[med-svn] [r-bioc-genomicranges] branch master updated (c9daa6e -> 59ae22f)

[Andreas Tille]

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

      from  c9daa6e   New upstream version, upload to unstable
       new  68b3305   New upstream version 1.30.0
       new  409b1f6   Update upstream source from tag 'upstream/1.30.0'
       new  a03f79f   New upstream version
       new  59ae22f   Bump versioned Build-Depends: r-bioc-iranges (>= >= 2.11.16)

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                                 |  10 +-
 NAMESPACE                                   |  37 ++-
 NEWS                                        |  59 ++++-
 R/GNCList-class.R                           |   2 +-
 R/GPos-class.R                              | 391 ++++++++++------------------
 R/GRanges-class.R                           |  84 +++---
 R/GRangesList-class.R                       |  19 +-
 R/GenomicRanges-class.R                     |  30 +--
 R/GenomicRanges-comparison.R                |   8 +-
 R/RangedData-methods.R                      |   7 -
 R/findOverlaps-methods.R                    |  92 ++++---
 R/genomic-range-squeezers.R                 |  28 ++
 R/inter-range-methods.R                     |   5 +-
 R/intra-range-methods.R                     |  13 +-
 R/nearest-methods.R                         |  34 ++-
 R/range-squeezers.R                         |  49 ----
 R/setops-methods.R                          |   6 +-
 R/strand-utils.R                            |  28 +-
 build/vignette.rds                          | Bin 697 -> 698 bytes
 debian/changelog                            |   7 +
 debian/control                              |   2 +-
 inst/doc/ExtendingGenomicRanges.pdf         | Bin 103036 -> 140031 bytes
 inst/doc/GRanges_and_GRangesList_slides.pdf | Bin 250940 -> 250940 bytes
 inst/doc/GenomicRangesHOWTOs.pdf            | Bin 195126 -> 234135 bytes
 inst/doc/GenomicRangesIntroduction.Rnw      |   3 +-
 inst/doc/GenomicRangesIntroduction.pdf      | Bin 159556 -> 189468 bytes
 inst/doc/Ten_things_slides.pdf              | Bin 138327 -> 138321 bytes
 inst/unitTests/test_GNCList-class.R         |  20 +-
 man/GPos-class.Rd                           | 104 ++++----
 man/GRanges-class.Rd                        | 350 ++++++++++++-------------
 man/GRangesList-class.Rd                    |   2 +
 man/GenomicRanges-comparison.Rd             |  73 +++---
 man/findOverlaps-methods.Rd                 |   6 +-
 man/genomic-range-squeezers.Rd              |  94 +++++++
 man/intra-range-methods.Rd                  |   1 -
 man/makeGRangesFromDataFrame.Rd             |  10 +-
 man/range-squeezers.Rd                      | 114 --------
 vignettes/GenomicRangesIntroduction.Rnw     |   3 +-
 38 files changed, 817 insertions(+), 874 deletions(-)
 create mode 100644 R/genomic-range-squeezers.R
 delete mode 100644 R/range-squeezers.R
 create mode 100644 man/genomic-range-squeezers.Rd
 delete mode 100644 man/range-squeezers.Rd

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