[med-svn] [r-bioc-ensembldb] branch upstream updated (cc1e361 -> 616aa15)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

      from  cc1e361   New upstream version 2.0.4
       new  616aa15   New upstream version 2.2.0

The 1 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
 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(-)
 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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