[med-svn] [r-bioc-genomicfeatures] branch master updated (f734b23 -> 5bcc4a4)

[Andreas Tille]

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

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

      from  f734b23   New upstream version
       new  adf7bf6   Remove unneeded Testsuite field, Standards-Version: 4.1.1
       new  ec658d1   Testsuite: autopkgtest-pkg-r
       new  793c8d9   Upload to unstable
       new  de72f12   Secure URI in watch file
       new  5f7c220   New upstream version 1.30.0+dfsg
       new  863e80f   Update upstream source from tag 'upstream/1.30.0+dfsg'
       new  8a892ed   New upstream version
       new  422b266   New Build-Depends: r-cran-rmysql
       new  5bcc4a4   Upload to unstable

The 9 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                                        |  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
 debian/changelog                                   |  14 +-
 debian/control                                     |   6 +-
 debian/watch                                       |   2 +-
 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 ++--
 44 files changed, 1296 insertions(+), 452 deletions(-)
 create mode 100644 R/makeTxDbFromEnsembl.R
 create mode 100644 man/exonicParts.Rd
 create mode 100644 man/makeTxDbFromEnsembl.Rd

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