Commit made by the Bioconductor Git-SVN bridge.
Consists of 30 commit(s).

Commit information:

    Commit id: ff39f6e740b94b731ea38357e21737434a9d479e
    Commit message:
    add suggestions from Nate
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-22T12:41:19-08:00

    Commit id: 97a838c5a86ba03712452d01eae75c0cde2a8582
    Commit message:
    cleanup -

      remove unnecessarily large test package
      replace with small test package
      be sure example code is parsed correctly
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-22T15:08:25-08:00

    Commit id: 97b3c231e59b6c177cf171dab55af2da5d785ee0
    Commit message:
    cleanup
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-22T17:24:01-08:00

    Commit id: fe55cd4701aafcb50acfb4438935e50ba3477cef
    Commit message:
    add another test file
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-22T17:25:59-08:00

    Commit id: 54df293a1cca235cc3fc0ea68e2dd8d4036ebefe
    Commit message:
    add option to disable biocViews checks
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-22T17:34:16-08:00

    Commit id: 37f31d99abf77d299e40a55a49bab7eaffa9ab67
    Commit message:
    check for T and F
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-23T16:59:51-08:00

    Commit id: d88b5821c6a317e35903c682a14ebe539ab6d0ad
    Commit message:
    formatting
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-23T17:12:14-08:00

    Commit id: 8cccdb3fd91497288ff52323202b053fd5bf37cb
    Commit message:
    broken commit
    Committed by dtenenba <dtenenba at fhcrc.org>
    Commit date: 2014-01-24T08:47:47-08:00

    Commit id: 6b3073ab158fdffff0aadff18c32f546bdf475bd
    Commit message:
    add NOTE about eval=FALSE chunks
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-24T09:58:04-08:00

    Commit id: e6d05b894f2fd638a1eaf39aab98826c665ae3e4
    Commit message:
    formatting cleanup, suppress more codetoolsBioC warnings
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-24T10:08:58-08:00

    Commit id: 0f962fec818615d934fac2a73a3415a4fc22b447
    Commit message:
    Check for incorrect use of Depends, such that a package depending on
    the checked package would have a problem unless the package in the incorrect
    depends was imported in NAMESPACE. Still need a unit test for this.
    Thanks to Martin for the basic idea of this.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-24T17:48:34-08:00

    Commit id: 668fe28fe9f7446e242e65e4152ee9af13a1fa0e
    Commit message:
    test files, algo notes
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-26T17:35:55-08:00

    Commit id: decf3680af9e1998210beb5ebb606336551a147e
    Commit message:
    cosmetic
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-26T22:53:05-08:00

    Commit id: 2f0bfa3405703c61cdbaec0d5887b1a9029950e1
    Commit message:
    more algos
    Committed by dtenenba <dtenenba at fhcrc.org>
    Commit date: 2014-01-27T08:21:56-08:00

    Commit id: 9c5fe6ecb65ee92d3669af9ac82323a8fac054dc
    Commit message:
    run normalizePath on package dir so that "R CMD BiocCheck ." will work
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-27T12:47:25-08:00

    Commit id: 51b578c8f82b64e759187cf8a821a4793224d437
    Commit message:
    Add unit test for checking bad dependencies.

    Some work on finding library(mypkg).
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-27T17:04:29-08:00

    Commit id: 3a4fca7b2cb4e96fc67d76856889e1c5726d842f
    Commit message:
    Fixed loophole in library(pkg) search.

    Deactivated a test until I can refactor some code.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-27T21:55:30-08:00

    Commit id: 3de3d3359f1b169cdcba1b1ead6d10fd0d0dbc23
    Commit message:
    unit tests now pass
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-28T10:51:36-08:00

    Commit id: d85a8179c4f993dd4bf77dbb7c12c83f1b5a5a32
    Commit message:
    integrate library/require checking
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-28T11:26:12-08:00

    Commit id: bba9c895901ab1b504fd55f3375039ef5b62266c
    Commit message:
    checking function lengths
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-28T15:46:26-08:00

    Commit id: 66a6cd26715cb6c26e7851a70e4c36c2487897aa
    Commit message:
    tidying
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-28T15:48:57-08:00

    Commit id: a3e8213227a5a1d969cdcb335f8b2b8b6036333d
    Commit message:
    Integrated function line counting

    Turns out this is pretty slow on longer source files (e.g. IRanges).
    Need to speed it up or remove it.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-29T15:08:30-08:00

    Commit id: f54fc3cf79e19709b4132b4e154e29a6540fd295
    Commit message:
    Getting function line counts is a bit faster but not yet fast enough.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-29T22:17:49-08:00

