07 -0400
Author date: 2014-06-13 10:41:07 -0400

Commit id: 5d03933
Commit message: added psva, fixed imports
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-13 10:40:56 -0400
Author date: 2014-06-13 10:40:56 -0400



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@91370 bc3139a8-67e5-0310-9ffc-ced21a209358
    j.leek committed Jun 13, 2014
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  2. Commit made by the Bioconductor Git-SVN bridge. 

    Consists of 2 commits.

Commit information:

Commit id: 055e3a6
Commit message: Merge branch 'master' of https://github.com/jtleek/sva-devel
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-13 10:41:07 -0400
Author date: 2014-06-13 10:41:07 -0400

Commit id: 5d03933
Commit message: added psva, fixed imports
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-13 10:40:56 -0400
Author date: 2014-06-13 10:40:56 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@91370 bc3139a8-67e5-0310-9ffc-ced21a209358
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Commits on Jun 23, 2014

  1. Commit made by the Bioconductor Git-SVN bridge. 

    Consists of 1 commit.

Commit information:

Commit id: 21bdbce
Commit message: removed dependency on fast.svd and added ability to change constant in svaseq
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-23 14:46:34 -0400
Author date: 2014-06-23 14:46:34 -0400



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Commit id: 21bdbce
Commit message: removed dependency on fast.svd and added ability to change constant in svaseq
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-23 14:46:34 -0400
Author date: 2014-06-23 14:46:34 -0400



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Commits on Jun 24, 2014

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Commit id: f88184b
Commit message: updated vignette
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-24 13:14:49 -0400
Author date: 2014-06-24 13:14:49 -0400



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Commit id: f88184b
Commit message: updated vignette
Committed by: jtleek
Author Name: jtleek
Commit date: 2014-06-24 13:14:49 -0400
Author date: 2014-06-24 13:14:49 -0400



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Commits on Sep 4, 2014

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Commit id: fc897f2

    added sva.check function

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-09-03 21:05:49 -0400
Author date: 2014-09-03 21:05:49 -0400


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Commit id: fc897f2

    added sva.check function

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-09-03 21:05:49 -0400
Author date: 2014-09-03 21:05:49 -0400


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Commits on Oct 2, 2014

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Commit id: fa99307

    fixed documentation of sva.check

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-10-01 21:26:11 -0400
Author date: 2014-10-01 21:26:11 -0400


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Commit id: fa99307

    fixed documentation of sva.check

Committed by: jtleek
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Commit date: 2014-10-01 21:26:11 -0400
Author date: 2014-10-01 21:26:11 -0400


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Commit id: bdae45f

    update vignette to fix combat problem

Committed by: jtleek
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Commit date: 2014-10-02 15:57:30 -0400
Author date: 2014-10-02 15:57:30 -0400


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Commit id: bdae45f

    update vignette to fix combat problem

Committed by: jtleek
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Commit date: 2014-10-02 15:57:30 -0400
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Commits on Oct 13, 2014

  1. Bump package versions prior to creating the 3.0 branch. 

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  3. Bumping versions after creating 3.0 release branch. 

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Commits on Nov 25, 2014

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Commit id: bdd9758

    Merge branch 'master' of https://github.com/jtleek/sva-devel

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:59 -0500
Author date: 2014-11-25 10:13:59 -0500

Commit id: 4b1d957

    updated n.sv to do min(m,n) when using method=be

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:44 -0500
Author date: 2014-11-25 10:13:44 -0500


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Commit id: bdd9758

    Merge branch 'master' of https://github.com/jtleek/sva-devel

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:59 -0500
Author date: 2014-11-25 10:13:59 -0500

Commit id: 4b1d957

    updated n.sv to do min(m,n) when using method=be

Committed by: jtleek
Author Name: jtleek
Commit date: 2014-11-25 10:13:44 -0500
Author date: 2014-11-25 10:13:44 -0500


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Commits on Dec 4, 2014

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Commit id: 21cee1c

    Merge pull request jtleek#1 from wevanjohnson/master

    Added a long overdue error message to ComBat when the experimental design is confounded
Committed by: Jeff L.
Author Name: Jeff L.
Commit date: 2014-12-04 10:31:35 -0500
Author date: 2014-12-04 10:31:35 -0500

Commit id: 33a090d

    Added a long overdue error message thelling the user when the experimental design is confounded.

Committed by: wevanjohnson
Author Name: wevanjohnson
Commit date: 2014-12-03 21:31:17 -0500
Author date: 2014-12-03 21:31:17 -0500


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Commit id: 21cee1c

    Merge pull request jtleek#1 from wevanjohnson/master

    Added a long overdue error message to ComBat when the experimental design is confounded
Committed by: Jeff L.
Author Name: Jeff L.
Commit date: 2014-12-04 10:31:35 -0500
Author date: 2014-12-04 10:31:35 -0500

Commit id: 33a090d

    Added a long overdue error message thelling the user when the experimental design is confounded.

