[med-svn] [r-bioc-iranges] branch master updated (e30a819 -> 3e0ab08)

[Andreas Tille]

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

      from  e30a819   Remove unnecessary testsuite autopkgtest header; upload to unstable
       new  e7bd5e0   New upstream version 2.12.0
       new  5d0fe47   Update upstream source from tag 'upstream/2.12.0'
       new  767e3df   New upstream version
       new  3e0ab08   Upload to unstable

The 4 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 ++--
 debian/changelog                           |   6 +
 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 +-
 59 files changed, 1798 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

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