[med-svn] [r-bioc-delayedarray] branch master updated (fb6def2 -> 3d874ac)

[Andreas Tille]

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

      from  fb6def2   Moved packaging from SVN to Git, upload to unstable
       new  c54872c   New upstream version 0.4.1
       new  3ce4e78   Update upstream source from tag 'upstream/0.4.1'
       new  649877c   New upstream version
       new  3d874ac   Team upload to unstable

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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                             |  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
 debian/changelog                        |   7 +
 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 ++
 42 files changed, 4589 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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