Committed by: wevanjohnson
Author Name: wevanjohnson
Commit date: 2014-12-03 21:31:17 -0500
Author date: 2014-12-03 21:31:17 -0500


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Commits on Feb 25, 2015

  1. Commit made by the Bioconductor Git-SVN bridge. 

    Consists of 4 commits.

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Commit id: fdcf505

    Merge pull request jtleek#4 from andrewejaffe/master

    fixed bug with vfilter
Committed by: Jeff L.
Author Name: Jeff L.
Commit date: 2015-02-25 11:05:34 -0500
Author date: 2015-02-25 11:05:34 -0500

Commit id: 39deb94

    Delete dequal.R

Committed by: andrewejaffe
Author Name: andrewejaffe
Commit date: 2015-02-22 14:06:49 -0500
Author date: 2015-02-22 14:06:49 -0500

Commit id: 8f0ee22

    fixed bug with vfilter

    when estimating the number of SVs, using vfilter would throw an error
    
Committed by: Andrew Jaffe
Author Name: Andrew Jaffe
Commit date: 2015-02-22 13:54:19 -0500
Author date: 2015-02-22 13:54:19 -0500

Commit id: dac64b6

    added DEqual plot

    added function to inspect RNA quality bias in differential expression
    analysis
    
Committed by: Andrew Jaffe
Author Name: Andrew Jaffe
Commit date: 2015-02-19 20:52:17 -0500
Author date: 2015-02-19 20:52:17 -0500


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Commit id: fdcf505

    Merge pull request jtleek#4 from andrewejaffe/master

    fixed bug with vfilter
Committed by: Jeff L.
Author Name: Jeff L.
Commit date: 2015-02-25 11:05:34 -0500
Author date: 2015-02-25 11:05:34 -0500

Commit id: 39deb94

    Delete dequal.R

Committed by: andrewejaffe
Author Name: andrewejaffe
Commit date: 2015-02-22 14:06:49 -0500
Author date: 2015-02-22 14:06:49 -0500

Commit id: 8f0ee22

    fixed bug with vfilter

    when estimating the number of SVs, using vfilter would throw an error
    
Committed by: Andrew Jaffe
Author Name: Andrew Jaffe
Commit date: 2015-02-22 13:54:19 -0500
Author date: 2015-02-22 13:54:19 -0500

Commit id: dac64b6

    added DEqual plot

    added function to inspect RNA quality bias in differential expression
    analysis
    
Committed by: Andrew Jaffe
Author Name: Andrew Jaffe
Commit date: 2015-02-19 20:52:17 -0500
Author date: 2015-02-19 20:52:17 -0500


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Commit id: 97f8f19

    Merge pull request jtleek#2 from wevanjohnson/master

    Made several modifications to ComBat to streamline the design matrix set...
Committed by: Jeff L.
Author Name: Jeff L.
Commit date: 2015-02-25 11:07:42 -0500
Author date: 2015-02-25 11:07:42 -0500

Commit id: d366c9c

    Made several modifications to ComBat to streamline the design matrix setup and to prepare for future modifications (mean-only batch adjustment, multiple batches, confounded designs, etc). More specifically, I did the following: (1) added a default value for the 'mod' parameter (mod=NULL), (2) removed the numCovs argument; the user is required to supply the covariate matrix, so distinguishing between categorical and numerical covariates is no longer necessary, (3) removed the dependancy on helper functions such as filter.absent (this is not currently used anyway), build.design, design.mat, list.batch, and (4) removed the statment that 'multiple batches are allowed'. This version of ComBat does not robustly handle multiple batches.

Committed by: wevanjohnson
Author Name: wevanjohnson
Commit date: 2014-12-17 16:16:06 -0500
Author date: 2014-12-17 16:16:06 -0500


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Commit id: 97f8f19

    Merge pull request jtleek#2 from wevanjohnson/master

    Made several modifications to ComBat to streamline the design matrix set...
Committed by: Jeff L.
Author Name: Jeff L.
Commit date: 2015-02-25 11:07:42 -0500
Author date: 2015-02-25 11:07:42 -0500

Commit id: d366c9c

    Made several modifications to ComBat to streamline the design matrix setup and to prepare for future modifications (mean-only batch adjustment, multiple batches, confounded designs, etc). More specifically, I did the following: (1) added a default value for the 'mod' parameter (mod=NULL), (2) removed the numCovs argument; the user is required to supply the covariate matrix, so distinguishing between categorical and numerical covariates is no longer necessary, (3) removed the dependancy on helper functions such as filter.absent (this is not currently used anyway), build.design, design.mat, list.batch, and (4) removed the statment that 'multiple batches are allowed'. This version of ComBat does not robustly handle multiple batches.

