[med-svn] [r-bioc-summarizedexperiment] 11/12: Updated version 1.6.3 from 'upstream/1.6.3'

[Andreas Tille]

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

commit 100637c445fc84be5ee64826927cc89ca7661b6c
Merge: a7f2e99 28bc7c1
Author: Andreas Tille <tille at debian.org>
Date:   Mon Oct 2 11:52:34 2017 +0200

    Updated version 1.6.3 from 'upstream/1.6.3'
    
    with Debian dir 753f0c4ff456ae6fca17d6a2004933362caec531

 DESCRIPTION                                        |   30 +
 NAMESPACE                                          |  123 +
 NEWS                                               |  120 +
 NOTES                                              |   35 +
 R/Assays-class.R                                   |  377 +++
 R/RangedSummarizedExperiment-class.R               |  572 ++++
 R/SummarizedExperiment-class.R                     |  844 ++++++
 R/coverage-methods.R                               |   15 +
 R/findOverlaps-methods.R                           |   42 +
 R/inter-range-methods.R                            |   22 +
 R/intra-range-methods.R                            |   79 +
 R/makeSummarizedExperimentFromDataFrame.R          |   32 +
 R/makeSummarizedExperimentFromExpressionSet.R      |  265 ++
 R/nearest-methods.R                                |  117 +
 R/readKallisto.R                                   |  196 ++
 R/saveHDF5SummarizedExperiment.R                   |  127 +
 R/zzz.R                                            |    2 +
 build/vignette.rds                                 |  Bin 0 -> 209 bytes
 inst/doc/SummarizedExperiment.R                    |  101 +
 inst/doc/SummarizedExperiment.Rmd                  |  345 +++
 inst/doc/SummarizedExperiment.html                 |  541 ++++
 inst/extdata/kallisto/abundance.h5                 |  Bin 0 -> 1086722 bytes
 inst/extdata/kallisto/abundance.tsv                | 2859 ++++++++++++++++++++
 inst/extdata/kallisto/abundance.txt                |   16 +
 inst/extdata/kallisto/run_info.json                |    8 +
 inst/scripts/Find_and_update_objects/README        |   68 +
 .../collect_rda_objects_to_update.R                |  133 +
 .../data_store_RDA_OBJECTS_TO_UPDATE               |   30 +
 .../pkgs_RDA_OBJECTS_TO_UPDATE                     |    9 +
 .../Find_and_update_objects/scan_rda_files.R       |   68 +
 .../Find_and_update_objects/update_rda_objects.R   |   70 +
 inst/unitTests/test_Assays-class.R                 |   88 +
 .../test_RangedSummarizedExperiment-class.R        |  375 +++
 inst/unitTests/test_SummarizedExperiment-class.R   |  339 +++
 inst/unitTests/test_coverage-methods.R             |   56 +
 inst/unitTests/test_findOverlaps-methods.R         |   92 +
 inst/unitTests/test_inter-range-methods.R          |   52 +
 inst/unitTests/test_intra-range-methods.R          |   94 +
 .../test_makeSummarizedExperimentFromDataFrame.R   |   56 +
 ...est_makeSummarizedExperimentFromExpressionSet.R |  187 ++
 inst/unitTests/test_nearest-methods.R              |   70 +
 man/Assays-class.Rd                                |  172 ++
 man/RangedSummarizedExperiment-class.Rd            |  335 +++
 man/SummarizedExperiment-class.Rd                  |  454 ++++
 man/coverage-methods.Rd                            |   80 +
 man/findOverlaps-methods.Rd                        |  105 +
 man/inter-range-methods.Rd                         |   95 +
 man/intra-range-methods.Rd                         |  151 ++
 man/makeSummarizedExperimentFromDataFrame.Rd       |   87 +
 man/makeSummarizedExperimentFromExpressionSet.Rd   |  112 +
 man/nearest-methods.Rd                             |  149 +
 man/readKallisto.Rd                                |  120 +
 man/saveHDF5SummarizedExperiment.Rd                |  144 +
 tests/run_unitTests.R                              |    2 +
 vignettes/SummarizedExperiment.Rmd                 |  345 +++
 55 files changed, 11006 insertions(+)

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