[med-svn] [r-bioc-ensembldb] 02/06: Update upstream source from tag 'upstream/2.2.0'

[Andreas Tille]

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

commit f7ee24c846959b258c8901890f843fd5d994e9f5
Merge: da2da89 616aa15
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 9 10:13:24 2017 +0100

    Update upstream source from tag 'upstream/2.2.0'
    
    Update to upstream version '2.2.0'
    with Debian dir 691cb6cb57d2e65ca33c34be3a573569448e1eef

 DESCRIPTION                                  |  17 +-
 NAMESPACE                                    |  20 +-
 R/Classes.R                                  |  35 +++-
 R/Generics.R                                 |   6 +
 R/Methods-Filter.R                           |  86 ++++++++
 R/Methods.R                                  | 106 +++++++++-
 R/dbhelpers.R                                |  17 +-
 R/functions-EnsDb.R                          |  78 +++++++
 R/functions-Filter.R                         |  67 ++++--
 R/functions-create-EnsDb.R                   | 108 +++++++---
 build/vignette.rds                           | Bin 367 -> 376 bytes
 inst/NEWS                                    |  42 +++-
 inst/doc/MySQL-backend.R                     |   8 +-
 inst/doc/MySQL-backend.Rmd                   |  14 +-
 inst/doc/MySQL-backend.html                  |  13 +-
 inst/doc/ensembldb.R                         | 107 +++++++---
 inst/doc/ensembldb.Rmd                       | 242 ++++++++++++++-------
 inst/doc/ensembldb.html                      | 300 +++++++++++++++++++--------
 inst/doc/proteins.R                          |  30 ++-
 inst/doc/proteins.Rmd                        |  64 +++---
 inst/doc/proteins.html                       |  21 +-
 inst/perl/get_gene_transcript_exon_tables.pl |  47 ++++-
 inst/scripts/checkEnsDbs.R                   |   2 +
 man/EnsDb-class.Rd                           |  10 +-
 man/EnsDb-exonsBy.Rd                         |  17 +-
 man/EnsDb.Rd                                 |  17 +-
 man/Filter-classes.Rd                        |  34 ++-
 man/ProteinFunctionality.Rd                  |  46 ++--
 man/convertFilter.Rd                         |  64 ++++++
 man/global-filters.Rd                        |  94 +++++++++
 man/hasProteinData-EnsDb-method.Rd           |   4 +-
 man/listEnsDbs.Rd                            |  16 +-
 man/useMySQL-EnsDb-method.Rd                 |  16 +-
 tests/testthat/test_Classes.R                |   6 +
 tests/testthat/test_Methods-Filter.R         |  40 ++++
 tests/testthat/test_Methods.R                |  39 +++-
 tests/testthat/test_functions-EnsDb.R        |  59 ++++++
 tests/testthat/test_functions-Filter.R       |  52 +++++
 tests/testthat/test_functions-utils.R        |  22 ++
 vignettes/MySQL-backend.Rmd                  |  14 +-
 vignettes/MySQL-backend.org                  |   5 +-
 vignettes/ensembldb.Rmd                      | 242 ++++++++++++++-------
 vignettes/ensembldb.org                      |  73 ++++++-
 vignettes/images/dblayout.png                | Bin 204300 -> 389708 bytes
 vignettes/proteins.Rmd                       |  64 +++---
 vignettes/proteins.org                       |   2 +-
 46 files changed, 1855 insertions(+), 511 deletions(-)

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