Committed by: wevanjohnson
Author Name: wevanjohnson
Commit date: 2014-12-17 16:16:06 -0500
Author date: 2014-12-17 16:16:06 -0500


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@99795 bc3139a8-67e5-0310-9ffc-ced21a209358
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Commits on Mar 3, 2015

  1. Commit made by the Bioconductor Git-SVN bridge. 

    Commit id: a7cb4b2

    Merge pull request jtleek#5 from wevanjohnson/master

    Added unit tests for ComBat

Commit id: 7632f0c

    Made the following changes: 1) added unit tests for ComBat to check ComBat errors for confounded designs and for the output on simulated and the bladder cancer data. 2) Streamlined some of the ComBat errors (just shortened the text). 3) Added myself as a maintainer of the package since I am the only one updating/maintaining the ComBat part of the package.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@100106 bc3139a8-67e5-0310-9ffc-ced21a209358
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  2. Commit made by the Bioconductor Git-SVN bridge. 

    Commit id: a7cb4b2

    Merge pull request jtleek#5 from wevanjohnson/master

    Added unit tests for ComBat

Commit id: 7632f0c

    Made the following changes: 1) added unit tests for ComBat to check ComBat errors for confounded designs and for the output on simulated and the bladder cancer data. 2) Streamlined some of the ComBat errors (just shortened the text). 3) Added myself as a maintainer of the package since I am the only one updating/maintaining the ComBat part of the package.



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@100106 bc3139a8-67e5-0310-9ffc-ced21a209358
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Commits on Apr 16, 2015

  1. Bump versions prior to creating 3.1 branch. 

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  2. Bump versions prior to creating 3.1 branch. 

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  3. Bump versions in trunk after creation of 3.1 branch. 

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    d.tenenbaum committed Apr 16, 2015
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  4. Bump versions in trunk after creation of 3.1 branch. 

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Commits on Aug 4, 2015

  1. Commit made by the Bioconductor Git-SVN bridge. 

    Commit id: 7fb36db

    Merge pull request jtleek#7 from wevanjohnson/master

    Added a mean.only option to ComBat

Commit id: 29446f0

    Added a mean.only option to ComBat to only adjust the mean of the batch effect (default adjusts mean and variance)


Commit id: f677116

    Added a mean.only option to ComBat to only adjust the mean of the batch effect (default adjusts mean and varianceA)


Commit id: 6d5ae07

    Merge pull request jtleek#1 from jtleek/master

    Brought in changes from jtleek to update my fork


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@107119 bc3139a8-67e5-0310-9ffc-ced21a209358
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  2. Commit made by the Bioconductor Git-SVN bridge. 

    Commit id: 7fb36db

    Merge pull request jtleek#7 from wevanjohnson/master

    Added a mean.only option to ComBat

Commit id: 29446f0

    Added a mean.only option to ComBat to only adjust the mean of the batch effect (default adjusts mean and variance)


Commit id: f677116

    Added a mean.only option to ComBat to only adjust the mean of the batch effect (default adjusts mean and varianceA)


Commit id: 6d5ae07

    Merge pull request jtleek#1 from jtleek/master

    Brought in changes from jtleek to update my fork


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Commits on Oct 13, 2015

  1. Bumped versions of all packages prior to creating 3.2 branch. 

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  2. Bumped versions of all packages prior to creating 3.2 branch. 

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  3. Bumped version number of all packages after creation of 3.2 branch. 

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  4. Bumped version number of all packages after creation of 3.2 branch. 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@109592 bc3139a8-67e5-0310-9ffc-ced21a209358
    @dtenenba
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Commits on May 3, 2016

  1. Bump versions prior to creation of 3.3 branch 

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    d.tenenbaum committed May 3, 2016
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  2. Bump versions prior to creation of 3.3 branch 

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    @dtenenba
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  3. bump version after creating 3.3 branch 

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    d.tenenbaum committed May 3, 2016
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  4. bump version after creating 3.3 branch 

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    @dtenenba
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Commits on Oct 17, 2016

  1. bump x.y.z versions to even 'y' prior to creation of 3_4 branch 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@122710 bc3139a8-67e5-0310-9ffc-ced21a209358
    hpages@fhcrc.org committed Oct 17, 2016
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  2. bump x.y.z versions to even 'y' prior to creation of 3_4 branch 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@122710 bc3139a8-67e5-0310-9ffc-ced21a209358
    Herve Pages committed Oct 17, 2016
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  3. bump x.y.z versions to odd 'y' after creation of 3_4 branch 

