Accepted: gromacs 3.3.3-2 (source)

[Ubuntu Installer]

Accepted:
 OK: gromacs_3.3.3.orig.tar.gz
 OK: gromacs_3.3.3-2.diff.gz
 OK: gromacs_3.3.3-2.dsc
     -> Component: universe Section: science

Origin: Debian/unstable
Format: 1.7
Date: Fri,  28 Mar 2008 09:49:09 +0000
Source: gromacs
Binary: gromacs, gromacs-data, gromacs-dev, gromacs-mpich, gromacs-lam, gromacs-openmpi
Architecture: source
Version: 3.3.3-2
Distribution: hardy
Urgency: low
Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
Changed-By: Jordan Mantha <mantha at ubuntu.com>
Description: 
 gromacs    - Molecular dynamics simulator, with building and analysis tools
Closes: 456860 470000
Changes: 
 gromacs (3.3.3-2) unstable; urgency=low
 .
   * debian/control: Eliminate unneeded Build-Depends on libxml-dev.
     Spotted by Pierre Habouzit.  (Closes: #470000)
   * debian/rules: Force --with-gsl in configuration.
 .
 gromacs (3.3.3-1) unstable; urgency=low
 .
   [ Nicholas Breen ]
   * New upstream release.
   * debian/rules, debian/control: Reconfigure gromacs-doc as gromacs-data.
     This moves all architecture independent files into a single package,
     including many topology files formerly shipped in gromacs instead.
     - Rename debian/*gromacs-doc* to debian/*gromacs-data* .
     - debian/gromacs-doc.preinst: no longer necessary, removed.
   * Remove PDF manual for the time being, as modifiable sources are not
     currently available.
     - debian/gromacs.README.Debian, debian/man/gromacs.7: Provide pointers
       to its location online instead.
     - debian/control: Drop build dependency on sharutils, which was used
       only to provide the manual.
     - debian/gromacs-data.doc-base: Remove reference to PDF.
   * debian/control: Add Build-Depends on libgsl0-dev to support addition
     of /usr/bin/g_kinetics.
   * debian/gromacs.README.Debian: Update suggested MPI implementations.
   * debian/man: write preliminary man pages for undocumented new commands,
     g_kinetics.1 g_spatial.1 g_sdf.1
   * debian/patches/10_manpages: Update with ROFF fixes to 18 files; fix a 
     few minor typos; resync patch against upstream CVS.
   * debian/man/mdrun_mpi.{mpich,lam,openmpi}.1: Propagate those fixes.
   * debian/lintian-overrides.gromacs: Drop binary-without-manpage override.
   * debian/linda-overrides.gromacs, debian/rules: Remove linda override.
 .
   [ Daniel Leidert ]
   * debian/man/average.1: Minor ROFF improvements, hyphen/minus and typo
     fixes.
   * debian/man/g_nmtraj.1: Ditto.
   * debian/man/luck.1: Ditto.
 .
 gromacs (3.3.3~pre1-1) unstable; urgency=low
 .
   [ Nicholas Breen ]
   * New upstream release.
     - Remove obsolete patches now incorporated upstream:
       50_xtcio_double_range_checking, 51_180_degree_angle,
       52_pme_spline, 53_pbc_compiler.
   * debian/rules: 
     - Clean up patch syntax to prevent double compilations.
     - Add .NOTPARALLEL target to prevent the various MPI builds from
       compiling on the same source tree simultaneously, while still
       allowing -j options to be passed to sublevel targets.
     - Improve DEB_BUILD_OPTIONS=parallel=X handling, now in line with
       the example proposed for policy.
     - Disable FORTRAN inner loops for gromacs-openmpi on alpha.  This
       is a temporary workaround to avoid lingering linking problems
       regarding libmpi.so and the update-alternatives system.
     - Add support for DEB_BUILD_OPTIONS=noopt.
     - Additional rewrite work (see below): use new format for build
       commands, but split for individual MPI implementations.
     - Run autotools between patch and configuration steps.
     - New format for MPI library suffix configuration.
   * debian/control:
     - Add versioned Build-Depends on libmpich1.0-dev for its 
       g77 -> gfortran transition.
     - Add Build-Depends on autoconf and automake, and Build-Conflicts
       on autoconf2.13, to support updated mpisuffix patch.
     - Downgrade gromacs-doc Depends: on gromacs to a Recommends:, as -doc
       now ships its own copyright file.
   * debian/patches/04_autoconf_mpisuffix.dpatch: Apply dleidert's improved
     patch to allow arbitrary overrides of LIBSUFFIX; reduce patch to only
     the directly changed code in configure.ac, and add an invocation of
     autotools during the build process rather than patching configure
     itself directly.
   * debian/gromacs-{doc,dev}.preinst: Remove symlinks for package doc
     directories on upgrade, in order to replace them with actual directories.
 .
   [ Daniel Leidert ]
   * debian/control (Suggests): Fixed a debcheck issue - gromacs-openmpi should
     only be suggested on supported architectures.
   * debian/copyright: Added copyright information to satisfy lintian.
   * debian/gromacs-doc.doc-base (Section): Fixed accordingly to menu policy.
     (Format): Fixed path to HTML files.
   * debian/rules: Major rewrite. Changes/improvements include:
     - drop dpatch target definitions in favour of dpatch.make
     - put all configure flags to the top of the file
     - moved all configure related commands into configure-stamp
     - moved all build related commands into build-stamp
     - moved all install related commands into separate install targets
     - configure and build in sub-directories to avoid $(MAKE) clean calls
     - clean target removes build/ instead to run clean/distclean
     - replaced ln with dh_link and gzip with dh_installman
     - adjusted target requirements for binary* and install*
     - install a /usr/share/doc/$package directory for gromacs-doc and -dev
       too; put the HTML into the -doc documentation directory; add links to
       the HTML directory for the gromacs and the -dev package pointing to the
       -doc directory
     - fixed .PHONY target for above
   * debian/watch: Added pre-release version handling.
 .
 gromacs (3.3.2-3) unstable; urgency=low
 .
   * Package transferred to Debichem team maintenance.
   * debian/control:
     - Switched Maintainer to Debichem Team, moved myself to
       Uploaders.  Added Vcs-Browser, Vcs-Svn fields.
     - Increase Standards-Version to 3.7.3.  No changes required.
     - Build-Depend on libopenmpi-dev >= 1.2.4-5 (Closes: #456860).
   * debian/rules: include kfreebsd-* variants explicitly in OPENMPI_ARCH.
   * debian/patches/11_readme.dpatch: change edited README to an explicit
     patch, rather than modifying it directly in the .diff.gz.
   * Multiple bugfixes from upstream CVS:
     - 51_180_degree_angle.dpatch: apply upstream patches to avoid crashes
       crashes when operating on precisely linear 2-bond pairs.
       (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=172,
            http://bugzilla.gromacs.org/show_bug.cgi?id=177)
     - 52_pme_spline.dpatch: calculate mesh contribution when charges
       are 0 in A state, but non-zero in B state.
       (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=175)
     - 53_pbc_compiler: Solve regression in gmxlib/pbc.c introduced by a
       previous compiler workaround.
       (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=179)
   * debian/gromacs-doc.doc-base: remove extraneous spaces.
Files: 
 57f0dbb0834272abb5cfb365a3a9c9a7 1230 science extra gromacs_3.3.3-2.dsc
 dc31420bb5947f013db568776b4434b6 41165 science extra gromacs_3.3.3-2.diff.gz
 33f5f434d69b45bc51c5af36f5719618 8013789 science extra gromacs_3.3.3.orig.tar.gz