[med-svn] [r-bioc-delayedarray] branch upstream updated (c0833a2 -> c54872c)

[Andreas Tille]

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

      from  c0833a2   New upstream version 0.2.7
       new  c54872c   New upstream version 0.4.1

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                             |  18 +-
 NAMESPACE                               |  52 ++-
 R/Array-class.R                         |  68 +++
 R/ArrayBlocks-class.R                   | 177 --------
 R/ArrayGrid-class.R                     | 574 ++++++++++++++++++++++++
 R/ConformableSeedCombiner-class.R       |  93 ++++
 R/DelayedArray-class.R                  | 624 +++++++++++++-------------
 R/DelayedArray-stats.R                  |  56 ++-
 R/DelayedArray-utils.R                  | 136 +-----
 R/DelayedMatrix-utils.R                 |  21 +-
 R/RleArray-class.R                      | 392 +++++++++++-----
 R/SeedBinder-class.R                    |  96 ++++
 R/bind-arrays.R                         | 162 +++++++
 R/block_processing.R                    | 114 +++--
 R/cbind-methods.R                       | 163 -------
 R/realize.R                             |  72 +--
 R/show-utils.R                          |  88 ++--
 R/subset_seed_as_array.R                | 128 ++++++
 R/utils.R                               | 172 ++++---
 TODO                                    |   3 +
 build/vignette.rds                      | Bin 0 -> 291 bytes
 inst/doc/Working_with_large_arrays.R    | 115 +++++
 inst/doc/Working_with_large_arrays.Rnw  | 764 ++++++++++++++++++++++++++++++++
 inst/doc/Working_with_large_arrays.pdf  | Bin 0 -> 182894 bytes
 inst/unitTests/test_ArrayBlocks-class.R |  71 ---
 inst/unitTests/test_ArrayGrid-class.R   | 270 +++++++++++
 inst/unitTests/test_RleArray-class.R    |  45 ++
 inst/unitTests/test_bind-arrays.R       |  96 ++++
 man/Array-class.Rd                      |  26 ++
 man/ArrayBlocks-class.Rd                |  19 -
 man/ArrayGrid-class.Rd                  | 142 ++++++
 man/DelayedArray-class.Rd               |  77 +++-
 man/DelayedArray-utils.Rd               |  10 +-
 man/RleArray-class.Rd                   |  32 +-
 man/bind-arrays.Rd                      |  58 +++
 man/block_processing.Rd                 |  26 ++
 man/cbind-methods.Rd                    |  91 ----
 man/realize.Rd                          |  12 +-
 man/subset_seed_as_array.Rd             |  55 +++
 vignettes/Working_with_large_arrays.Rnw | 764 ++++++++++++++++++++++++++++++++
 vignettes/slides.sty                    |  34 ++
 41 files changed, 4582 insertions(+), 1334 deletions(-)
 create mode 100644 R/Array-class.R
 delete mode 100644 R/ArrayBlocks-class.R
 create mode 100644 R/ArrayGrid-class.R
 create mode 100644 R/ConformableSeedCombiner-class.R
 create mode 100644 R/SeedBinder-class.R
 create mode 100644 R/bind-arrays.R
 delete mode 100644 R/cbind-methods.R
 create mode 100644 R/subset_seed_as_array.R
 create mode 100644 build/vignette.rds
 create mode 100644 inst/doc/Working_with_large_arrays.R
 create mode 100644 inst/doc/Working_with_large_arrays.Rnw
 create mode 100644 inst/doc/Working_with_large_arrays.pdf
 delete mode 100644 inst/unitTests/test_ArrayBlocks-class.R
 create mode 100644 inst/unitTests/test_ArrayGrid-class.R
 create mode 100644 inst/unitTests/test_RleArray-class.R
 create mode 100644 inst/unitTests/test_bind-arrays.R
 create mode 100644 man/Array-class.Rd
 delete mode 100644 man/ArrayBlocks-class.Rd
 create mode 100644 man/ArrayGrid-class.Rd
 create mode 100644 man/bind-arrays.Rd
 create mode 100644 man/block_processing.Rd
 delete mode 100644 man/cbind-methods.Rd
 create mode 100644 man/subset_seed_as_array.Rd
 create mode 100644 vignettes/Working_with_large_arrays.Rnw
 create mode 100644 vignettes/slides.sty

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