[med-svn] [r-bioc-genomicfeatures] 06/09: Update upstream source from tag 'upstream/1.30.0+dfsg'

[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-genomicfeatures.

commit 863e80fd387748451abf085daf8f522b59cb15de
Merge: de72f12 5f7c220
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 9 09:33:18 2017 +0100

    Update upstream source from tag 'upstream/1.30.0+dfsg'
    
    Update to upstream version '1.30.0+dfsg'
    with Debian dir 8b6f795437fc6e9700a99853e07529459a2ac449

 DESCRIPTION                                        |  32 ++-
 NAMESPACE                                          |   9 +-
 NEWS                                               |  44 +++
 R/Ensembl.utils.R                                  |  70 +++--
 R/TxDb-SELECT-helpers.R                            |  15 +-
 R/TxDb-class.R                                     |  58 ++--
 R/TxDb-schema.R                                    |  20 +-
 R/coordinate-mapping-methods.R                     |   6 +-
 R/exonicParts.R                                    |  18 +-
 R/extractTranscriptSeqs.R                          |  62 ++---
 R/makeTxDb.R                                       | 180 ++++++------
 R/makeTxDbFromEnsembl.R                            | 301 +++++++++++++++++++++
 R/makeTxDbFromGRanges.R                            |  70 ++++-
 R/transcriptsByOverlaps.R                          |  12 +-
 build/vignette.rds                                 | Bin 292 -> 293 bytes
 inst/doc/GenomicFeatures.R                         |  67 +++--
 inst/doc/GenomicFeatures.Rnw                       |  57 ++--
 inst/doc/GenomicFeatures.pdf                       | Bin 166472 -> 214029 bytes
 inst/extdata/GFF3_files/a.sqlite                   | Bin 247808 -> 286720 bytes
 .../GFF3_files/dmel-1000-r5.11.filtered.sqlite     | Bin 45056 -> 69632 bytes
 .../extdata/GTF_files/Aedes_aegypti.partial.sqlite | Bin 66560 -> 98304 bytes
 inst/script/makeTxDbs.R                            |  92 ++++++-
 man/DEFAULT_CIRC_SEQS.Rd                           |   3 +-
 man/TxDb-class.Rd                                  |  23 +-
 man/coordinate-mapping-methods.Rd                  |   3 +-
 man/coverageByTranscript.Rd                        |  19 +-
 man/disjointExons.Rd                               |  11 +-
 man/exonicParts.Rd                                 | 163 +++++++++++
 man/extractTranscriptSeqs.Rd                       |   8 +-
 man/extractUpstreamSeqs.Rd                         |  19 +-
 man/makeTxDb.Rd                                    |  40 +--
 man/makeTxDbFromBiomart.Rd                         |  34 +--
 man/makeTxDbFromEnsembl.Rd                         |  79 ++++++
 man/makeTxDbFromGFF.Rd                             |   6 +-
 man/makeTxDbFromGRanges.Rd                         |  14 +-
 man/makeTxDbFromUCSC.Rd                            |  11 +-
 man/transcriptLengths.Rd                           |  21 +-
 man/transcripts.Rd                                 |  33 +--
 man/transcriptsBy.Rd                               |  10 +-
 man/transcriptsByOverlaps.Rd                       |  59 ++--
 vignettes/GenomicFeatures.Rnw                      |  57 ++--
 41 files changed, 1279 insertions(+), 447 deletions(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-genomicfeatures.git