[med-svn] [r-bioc-rtracklayer] branch master updated (8039287 -> 5b54297)

[Andreas Tille]

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

      from  8039287   Upload to unstable
       new  6942ae9   New upstream version 1.38.0
       new  c386cc0   Update upstream source from tag 'upstream/1.38.0'
       new  440bd81   New upstream version
       new  a7ec61c   Adapt patches
       new  5b54297   Upload to unstable

The 5 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                                   |  15 +++++++-------
 NAMESPACE                                     |   2 +-
 R/bed.R                                       |   5 +++--
 R/bigWig.R                                    |  18 +++++++++++++++--
 R/browser.R                                   |   4 ++--
 R/chain.R                                     |  20 ++++++++++++++++--
 R/gff.R                                       |   3 +--
 R/ucsc.R                                      |   7 ++++++-
 R/wig.R                                       |  14 +++++++++++--
 debian/changelog                              |   6 ++++++
 debian/patches/use_debian_packaged_zlib.patch |  12 +++++------
 inst/doc/rtracklayer.pdf                      | Bin 311311 -> 311498 bytes
 inst/tests/test.bedGraph                      |  18 ++++++++---------
 man/BEDFile-class.Rd                          |   1 +
 man/BigWigFile.Rd                             |  21 ++++++++++++++++---
 man/GFFFile-class.Rd                          |   1 -
 man/GenomicData.Rd                            |   1 -
 man/TwoBitFile-class.Rd                       |   2 +-
 man/browseGenome.Rd                           |   6 +++---
 man/export.Rd                                 |   1 -
 src/Makevars                                  |   2 +-
 src/Makevars.in                               |   2 +-
 src/bigWig.c                                  |   5 +++--
 src/chain_io.c                                |  11 +++++-----
 src/ucsc/bPlusTree.c                          |   4 +---
 src/ucsc/bbiRead.c                            |   7 +++----
 src/ucsc/dnautil.c                            |  28 ++++++++++++--------------
 src/ucsc/net.c                                |   4 ++--
 src/ucsc/udc.c                                |  12 +++++------
 src/utils.c                                   |   1 -
 30 files changed, 146 insertions(+), 87 deletions(-)

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