[med-svn] [r-bioc-iranges] 02/04: Update upstream source from tag 'upstream/2.12.0'

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-bioc-iranges.

commit 5d0fe47e5eaf4ec26582bd44a60bd0afe2b0c853
Merge: e30a819 e7bd5e0
Author: Andreas Tille <tille at debian.org>
Date:   Wed Nov 8 10:26:28 2017 +0100

    Update upstream source from tag 'upstream/2.12.0'
    
    Update to upstream version '2.12.0'
    with Debian dir b1e8ca4ab3e34673ac532e6aabe8cca30937816b

 DESCRIPTION                                |  25 +-
 NAMESPACE                                  |  47 ++--
 NEWS                                       | 109 +++++++-
 R/AtomicList-impl.R                        |  16 +-
 R/AtomicList-utils.R                       |  34 ++-
 R/CompressedList-class.R                   |  42 +---
 R/Grouping-class.R                         |   7 +-
 R/IPos-class.R                             | 354 ++++++++++++++++++++++++++
 R/IRanges-class.R                          |  65 ++++-
 R/List-class-leftovers.R                   |   4 +-
 R/NCList-class.R                           |  50 ++--
 R/RangedData-class.R                       |  20 +-
 R/RangedSelection-class.R                  |   4 +-
 R/Ranges-class.R                           |  23 ++
 R/Ranges-comparison.R                      |  72 +++++-
 R/RangesList-class.R                       |  28 ++-
 R/Rle-class-leftovers.R                    |   5 +-
 R/RleViewsList-class.R                     |  12 +-
 R/Views-class.R                            |   6 +-
 R/ViewsList-class.R                        |   7 +-
 R/bind-arrays.R                            | 162 ------------
 R/coverage-methods.R                       |   9 +
 R/extractList.R                            |   2 +
 R/findOverlaps-methods.R                   | 389 ++++++++++++++++++-----------
 R/inter-range-methods.R                    |  27 +-
 R/intra-range-methods.R                    |  26 ++
 R/nearest-methods.R                        |   4 +-
 R/range-squeezers.R                        |  27 ++
 R/setops-methods.R                         |  55 ++--
 inst/doc/IRangesOverview.pdf               | Bin 230670 -> 230876 bytes
 inst/unitTests/test_DataFrameList.R        |  11 +-
 inst/unitTests/test_IRanges-class.R        |   6 -
 inst/unitTests/test_NCList-class.R         |  75 +++---
 inst/unitTests/test_bind-arrays.R          |  96 -------
 inst/unitTests/test_findOverlaps-methods.R |  36 ++-
 man/AtomicList-utils.Rd                    |  27 +-
 man/DataFrame-utils.Rd                     |   4 +-
 man/DataFrameList-class.Rd                 |   3 +-
 man/Grouping-class.Rd                      |   1 -
 man/IPos-class.Rd                          | 232 +++++++++++++++++
 man/IRanges-class.Rd                       |  11 +
 man/IRangesList-class.Rd                   |   2 +-
 man/NCList-class.Rd                        |   2 -
 man/RangedData-class.Rd                    |  22 +-
 man/Ranges-class.Rd                        |  22 +-
 man/Ranges-comparison.Rd                   |  40 ++-
 man/RangesList-class.Rd                    |  24 +-
 man/RleViewsList-class.Rd                  |   4 +-
 man/Views-class.Rd                         |   1 -
 man/ViewsList-class.Rd                     |   3 -
 man/bind-arrays.Rd                         |  56 -----
 man/findOverlaps-methods.Rd                | 194 +++++++-------
 man/inter-range-methods.Rd                 |   8 +-
 man/intra-range-methods.Rd                 |   1 +
 man/range-squeezers.Rd                     | 108 ++++++++
 man/setops-methods.Rd                      |  11 +
 src/NCList.c                               |  63 +++--
 src/coverage_methods.c                     |   2 +-
 58 files changed, 1792 insertions(+), 904 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-iranges.git