[med-svn] [r-bioc-ensembldb] 07/10: Updated version 1.6.2 from 'upstream/1.6.2'

[Andreas Tille]

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

commit 26d20be8cc65fd56795041cf92b4968d24dba0ef
Merge: 692c2bc 0f017c8
Author: Andreas Tille <tille at debian.org>
Date:   Tue Oct 3 09:14:21 2017 +0200

    Updated version 1.6.2 from 'upstream/1.6.2'
    
    with Debian dir 5899248017e85f1278f9bf1bbf0bab419c519446

 DESCRIPTION                                  |   37 +
 NAMESPACE                                    |   63 +
 R/Classes.R                                  |  404 +++
 R/EnsDbFromGTF.R                             | 1138 ++++++++
 R/Generics.R                                 |  147 +
 R/Methods-Filter.R                           |  933 +++++++
 R/Methods.R                                  | 1758 ++++++++++++
 R/dbhelpers.R                                |  589 ++++
 R/functions-utils.R                          |   83 +
 R/loadEnsDb.R                                |    5 +
 R/makeEnsemblDbPackage.R                     |  213 ++
 R/runEnsDbApp.R                              |   10 +
 R/select-methods.R                           |  319 +++
 R/seqname-utils.R                            |  258 ++
 R/zzz.R                                      |   15 +
 build/vignette.rds                           |  Bin 0 -> 325 bytes
 inst/NEWS                                    |  488 ++++
 inst/YGRanges.RData                          |  Bin 0 -> 47220 bytes
 inst/chrY/ens_chromosome.txt                 |    2 +
 inst/chrY/ens_exon.txt                       | 2700 +++++++++++++++++++
 inst/chrY/ens_gene.txt                       |  496 ++++
 inst/chrY/ens_metadata.txt                   |   12 +
 inst/chrY/ens_tx.txt                         |  732 +++++
 inst/chrY/ens_tx2exon.txt                    | 3745 ++++++++++++++++++++++++++
 inst/doc/MySQL-backend.R                     |   30 +
 inst/doc/MySQL-backend.Rmd                   |   74 +
 inst/doc/MySQL-backend.html                  |  209 ++
 inst/doc/ensembldb.R                         |  386 +++
 inst/doc/ensembldb.Rmd                       |  920 +++++++
 inst/doc/ensembldb.html                      | 1300 +++++++++
 inst/perl/get_gene_transcript_exon_tables.pl |  278 ++
 inst/pkg-template/DESCRIPTION                |   15 +
 inst/pkg-template/NAMESPACE                  |    9 +
 inst/pkg-template/R/zzz.R                    |   18 +
 inst/pkg-template/man/package.Rd             |   40 +
 inst/shinyHappyPeople/server.R               |  242 ++
 inst/shinyHappyPeople/ui.R                   |  154 ++
 inst/test/testFunctionality.R                |  293 ++
 inst/test/testInternals.R                    |  146 +
 inst/txt/ENST00000200135.fa.gz               |  Bin 0 -> 13986 bytes
 inst/txt/ENST00000335953.fa.gz               |  Bin 0 -> 60063 bytes
 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_returnCols.R             |  319 +++
 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/EnsDb-AnnotationDbi.Rd                   |  223 ++
 man/EnsDb-class.Rd                           |  368 +++
 man/EnsDb-exonsBy.Rd                         |  568 ++++
 man/EnsDb-lengths.Rd                         |  110 +
 man/EnsDb-seqlevels.Rd                       |  149 +
 man/EnsDb-sequences.Rd                       |  118 +
 man/EnsDb-utils.Rd                           |  118 +
 man/EnsDb.Rd                                 |   50 +
 man/GeneidFilter-class.Rd                    |  451 ++++
 man/SeqendFilter.Rd                          |  237 ++
 man/listEnsDbs.Rd                            |   53 +
 man/makeEnsemblDbPackage.Rd                  |  311 +++
 man/runEnsDbApp.Rd                           |   41 +
 man/useMySQL-EnsDb-method.Rd                 |   56 +
 tests/runTests.R                             |    1 +
 vignettes/MySQL-backend.Rmd                  |   74 +
 vignettes/MySQL-backend.org                  |   88 +
 vignettes/ensembldb.Rmd                      |  920 +++++++
 vignettes/ensembldb.org                      | 1369 ++++++++++
 vignettes/images/dblayout.png                |  Bin 0 -> 444031 bytes
 vignettes/issues.org                         |  183 ++
 79 files changed, 26794 insertions(+)

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