[med-svn] [r-bioc-ensembldb] branch master updated (da2da89 -> 287bfb1)

[Andreas Tille]

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

      from  da2da89   Upload to unstable
       new  616aa15   New upstream version 2.2.0
       new  f7ee24c   Update upstream source from tag 'upstream/2.2.0'
       new  e5584f4   New upstream version
       new  126467b   New versioned Build-Depends: r-bioc-genomicfeatures (>= 1.29.10)
       new  7cef8c1   r-bioc-annotationfilter (>= 1.1.9)
       new  287bfb1   Upload to unstable

The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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
 debian/changelog                             |   8 +
 debian/control                               |   4 +-
 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 +-
 48 files changed, 1865 insertions(+), 513 deletions(-)
 create mode 100644 R/functions-EnsDb.R
 create mode 100644 man/convertFilter.Rd
 create mode 100644 man/global-filters.Rd
 create mode 100644 tests/testthat/test_functions-EnsDb.R

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