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    hpages@fhcrc.org committed Oct 17, 2016
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  4. bump x.y.z versions to odd 'y' after creation of 3_4 branch 

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    Herve Pages committed Oct 17, 2016
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Commits on Apr 24, 2017

  1. bump x.y.z versions to even y prior to creation of 3_5 branch 

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
    hpages@fhcrc.org committed Apr 24, 2017
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  2. bump x.y.z versions to even y prior to creation of 3_5 branch 

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    Herve Pages committed Apr 24, 2017
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  3. bump x.y.z versions to odd y after creation of 3_5 branch 

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    hpages@fhcrc.org committed Apr 24, 2017
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  4. bump x.y.z versions to odd y after creation of 3_5 branch 

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    Herve Pages committed Apr 24, 2017
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Commits on Apr 28, 2017

  1. Merge pull request jtleek#26 from cafletezbrant/master 

    Fixed the bug from a month ago
    @jtleek
    jtleek authored Apr 28, 2017
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Commits on Jun 5, 2017

  1. Resolved branch conflicts 

    From: Leonardo Collado Torres <lcollado@jhsph.edu>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130117 bc3139a8-67e5-0310-9ffc-ced21a209358
    l.collado-torres committed Jun 5, 2017
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  2. Resolved branch conflicts 

    From: Leonardo Collado Torres <lcollado@jhsph.edu>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130117 bc3139a8-67e5-0310-9ffc-ced21a209358
    @lcolladotor
    lcolladotor committed Jun 5, 2017
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  3. v3.25.1 -- merged https://github.com/jtleek/sva-devel with svn's history

    @lcolladotor
    lcolladotor committed Jun 5, 2017
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  4. v3.25.1 -- merged https://github.com/jtleek/sva-devel with svn's history 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130118 bc3139a8-67e5-0310-9ffc-ced21a209358
    @lcolladotor
    lcolladotor committed Jun 5, 2017
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  5. Fix my email

    @lcolladotor
    lcolladotor committed Jun 5, 2017
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  6. Fix my email 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130119 bc3139a8-67e5-0310-9ffc-ced21a209358
    @lcolladotor
    lcolladotor committed Jun 5, 2017
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Commits on Jun 13, 2017

  1. v3.25.2 -- resolve some notes/errors/warnings from R CMD check

    @lcolladotor
    lcolladotor committed Jun 13, 2017
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  2. v3.25.2 -- resolve some notes/errors/warnings from R CMD check 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130304 bc3139a8-67e5-0310-9ffc-ced21a209358
    @lcolladotor
    lcolladotor committed Jun 13, 2017
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Commits on Jun 15, 2017

  1. v3.25.3 -- fixed another error and a note

    @lcolladotor
    lcolladotor committed Jun 15, 2017
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  2. v3.25.3 -- fixed another error and a note 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130416 bc3139a8-67e5-0310-9ffc-ced21a209358
    @lcolladotor
    lcolladotor committed Jun 15, 2017
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Commits on Jun 19, 2017

  1. v3.25.4 -- fixed a namespace warning

    @lcolladotor
    lcolladotor committed Jun 19, 2017
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  2. v3.25.4 -- fixed a namespace warning 

    git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/sva@130528 bc3139a8-67e5-0310-9ffc-ced21a209358
    @lcolladotor
    lcolladotor committed Jun 19, 2017
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Commits on Aug 21, 2017

  1. Merge remote-tracking branch 'upstream/master'

    @lcolladotor
    lcolladotor committed Aug 21, 2017
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Commits on Oct 6, 2017

  1. Update ComBat.R 

    Changed two occurences of `cat()` to `message()` in ComBat so they can be suppressed. All the other printing in ComBat already uses `message()`.
    @kasperdanielhansen
    kasperdanielhansen authored Oct 6, 2017
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  2. Merge pull request jtleek#32 from kasperdanielhansen/patch-2 

    Update ComBat.R
    @jtleek
    jtleek authored Oct 6, 2017
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Commits on Oct 30, 2017

  1. bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

    @hpages
    hpages committed Oct 30, 2017
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  2. bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

    @hpages
    hpages committed Oct 30, 2017
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  3. Merge remote-tracking branch 'upstream/master'

    @lcolladotor
    lcolladotor committed Oct 30, 2017
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Commits on May 14, 2018

  1. Improve consistency among message, warnings, and errors 

    Now message() is uniformly used instead of cat(), warning() is used
for warnings instead of cat(), correct spacing is added between
arguments where appropriate, and error messages do not have trailing
newlines, since stop() already adds one.
    @DarwinAwardWinner
    DarwinAwardWinner committed May 14, 2018
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