[med-svn] [r-bioc-iranges] branch upstream updated (bf67f3d -> e7bd5e0)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository r-bioc-iranges.

      from  bf67f3d   New upstream version 2.10.5
       new  e7bd5e0   New upstream version 2.12.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 create mode 100644 R/IPos-class.R
 delete mode 100644 R/bind-arrays.R
 create mode 100644 R/range-squeezers.R
 delete mode 100644 inst/unitTests/test_bind-arrays.R
 create mode 100644 man/IPos-class.Rd
 delete mode 100644 man/bind-arrays.Rd
 create mode 100644 man/range-squeezers.Rd

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