    Commit id: 81346d7113ac4f7fa67d10d7c2d2e2d16c6a941c
    Commit message:
    getFunctionLengths() is much faster
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-30T10:29:07-08:00

    Commit id: 570e8f74aa4ce999720515388a507da2f375b82e
    Commit message:
    Check for <<-
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-30T10:48:16-08:00

    Commit id: 2483ae1bbee7e00c4fb9656564ad12feeb88cfb7
    Commit message:
    updated todos
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-30T10:53:08-08:00

    Commit id: 95262891bec40a309a31a5965ac3dada2f62a414
    Commit message:
    Check that man pages documenting exported objects have _running_ examples.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-30T15:35:03-08:00

    Commit id: 1d223998db1cd6b2ca70cea1ee8b7535a1a49d75
    Commit message:
    add important todo
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-30T16:43:28-08:00

    Commit id: 6dd43a4dd76db7db85f3ebefa7a17173a3b2e434
    Commit message:
    Modify installation procedure so path to Rscript is not hardcoded

    Instead, use a path based on R_HOME.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-30T17:41:20-08:00

    Commit id: a4db33a7b5d697cd917bf8de7e801c113cbebf15
    Commit message:
    windows-only tweaks to installer
    Committed by dtenenba <dtenenba at fhcrc.org>
    Commit date: 2014-01-30T18:57:01-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCheck@85934 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' of https://github.com/Bioconductor/BiocCheck
Commit made by the Bioconductor Git-SVN bridge.
Consists of 8 commit(s).

Commit information:

    Commit id: e0d84522c9138edc91b46d55022f600b8a1c8a83
    Commit message:
    Changed some severities:

    >= 50% eval=FALSE vignette chunks is now a warning.
    No running examples in man pages of exported examples is now a note.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-31T09:47:14-08:00

    Commit id: 7fa6b84a64c8b64472474d235724d1f7124413a0
    Commit message:
    Check that package NEWS is present and well-formatted.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-31T10:24:21-08:00

    Commit id: 3eecaa257949b1f583e196a247f81e19ceec5ade
    Commit message:
    update todos
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-01-31T15:14:10-08:00

    Commit id: b0068aea0234d980d4c37e2b048969287b3b1a9d
    Commit message:
    update todos
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-04T15:21:01-08:00

    Commit id: 774e6d230149a08e82c9ffd217425515b7eef61e
    Commit message:
    show relevant url when warning about missing dll registration
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-05T10:48:20-08:00

    Commit id: 0eda16dca475a24b61ba79197a9875c05fdf03bb
    Commit message:
    emit NOTE with % of lines > 80 chars long
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-05T12:35:55-08:00

    Commit id: 43fbc824e9daa90e4cba7ef120d89ceabb80ab97
    Commit message:
    check for tabs and indentation with a non-multiple of 4 spaces
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-05T13:19:48-08:00

    Commit id: 7c38848e302c0fb789f03fb513e4ae468c218bf8
    Commit message:
    Merge branch 'master' of https://github.com/Bioconductor/BiocCheck
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-05T13:20:43-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCheck@86120 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'maindev'
Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commit(s).

Commit information:

    Commit id: ac4205f479827315cabfa4c2dfe8692b14a8fdef
    Commit message:
    update TODOS
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-05T13:28:41-08:00

    Commit id: e418855acc8017ab46da89ff931bad297c7b08ec
    Commit message:
    Change the sense of user messages

    so they are consistent with
    REQUIRED (not ERROR) and RECOMMENDED (not WARNING).
    Change associated functions and variables.
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-06T15:12:37-08:00

    Commit id: 1351d596da6ad51f39567889b242e6e93d1c6661
    Commit message:
    Merge branch 'maindev'
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-06T15:14:05-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCheck@86184 bc3139a8-67e5-0310-9ffc-ced21a209358
update todos
Merge branch 'master' of https://github.com/Bioconductor/BiocCheck
Commit made by the Bioconductor Git-SVN bridge.
Consists of 2 commit(s).

Commit information:

    Commit id: 49cf332c92046d44e5f336da1f68de25bd98cef4
    Commit message:
    update todos
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-06T15:24:26-08:00

    Commit id: 6506e7cce8dc36cd55f5bcc57b781d7c84c5c718
    Commit message:
    Merge branch 'master' of https://github.com/Bioconductor/BiocCheck
    Committed by Dan Tenenbaum <dtenenba at fhcrc.org>
    Commit date: 2014-02-06T15:24:38-08:00

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCheck@86185 bc3139a8-67e5-0310-9ffc-ced21a209358
Add BiocCheck man page, cleanup

add, export usage() function
pass R CMD check and BiocCheck
Merge branch 'master' of https://github.com/Bioconductor/BiocCheck