[med-svn] [r-bioc-s4vectors] branch upstream updated (5952411 -> 1e3bcb7)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository r-bioc-s4vectors.

      from  5952411   New upstream version 0.14.7
       new  1e3bcb7   New upstream version 0.16.0

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 DESCRIPTION                               |  30 ++-
 NAMESPACE                                 |  47 +++--
 NEWS                                      |  54 ++++-
 R/DataFrame-class.R                       |  15 +-
 R/FilterRules-class.R                     |  13 +-
 R/{Linteger-class.R => LLint-class.R}     | 151 +++++++-------
 R/List-class.R                            | 107 ++++++----
 R/Pairs-class.R                           |  32 ++-
 R/Rle-class.R                             |  28 +--
 R/Rle-utils.R                             |   6 +-
 R/Vector-class.R                          |   2 +-
 R/aggregate-methods.R                     |   2 +-
 R/{str-utils.R => character-utils.R}      |   0
 R/{int-utils.R => integer-utils.R}        |   0
 R/logical-utils.R                         |  32 ---
 R/subsetting-utils.R                      |  49 ++---
 R/zzz.R                                   |   6 +-
 TODO                                      |   6 +-
 inst/doc/RleTricks.pdf                    | Bin 42909 -> 43115 bytes
 inst/doc/S4QuickOverview.pdf              | Bin 175848 -> 175848 bytes
 inst/include/S4Vectors_defines.h          |   2 +-
 inst/include/S4Vectors_interface.h        |  49 ++++-
 inst/include/_S4Vectors_stubs.c           |  52 ++++-
 inst/unitTests/test_List-class.R          |   6 +-
 man/{Linteger-class.Rd => LLint-class.Rd} | 152 +++++++-------
 man/List-utils.Rd                         |   4 +
 man/Rle-class.Rd                          |   1 -
 man/Rle-runstat.Rd                        |   6 +-
 man/Vector-class.Rd                       |   2 +
 man/{str-utils.Rd => character-utils.Rd}  |   2 +-
 src/AEbufs.c                              |  69 ++++---
 src/{Linteger_class.c => LLint_class.c}   | 190 +++++++++---------
 src/R_init_S4Vectors.c                    |  54 ++---
 src/Rle_class.c                           |  44 ++---
 src/Rle_utils.c                           |   4 +-
 src/S4Vectors.h                           |  87 +++++---
 src/{str_utils.c => character_utils.c}    |   2 +-
 src/{int_utils.c => integer_utils.c}      |   0
 src/logical_utils.c                       | 316 +++++++++++++-----------------
 src/safe_arithm.c                         |  24 +--
 src/vector_utils.c                        |   2 +-
 41 files changed, 905 insertions(+), 743 deletions(-)
 rename R/{Linteger-class.R => LLint-class.R} (51%)
 rename R/{str-utils.R => character-utils.R} (100%)
 rename R/{int-utils.R => integer-utils.R} (100%)
 delete mode 100644 R/logical-utils.R
 rename man/{Linteger-class.Rd => LLint-class.Rd} (62%)
 rename man/{str-utils.Rd => character-utils.Rd} (99%)
 rename src/{Linteger_class.c => LLint_class.c} (77%)
 rename src/{str_utils.c => character_utils.c} (99%)
 rename src/{int_utils.c => integer_utils.c} (100%)

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