[med-svn] [r-bioc-savr] 05/06: Updated version 1.12.0 from 'upstream/1.12.0'

[Andreas Tille]

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

commit 65afe7f4e57e194201f7ab9bed0ae7189c5f76d4
Merge: c37a6de 677212c
Author: Andreas Tille <tille at debian.org>
Date:   Mon Oct 2 10:21:26 2017 +0200

    Updated version 1.12.0 from 'upstream/1.12.0'
    
    with Debian dir 7541790ef639c8ca5a568f707134740acd7332a8

 CHANGES                                            |  43 ++
 DESCRIPTION                                        |  18 +
 NAMESPACE                                          |  29 +
 R/AllClasses.R                                     | 274 +++++++++
 R/AllGenerics.R                                    | 356 +++++++++++
 R/SavR-accessors.R                                 |  82 +++
 R/savR-methods.R                                   | 666 +++++++++++++++++++++
 R/savR-package.R                                   |  24 +
 R/show-methods.R                                   |  17 +
 README.md                                          |  15 +
 build/vignette.rds                                 | Bin 0 -> 194 bytes
 inst/doc/savR.R                                    | 101 ++++
 inst/doc/savR.Rnw                                  | 196 ++++++
 inst/doc/savR.pdf                                  | Bin 0 -> 128971 bytes
 .../MiSeq/InterOp/CorrectedIntMetricsOut.bin       | Bin 0 -> 149570 bytes
 .../extdata/MiSeq/InterOp/ExtractionMetricsOut.bin | Bin 0 -> 118410 bytes
 inst/extdata/MiSeq/InterOp/QMetricsOut.bin         | Bin 0 -> 641898 bytes
 inst/extdata/MiSeq/InterOp/TileMetricsOut.bin      | Bin 0 -> 6482 bytes
 inst/extdata/MiSeq/RunInfo.xml                     |  13 +
 man/buildReports.Rd                                |  32 +
 man/clusterQualityGtN.Rd                           |  34 ++
 man/clusters.Rd                                    |  27 +
 man/correctedIntensities.Rd                        |  38 ++
 man/cycles.Rd                                      |  26 +
 man/directions.Rd                                  |  26 +
 man/errorMetrics.Rd                                |  36 ++
 man/extractionMetrics.Rd                           |  36 ++
 man/flowcellLayout.Rd                              |  27 +
 man/illuminaFlowCellLayout-class.Rd                |  22 +
 man/illuminaRead-class.Rd                          |  18 +
 man/location.Rd                                    |  26 +
 man/pfBoxplot.Rd                                   |  20 +
 man/pfClusters.Rd                                  |  28 +
 man/plotFWHM.Rd                                    |  34 ++
 man/plotIntensity.Rd                               |  33 +
 man/plotQGT30.Rd                                   |  25 +
 man/qualityHeatmap.Rd                              |  30 +
 man/qualityMetrics.Rd                              |  34 ++
 man/reads.Rd                                       |  27 +
 man/run.Rd                                         |  26 +
 man/savCorrectedIntensityFormat-class.Rd           |  22 +
 man/savData-class.Rd                               |  17 +
 man/savErrorFormat-class.Rd                        |  21 +
 man/savExtractionFormat-class.Rd                   |  23 +
 man/savFormat-class.Rd                             |  22 +
 man/savProject-class.Rd                            |  26 +
 man/savQualityFormat-class.Rd                      |  20 +
 man/savQualityFormatV5-class.Rd                    |  20 +
 man/savR-package.Rd                                |  30 +
 man/savR.Rd                                        |  30 +
 man/savTileFormat-class.Rd                         |  29 +
 man/tileMetrics.Rd                                 |  50 ++
 tests/testthat.R                                   |   4 +
 tests/testthat/test_accessors.R                    |  34 ++
 tests/testthat/test_load.R                         |  69 +++
 vignettes/savR.Rnw                                 | 196 ++++++
 56 files changed, 3052 insertions(+)

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