[med-svn] [r-cran-bio3d] branch master updated (501a405 -> 004d335)

[Andreas Tille]

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tille pushed a change to branch master
in repository r-cran-bio3d.

      from  501a405   Moved packaging from SVN to Git
       new  dc60a34   New upstream version 2.3-3
       new  50061da   Updated version 2.3-3 from 'upstream/2.3-3'
       new  eeecfe6   New upstream version
       new  8a42195   Standards-Version: 4.1.0 (no changes needed)
       new  708bb7a   Add debian/README.source to document binary data
       new  004d335   Upload to unstable

The 6 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                   |   6 +-
 MD5                           |  71 ++++++++--------
 R/atom.select.pdb.R           |  14 +++-
 R/atom2ele.R                  |  65 ++++++++++++--
 R/cnapath.R                   |   4 +-
 R/community.aln.R             |   6 ++
 R/get.pdb.R                   |  14 ++--
 R/hmmer.R                     |  10 +++
 R/pdbs2sse.R                  |  42 ++++++++--
 R/plot.blast.R                |   2 +-
 R/plot.dmat.R                 |  14 ++--
 R/plot.matrix.loadings.R      |  86 ++++++++++---------
 R/plot.pca.scree.R            |   2 +-
 R/read.cif.R                  |   2 +-
 R/read.pdb.R                  |   2 +-
 R/uniprot.R                   |  26 +++++-
 build/vignette.rds            | Bin 203 -> 203 bytes
 debian/README.source          |  38 +++++++++
 debian/changelog              |   7 +-
 debian/control                |   2 +-
 inst/doc/bio3d_vignettes.html | 191 ++++++++++++++++++++++++++++++++++--------
 man/atom.select.Rd            |   4 +-
 man/atom2ele.Rd               |  16 ++--
 man/bio3d.package.Rd          |   4 +-
 man/cna.Rd                    |   6 +-
 man/cnapath.Rd                |   6 ++
 man/community.aln.Rd          |   7 +-
 man/community.tree.Rd         |   5 ++
 man/identify.cna.Rd           |   5 ++
 man/layout.cna.Rd             |   5 ++
 man/mustang.Rd                |   6 ++
 man/network.amendment.Rd      |   7 +-
 man/plot.cna.Rd               |  11 +--
 man/plot.matrix.loadings.Rd   |   4 +-
 man/plot.pca.Rd               |   2 +-
 man/print.cna.Rd              |   5 ++
 man/prune.cna.Rd              |   5 ++
 man/vmd.cna.Rd                |   5 ++
 src/init.c                    |  28 +++++++
 src/read_cif.cpp              |  14 ++--
 40 files changed, 566 insertions(+), 183 deletions(-)
 create mode 100644 debian/README.source
 create mode 100644 src/init.c

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