[med-svn] [phyml] branch master updated (ca7dd1a -> 10a15d8)

[Andreas Tille]

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

tille pushed a change to branch master
in repository phyml.

      from  ca7dd1a   Avoid initialisation an array with a scalar value
       new  6bfa298   Imported Upstream version 3.2.0+dfsg
       new  3a8c751   Adapt patched to previous version
       new  4ca2f9c   hardening=+all,-pie (Build fails with +pie)
       new  10a15d8   Wrapper to use MPI if appropriate

The 4 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:
 NEWS                                               |    0
 README                                             |   30 +-
 autogen.sh                                         |    0
 config.h.in                                        |    3 -
 configure.ac                                       |   24 +-
 debian/changelog                                   |    7 +-
 debian/install                                     |    1 +
 debian/patches/fix_declaration_of_temp.patch       |   10 +-
 ...onfigure-ac-date => no-configure-ac-date.patch} |    4 +-
 debian/patches/no-stdc++.patch                     |    2 +-
 debian/patches/series                              |    4 +-
 debian/patches/sse_only_if_supported.patch         |    4 +-
 debian/rules                                       |    3 +
 debian/wrapper/phyml                               |    4 +-
 doc/fig/phyrexlog.pdf                              |  Bin 463638 -> 0 bytes
 doc/phyml-manual.pdf                               |  Bin 885797 -> 407931 bytes
 doc/phyml-manual.tex                               |  135 +-
 doc/ref.bib                                        |   74 -
 examples/phyrex_input_files/h1n1.nxs               |  613 -----
 examples/phyrex_input_files/usa_coord.txt          |   53 -
 src/Makefile.am                                    |   90 +-
 src/alrt.c                                         |  262 +-
 src/cl.c                                           |  109 +-
 src/cl.h                                           |    1 -
 src/date.c                                         |  789 ------
 src/date.h                                         |   41 -
 src/free.c                                         |  230 +-
 src/free.h                                         |   12 +-
 src/init.c                                         |  300 +--
 src/init.h                                         |   10 +-
 src/interface.c                                    |   27 +-
 src/invitee.c                                      |   60 +-
 src/invitee.h                                      |    2 +-
 src/io.c                                           | 1666 +++++++++---
 src/io.h                                           |    7 -
 src/lk.c                                           |  958 +++----
 src/m4.c                                           |    6 +-
 src/main.c                                         |   29 +-
 src/make.c                                         |  143 +-
 src/make.h                                         |   12 +-
 src/mcmc.c                                         |  370 +--
 src/mcmc.h                                         |    5 +-
 src/mg.c                                           | 2820 ++++++++++++++++++++
 src/mg.h                                           |   51 +
 src/mixt.c                                         |  829 +-----
 src/mixt.h                                         |   16 +-
 src/models.c                                       |   16 +-
 src/mpi_boot.c                                     |    2 +-
 src/optimiz.c                                      |  221 +-
 src/pars.c                                         |  182 +-
 src/phyrex.c                                       |  375 +--
 src/phyrex.h                                       |    4 +-
 src/rates.c                                        |    8 +-
 src/simu.c                                         |  715 +++--
 src/spr.c                                          | 1237 ++++-----
 src/spr.h                                          |   14 +-
 src/stats.c                                        |   13 +-
 src/stats.h                                        |    2 +-
 src/times.c                                        |  507 +---
 src/times.h                                        |    3 -
 src/utilities.c                                    | 2358 +++++++---------
 src/utilities.h                                    |  193 +-
 src/xml.c                                          | 1146 +-------
 src/xml.h                                          |    3 -
 64 files changed, 7569 insertions(+), 9246 deletions(-)
 create mode 100644 NEWS
 mode change 100755 => 100644 autogen.sh
 create mode 100644 debian/install
 rename debian/patches/{no-configure-ac-date => no-configure-ac-date.patch} (79%)
 delete mode 100644 doc/fig/phyrexlog.pdf
 delete mode 100644 examples/phyrex_input_files/h1n1.nxs
 delete mode 100644 examples/phyrex_input_files/usa_coord.txt
 delete mode 100644 src/date.c
 delete mode 100644 src/date.h

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