[med-svn] [r-bioc-ensembldb] 02/05: Updated version 2.0.4 from 'upstream/2.0.4'

[Andreas Tille]

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

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

commit f5ae402ab57af6915f235c75fac2a789df7dc412
Merge: a39ebab cc1e361
Author: Andreas Tille <tille at debian.org>
Date:   Thu Oct 19 19:08:51 2017 +0200

    Updated version 2.0.4 from 'upstream/2.0.4'
    
    with Debian dir d14ab85c88104fad41af8dcfd9f63b0a6537f459

 DESCRIPTION                                        |   39 +-
 NAMESPACE                                          |  275 ++++-
 R/Classes.R                                        |  722 ++++++------
 R/Deprecated.R                                     |  182 +++
 R/Generics.R                                       |  211 ++--
 R/Methods-Filter.R                                 | 1173 +++++--------------
 R/Methods.R                                        | 1207 ++++++++++++--------
 R/dbhelpers.R                                      |  629 ++++++----
 R/functions-Filter.R                               |  324 ++++++
 R/{EnsDbFromGTF.R => functions-create-EnsDb.R}     |  880 +++++++++++---
 R/functions-utils.R                                |  176 ++-
 R/loadEnsDb.R                                      |    5 -
 R/makeEnsemblDbPackage.R                           |  213 ----
 R/runEnsDbApp.R                                    |   10 -
 R/select-methods.R                                 |  220 ++--
 build/vignette.rds                                 |  Bin 325 -> 367 bytes
 inst/NEWS                                          |  121 +-
 inst/doc/MySQL-backend.R                           |    4 +-
 inst/doc/MySQL-backend.Rmd                         |   18 +-
 inst/doc/MySQL-backend.html                        |  137 ++-
 inst/doc/ensembldb.R                               |  204 ++--
 inst/doc/ensembldb.Rmd                             |  569 +++++----
 inst/doc/ensembldb.html                            |  744 +++++++-----
 inst/doc/proteins.R                                |   94 ++
 inst/doc/proteins.Rmd                              |  273 +++++
 inst/doc/proteins.html                             |  369 ++++++
 inst/extended_tests/extended_tests.R               |  855 ++++++++++++++
 inst/extended_tests/performance_tests.R            |  173 +++
 inst/gff/Devosia_geojensis.ASM96941v1.32.gff3.gz   |  Bin 0 -> 272773 bytes
 inst/gtf/Devosia_geojensis.ASM96941v1.32.gtf.gz    |  Bin 0 -> 269508 bytes
 inst/perl/get_gene_transcript_exon_tables.pl       |  122 +-
 inst/perl/test_script.pl                           |   78 ++
 inst/scripts/checkEnsDbs.R                         |   22 +
 inst/scripts/generate-EnsDBs.R                     |  321 ++++++
 inst/shinyHappyPeople/server.R                     |    6 +-
 inst/test/testFunctionality.R                      |  293 -----
 inst/test/testInternals.R                          |  146 ---
 inst/unitTests/test_Filters.R                      |  241 ----
 inst/unitTests/test_Functionality.R                |  507 --------
 inst/unitTests/test_GFF.R                          |  179 ---
 inst/unitTests/test_GRangeFilter.R                 |  102 --
 inst/unitTests/test_SymbolFilter.R                 |   58 -
 inst/unitTests/test_buildEdb.R                     |   45 -
 inst/unitTests/test_getGenomeFaFile.R              |   49 -
 inst/unitTests/test_get_sequence.R                 |  189 ---
 inst/unitTests/test_mysql.R                        |   24 -
 inst/unitTests/test_ordering.R                     |  280 -----
 inst/unitTests/test_performance.R                  |   62 -
 inst/unitTests/test_select.R                       |  229 ----
 inst/unitTests/test_transcript_lengths.R           |  140 ---
 inst/unitTests/test_ucscChromosomeNames.R          |  508 --------
 inst/unitTests/test_validity.R                     |   11 -
 inst/unitTests/test_xByOverlap.R                   |  102 --
 man/Deprecated.Rd                                  |   92 ++
 man/EnsDb-AnnotationDbi.Rd                         |   62 +-
 man/EnsDb-class.Rd                                 |   69 +-
 man/EnsDb-exonsBy.Rd                               |  217 ++--
 man/EnsDb-lengths.Rd                               |   40 +-
 man/EnsDb-seqlevels.Rd                             |   11 +-
 man/EnsDb-sequences.Rd                             |    3 +-
 man/EnsDb-utils.Rd                                 |   28 +-
 man/EnsDb.Rd                                       |    1 -
 man/Filter-classes.Rd                              |  350 ++++++
 man/GeneidFilter-class.Rd                          |  451 --------
 man/ProteinFunctionality.Rd                        |  115 ++
 man/SeqendFilter.Rd                                |  237 ----
 man/hasProteinData-EnsDb-method.Rd                 |   32 +
 man/listEnsDbs.Rd                                  |    7 +-
 man/makeEnsemblDbPackage.Rd                        |   10 +-
 man/useMySQL-EnsDb-method.Rd                       |    3 +-
 readme.md                                          |   16 +
 tests/runTests.R                                   |    1 -
 tests/testthat.R                                   |    6 +
 tests/testthat/test_Classes.R                      |   85 ++
 tests/testthat/test_Methods-Filter.R               |  515 +++++++++
 .../test_Methods-with-returnFilterColumns.R        |  276 ++---
 tests/testthat/test_Methods.R                      |  893 +++++++++++++++
 tests/testthat/test_Protein-related-tests.R        |  253 ++++
 tests/testthat/test_SymbolFilter.R                 |   99 ++
 tests/testthat/test_dbhelpers.R                    |  405 +++++++
 tests/testthat/test_extractTranscriptSeqs.R        |   65 ++
 tests/testthat/test_functions-Filter.R             |  226 ++++
 tests/testthat/test_functions-create-EnsDb.R       |  234 ++++
 tests/testthat/test_functions-utils.R              |  106 ++
 tests/testthat/test_select-methods.R               |  414 +++++++
 tests/testthat/test_seqLevelStyle.R                |  445 ++++++++
 tests/testthat/test_validity.R                     |   20 +
 vignettes/MySQL-backend.Rmd                        |   18 +-
 vignettes/MySQL-backend.org                        |   29 +-
 vignettes/ensembldb.Rmd                            |  569 +++++----
 vignettes/ensembldb.org                            | 1187 +++++++++++++++----
 vignettes/images/dblayout.png                      |  Bin 444031 -> 204300 bytes
 vignettes/proteins.Rmd                             |  273 +++++
 vignettes/proteins.org                             |  485 ++++++++
 94 files changed, 13852 insertions(+), 8037 deletions(-)

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