[med-svn] [r-bioc-genomicranges] branch upstream updated (c1b9488 -> 68b3305)

[Andreas Tille]

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

      from  c1b9488   Imported Upstream version 1.28.6
       new  68b3305   New upstream version 1.30.0

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
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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
 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 +-
 36 files changed, 809 insertions(+), 873 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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