[med-svn] [r-bioc-delayedarray] 02/04: Update upstream source from tag 'upstream/0.4.1'

[Andreas Tille]

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

commit 3ce4e780067f0cfecbf1e763c5cb1e8bc53f0ba9
Merge: fb6def2 c54872c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Nov 8 18:42:34 2017 +0100

    Update upstream source from tag 'upstream/0.4.1'
    
    Update to upstream version '0.4.1'
    with Debian dir b64d7e04e2f5f5f6276d767e2be2be38cb52e3d9

 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(-)

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